ubiquinone and ubiquinone-8

Unprecedented community containment measures were taken following the recent outbreak of COVID-19 in Italy. The aim of the study was to explore the self-reported future compliance of citizens with such measures and its relationship with potentially impactful psychological variables.. An online survey was completed by 931 people (18-76 years) distributed across the Italian territory. In addition to demographics, five dimensions were measured: self-reported compliance with containment measures over time (today, at 7, 14, 30, 60, 90, and 180 days from now) at three hypothetical risk levels (10, 50, 90% of likelihood of contracting the COVID-19), perceived risk, generalized anxiety, intolerance of uncertainty, and relevance of several psychological needs whose satisfaction is currently precluded.. The duration of containment measures plays a crucial role in tackling the spread of the disease as people will be less compliant over time. Psychological needs of citizens impacting on the compliance should be taken into account when planning an easing of the lockdown, along with interventions for protecting vulnerable groups from mental distress.. La apendicitis aguda (AA) es la urgencia quirúrgica abdominal más frecuente. No encontramos estudios específicos que evalúen el impacto de la pandemia causada por el coronavirus 2 (SARS-Cov-2) sobre la AA y su tratamiento quirúrgico. Analizamos la influencia de esta nueva patología sobre la AA.. Estudio observacional retrospectivo en pacientes intervenidos por AA desde enero hasta abril de 2020. Fueron clasificados según el momento de la apendicectomía, antes de la declaración del estado de alarma (Pre-COVID19) y después de la declaración del estado de alarma (Post-COVID19) en España. Se evaluaron variables demográficas, duración de la sintomatología, tipo de apendicitis, tiempo quirúrgico, estancia hospitalaria y complicaciones postoperatorias.. La pandemia por SARS-Cov-2 influye en el momento de diagnóstico de la apendicitis, así como en su grado de evolución y estancia hospitalaria. La peritonitis fue lo más frecuentemente observado. Una sospecha y orientación clínica más temprana, es necesaria para evitar un manejo inadecuado de este trastorno quirúrgico común.. The primary outcome is improvement in PaO. Findings will provide timely information on the safety, efficacy, and optimal dosing of t-PA to treat moderate/severe COVID-19-induced ARDS, which can be rapidly adapted to a phase III trial (NCT04357730; FDA IND 149634).. None.. The gut barrier is crucial in cirrhosis in preventing infection-causing bacteria that normally live in the gut from accessing the liver and other organs via the bloodstream. Herein, we characterised gut inflammation by measuring different markers in stool samples from patients at different stages of cirrhosis and comparing this to healthy people. These markers, when compared with equivalent markers usually measured in blood, were found to be very different in pattern and absolute levels, suggesting that there is significant gut inflammation in cirrhosis related to different immune system pathways to that seen outside of the gut. This provides new insights into gut-specific immune disturbances that predispose to complications of cirrhosis, and emphasises that a better understanding of the gut-liver axis is necessary to develop better targeted therapies.. La surveillance de l’intervalle QT a suscité beaucoup d’intérêt durant la pandémie de la COVID-19 en raison de l’utilisation de médicaments prolongeant l’intervalle QT et les préoccupations quant à la transmission virale par les électrocardiogrammes (ECG) en série. Nous avons posé l’hypothèse que la surveillance en continu de l’intervalle QT par télémétrie était associée à une meilleure détection des épisodes de prolongation de l’intervalle QT.. Nous avons introduit la télémétrie cardiaque en continu (TCC) à l’aide d’un algorithme de surveillance automatisée de l’intervalle QT dans nos unités de COVID-19. Les mesures automatisées quotidiennes de l’intervalle QT corrigé (auto-QTc) en fonction de la fréquence cardiaque maximale ont été enregistrées. Nous avons comparé la proportion des épisodes de prolongation marquée de l’intervalle QTc (QTc long), définie par un intervalle QTc ≥ 500 ms, chez les patients montrant une suspicion de COVID-19 ou ayant la COVID-19 qui avaient été admis avant et après la mise en place de la TCC (groupe témoin. La surveillance en continu de l’intervalle QT est supérieure à la norme de soins dans la détection des épisodes de QTc long et exige peu d’ECG. La réponse clinique aux épisodes de QTc long est sous-optimale.. Exposure to a model wildfire air pollution source modifies cardiovascular responses to HC challenge, suggesting air pollution sensitizes the body to systemic triggers.. Though the majority of HIV-infected adults who were on HAART had shown viral suppression, the rate of suppression was sub-optimal according to the UNAIDS 90-90-90 target to help end the AIDS pandemic by 2020. Nonetheless, the rate of immunological recovery in the study cohort was low. Hence, early initiation of HAART should be strengthened to achieve good virological suppression and immunological recovery.. Dust in Egyptian laying hen houses contains high concentrations of microorganisms and endotoxins, which might impair the health of birds and farmers when inhaled. Furthermore, laying hens in Egypt seem to be a reservoir for ESBL-producing Enterobacteriaceae. Thus, farmers are at risk of exposure to ESBL-producing bacteria, and colonized hens might transmit these bacteria into the food chain.. The lack of significant differences in the absolute changes and relative ratios of injury and repair biomarkers by contrast-associated AKI status suggests that the majority of mild contrast-associated AKI cases may be driven by hemodynamic changes at the kidney.. Most comparisons for different outcomes are based on very few studies, mostly low-powered, with an overall low CoE. Thus, the available evidence is considered insufficient to either support or refute CH effectiveness or to recommend one ICM over another. Therefore, further well-designed, larger RCTs are required.. PROSPERO database Identifier: CRD42016041953.. Untouched root canal at cross-section perimeter, the Hero 642 system showed 41.44% ± 5.62% and Reciproc R40 58.67% ± 12.39% without contact with instruments. Regarding the untouched area, Hero 642 system showed 22.78% ± 6.42% and Reciproc R40 34.35% ± 8.52%. Neither instrument achieved complete cross-sectional root canal debridement. Hero 642 system rotary taper 0.02 instruments achieved significant greater wall contact perimeter and area compared to reciprocate the Reciproc R40 taper 0.06 instrument.. Hero 642 achieved higher wall contact perimeter and area but, regardless of instrument size and taper, vital pulp during. The functional properties of the main mechanisms involved in the control of muscle Ca. This study showed that the anti-inflammatory effect of the iron-responsive product DHA in arthritis can be monitored by an iron-like radioactive tracer (. Attenuated vascular reactivity during pregnancy suggests that the systemic vasodilatory state partially depletes nitric oxide bioavailability. Preliminary data support the potential for MRI to identify vascular dysfunction in vivo that underlies PE. Level of Evidence 2 Technical Efficacy Stage 1 J. MAGN. RESON. IMAGING 2021;53:447-455.. La evaluación de riesgo es importante para predecir los resultados postoperatorios en pacientes con cáncer gastroesofágico. Este estudio de cohortes tuvo como objetivo evaluar los cambios en la composición corporal durante la quimioterapia neoadyuvante e investigar su asociación con complicaciones postoperatorias. MÉTODOS: Los pacientes consecutivos con cáncer gastroesofágico sometidos a quimioterapia neoadyuvante y cirugía con intención curativa entre 2016 y 2019, identificados a partir de una base de datos específica, se incluyeron en el estudio. Se utilizaron las imágenes de tomografía computarizada, antes y después de la quimioterapia neoadyuvante, para evaluar el índice de masa muscular esquelética, la sarcopenia y el índice de grasa visceral y subcutánea.. In this in vitro premature infant lung model, HF oscillation of BCPAP was associated with improved CO. Our results showed that HPC significantly promotes neurogenesis after MCAO and ameliorates neuronal injury.. Inflammatory markers are highly related to signs of systemic hypoperfusion in CS. Moreover, high PCT and IL-6 levels are associated with poor prognosis.. These findings indicate that Tetrapleura tetraptera fruit has a protective potential against stroke through modulation of redox and electrolyte imbalances, and attenuation of neurotransmitter dysregulation and other neurochemical dysfunctions. Tetrapleura tetraptera fruit could be a promising source for the discovery of bioactives for stroke therapy.

Topics: 3T3-L1 Cells; A Kinase Anchor Proteins; Acetates; Achilles Tendon; Acute Kidney Injury; Acute Pain; Acyclic Monoterpenes; Adenine Nucleotides; Adhesins, Escherichia coli; Adipocytes; Adipocytes, Brown; Adipogenesis; Administration, Inhalation; Administration, Oral; Adrenal Cortex Hormones; Adsorption; Adult; Aeromonas hydrophila; Africa; Aged; Aged, 80 and over; Agrobacterium tumefaciens; Air; Air Pollutants; Air Pollution; Air Pollution, Indoor; Algorithms; Alkaloids; Alkynes; Allosteric Regulation; Amines; Amino Acid Sequence; Amino Acids; Amino Acids, Branched-Chain; Aminoisobutyric Acids; Aminopyridines; Amyotrophic Lateral Sclerosis; Anaerobic Threshold; Angiography; Angiotensin II Type 1 Receptor Blockers; Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Animal Distribution; Animal Feed; Animal Nutritional Physiological Phenomena; Animals; Ankle Joint; Anti-Bacterial Agents; Anti-HIV Agents; Anti-Inflammatory Agents; Antibodies, Bacterial; Antifungal Agents; Antimalarials; Antineoplastic Agents; Antineoplastic Agents, Phytogenic; Antioxidants; Antiretroviral Therapy, Highly Active; Antiviral Agents; Aotidae; Apelin; Apoptosis; Arabidopsis Proteins; Argentina; Arginine; Artemisinins; Arthritis, Experimental; Arthritis, Rheumatoid; Arthroscopy; Aspergillus; Aspergillus niger; Asteraceae; Asthma; ATP Binding Cassette Transporter, Subfamily B, Member 1; ATP Binding Cassette Transporter, Subfamily G, Member 2; Auditory Cortex; Autoantibodies; Autophagy; Bacteria; Bacterial Infections; Bacterial Proteins; Bacterial Typing Techniques; Base Composition; Base Sequence; Basketball; Beclin-1; Benzhydryl Compounds; Benzimidazoles; Benzo(a)pyrene; Benzofurans; Benzoxazines; Bereavement; beta Catenin; beta-Lactamase Inhibitors; beta-Lactamases; beta-Lactams; Betacoronavirus; Betaine; Binding Sites; Biofilms; Biological Assay; Biological Availability; Biological Evolution; Biomarkers; Biomechanical Phenomena; Biopolymers; Biopsy; Bismuth; Blood Glucose; Blood Platelets; Blood Pressure; Body Composition; Body Weight; Bone Marrow; Bone Marrow Cells; Bone Regeneration; Boron; Botrytis; Brain Ischemia; Brain Neoplasms; Brain-Derived Neurotrophic Factor; Brazil; Breast Neoplasms; Breath Tests; Bronchoalveolar Lavage Fluid; Burkholderia; C-Reactive Protein; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Calcification, Physiologic; Calcium; Calcium Signaling; Calorimetry, Differential Scanning; Cameroon; Camptothecin; Candida; Candida albicans; Capillaries; Carbapenem-Resistant Enterobacteriaceae; Carbapenems; Carbohydrate Conformation; Carbon; Carbon Dioxide; Carbon Isotopes; Carcinoma, Ovarian Epithelial; Cardiac Output; Cardiomyopathy, Hypertrophic; Cardiotonic Agents; Cardiovascular Diseases; Caregivers; Carps; Case-Control Studies; Catalase; Catalysis; Cats; CD4 Lymphocyte Count; Cell Culture Techniques; Cell Differentiation; Cell Line, Tumor; Cell Membrane; Cell Movement; Cell Proliferation; Cell Survival; Cells, Cultured; Cellulose; Centrosome; Ceratopogonidae; Chickens; Child; China; Cholera Toxin; Choline; Cholinesterases; Chromatography, High Pressure Liquid; Chromatography, Liquid; Chromatography, Micellar Electrokinetic Capillary; Chromatography, Reverse-Phase; Chronic Disease; Cinnamates; Cities; Citrates; Climate Change; Clinical Trials, Phase III as Topic; Coal; Coal Mining; Cohort Studies; Coinfection; Colchicine; Colony Count, Microbial; Colorectal Neoplasms; Coloring Agents; Common Cold; Complement Factor H; Computational Biology; Computer Simulation; Continuous Positive Airway Pressure; Contrast Media; Coordination Complexes; Coronary Artery Bypass; Coronavirus 3C Proteases; Coronavirus Infections; Coronavirus Protease Inhibitors; Corynebacterium glutamicum; Cosmetics; COVID-19; Creatinine; Cross-Sectional Studies; Crotonates; Crystallography, X-Ray; Cues; Culicidae; Culture Media; Curcuma; Cyclopentanes; Cyclopropanes; Cymbopogon; Cystine; Cytochrome P-450 CYP2B6; Cytochrome P-450 CYP2C19; Cytochrome P-450 CYP2C19 Inhibitors; Cytokines; Databases, Genetic; Death; Dendritic Cells; Density Functional Theory; Depsides; Diabetes Mellitus, Type 2; Diamond; Diarylheptanoids; Dibenzofurans; Dibenzofurans, Polychlorinated; Diclofenac; Diet; Dietary Carbohydrates; Dietary Supplements; Diffusion Magnetic Resonance Imaging; Dioxins; Diphenylamine; Disease Outbreaks; Disease Susceptibility; Disulfides; Dithiothreitol; Dizocilpine Maleate; DNA Methylation; DNA-Binding Proteins; DNA, Bacterial; Dogs; Dose-Response Relationship, Drug; Double-Blind Method; Doublecortin Protein; Drosophila melanogaster; Droughts; Drug Carriers; Drug Combinations; Drug Delivery Systems; Drug Liberation; Drug Resistance; Drug Resistance, Bacterial; Drug Resistance, Neoplasm; Drug Screening Assays, Antitumor; Dust; Dynactin Complex; Dysferlin; Echo-Planar Imaging; Echocardiography; Edaravone; Egypt; Elasticity; Electrodes; Electrolytes; Emodin; Emtricitabine; Endometriosis; Endothelium, Vascular; Endotoxins; Energy Metabolism; Energy Transfer; Enterobacteriaceae; Enterococcus faecalis; Enterotoxigenic Escherichia coli; Environmental Monitoring; Enzyme Inhibitors; Epidemiologic Factors; Epigenesis, Genetic; Erythrocytes; Escherichia coli; Escherichia coli Infections; Escherichia coli Vaccines; Esophageal Neoplasms; Esophagectomy; Esophagogastric Junction; Esterases; Esterification; Ethanol; Ethiopia; Ethnicity; Eucalyptus; Evidence-Based Practice; Exercise; Exercise Tolerance; Extracorporeal Membrane Oxygenation; Family; Fatty Acids; Feedback; Female; Ferric Compounds; Fibrin Fibrinogen Degradation Products; Filtration; Fish Diseases; Flavonoids; Flavonols; Fluorodeoxyglucose F18; Follow-Up Studies; Food Microbiology; Food Preservation; Forests; Fossils; Free Radical Scavengers; Freund's Adjuvant; Fruit; Fungi; Gallium; Gender Identity; Gene Expression Regulation; Gene Expression Regulation, Neoplastic; Gene Expression Regulation, Plant; Gene Knockdown Techniques; Genes, Bacterial; Genes, Plant; Genetic Predisposition to Disease; Genitalia; Genotype; Glomerulonephritis, IGA; Glottis; Glucocorticoids; Glucose; Glucuronides; Glutathione Transferase; Glycogen Synthase Kinase 3 beta; Gram-Negative Bacterial Infections; Gram-Positive Bacterial Infections; Grassland; Guinea Pigs; Half-Life; Head Kidney; Heart Atria; Heart Rate; Heart Septum; HEK293 Cells; Hematopoietic Stem Cells; Hemodynamics; Hep G2 Cells; Hepacivirus; Hepatitis C; Hepatitis C, Chronic; Hepatocytes; Hesperidin; High-Frequency Ventilation; High-Temperature Requirement A Serine Peptidase 1; Hippocampus; Hirudins; History, 20th Century; History, 21st Century; HIV Infections; Homeostasis; Hominidae; Housing, Animal; Humans; Hydrocarbons, Brominated; Hydrogen Bonding; Hydrogen Peroxide; Hydrogen-Ion Concentration; Hydroxybutyrates; Hydroxyl Radical; Hypertension; Hypothyroidism; Image Interpretation, Computer-Assisted; Immunoconjugates; Immunogenic Cell Death; Indoles; Infant, Newborn; Infant, Premature; Infarction, Middle Cerebral Artery; Inflammation; Inflammation Mediators; Infrared Rays; Inhibitory Concentration 50; Injections, Intravenous; Interferon-gamma; Interleukin-23; Interleukin-4; Interleukin-6; Intermediate Filaments; Intermittent Claudication; Intestine, Small; Iridoid Glucosides; Iridoids; Iron; Isomerism; Isotope Labeling; Isoxazoles; Itraconazole; Kelch-Like ECH-Associated Protein 1; Ketoprofen; Kidney Failure, Chronic; Kinetics; Klebsiella pneumoniae; Lactams, Macrocyclic; Lactobacillus; Lactulose; Lakes; Lamivudine; Laparoscopy; Laparotomy; Laryngoscopy; Leucine; Limit of Detection; Linear Models; Lipid A; Lipopolysaccharides; Listeria monocytogenes; Liver; Liver Cirrhosis; Logistic Models; Longitudinal Studies; Losartan; Low Back Pain; Lung; Lupinus; Lupus Erythematosus, Systemic; Machine Learning; Macular Degeneration; Madin Darby Canine Kidney Cells; Magnetic Phenomena; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Magnetics; Malaria, Falciparum; Male; Mannans; MAP Kinase Signaling System; Mass Spectrometry; Melatonin; Membrane Glycoproteins; Membrane Proteins; Meniscectomy; Menisci, Tibial; Mephenytoin; Mesenchymal Stem Cells; Metal Nanoparticles; Metal-Organic Frameworks; Methionine; Mice; Mice, Inbred C57BL; Mice, Knockout; Mice, Nude; Mice, Obese; Mice, Transgenic; Microbial Sensitivity Tests; Microcirculation; MicroRNAs; Microscopy, Video; Microtubules; Microvascular Density; Microwaves; Middle Aged; Minimally Invasive Surgical Procedures; Models, Animal; Models, Biological; Models, Molecular; Models, Theoretical; Molecular Docking Simulation; Molecular Structure; Molecular Weight; Morus; Mouth Floor; Multicenter Studies as Topic; Multiple Sclerosis; Multiple Sclerosis, Relapsing-Remitting; Muscle, Skeletal; Myocardial Ischemia; Myocardium; NAD; NADP; Nanocomposites; Nanoparticles; Naphthols; Nasal Lavage Fluid; Nasal Mucosa; Neisseria meningitidis; Neoadjuvant Therapy; Neoplasm Invasiveness; Neoplasm Recurrence, Local; Neoplasms, Experimental; Neural Stem Cells; Neuroblastoma; Neurofilament Proteins; Neurogenesis; Neurons; New York; NF-E2-Related Factor 2; NF-kappa B; Nicotine; Nitriles; Nitrogen; Nitrogen Fixation; North America; Observer Variation; Occupational Exposure; Ochrobactrum; Oils, Volatile; Olea; Oligosaccharides; Omeprazole; Open Field Test; Optimism; Oregon; Oryzias; Osmolar Concentration; Osteoarthritis; Osteoblasts; Osteogenesis; Ovarian Neoplasms; Ovariectomy; Oxadiazoles; Oxidation-Reduction; Oxidative Stress; Oxygen; Ozone; p38 Mitogen-Activated Protein Kinases; Pakistan; Pandemics; Particle Size; Particulate Matter; Patient-Centered Care; Pelargonium; Peptides; Perception; Peripheral Arterial Disease; Peroxides; Pets; Pharmaceutical Preparations; Pharmacogenetics; Phenobarbital; Phenols; Phenotype; Phosphates; Phosphatidylethanolamines; Phosphines; Phospholipids; Phosphorus; Phosphorylation; Photoacoustic Techniques; Photochemotherapy; Photosensitizing Agents; Phylogeny; Phytoestrogens; Pilot Projects; Plant Components, Aerial; Plant Extracts; Plant Immunity; Plant Leaves; Plant Oils; Plants, Medicinal; Plasmodium berghei; Plasmodium falciparum; Platelet Activation; Platelet Function Tests; Pneumonia, Viral; Poaceae; Pogostemon; Poloxamer; Poly I; Poly(ADP-ribose) Polymerase Inhibitors; Polychlorinated Biphenyls; Polychlorinated Dibenzodioxins; Polycyclic Compounds; Polyethylene Glycols; Polylysine; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Population Dynamics; Portasystemic Shunt, Transjugular Intrahepatic; Positron Emission Tomography Computed Tomography; Postoperative Complications; Postprandial Period; Potassium Cyanide; Predictive Value of Tests; Prefrontal Cortex; Pregnancy; Prepulse Inhibition; Prevalence; Procalcitonin; Prodrugs; Prognosis; Progression-Free Survival; Proline; Proof of Concept Study; Prospective Studies; Protein Binding; Protein Conformation; Protein Domains; Protein Folding; Protein Multimerization; Protein Sorting Signals; Protein Structure, Secondary; Proton Pump Inhibitors; Protozoan Proteins; Psychometrics; Pulse Wave Analysis; Pyridines; Pyrrolidines; Quality of Life; Quantum Dots; Quinoxalines; Quorum Sensing; Radiopharmaceuticals; Rain; Random Allocation; Randomized Controlled Trials as Topic; Rats; Rats, Sprague-Dawley; Rats, Wistar; RAW 264.7 Cells; Reactive Oxygen Species; Receptor, Angiotensin, Type 1; Receptor, PAR-1; Receptors, CXCR4; Receptors, Estrogen; Receptors, Glucocorticoid; Receptors, Interleukin-1; Receptors, Interleukin-17; Receptors, Notch; Recombinant Fusion Proteins; Recombinant Proteins; Reducing Agents; Reflex, Startle; Regional Blood Flow; Regression Analysis; Reperfusion Injury; Reproducibility of Results; Republic of Korea; Respiratory Tract Diseases; Retrospective Studies; Reverse Transcriptase Inhibitors; Rhinitis, Allergic; Risk Assessment; Risk Factors; Rituximab; RNA, Messenger; RNA, Ribosomal, 16S; ROC Curve; Rosmarinic Acid; Running; Ruthenium; Rutin; Sarcolemma; Sarcoma; Sarcopenia; Sarcoplasmic Reticulum; SARS-CoV-2; Scavenger Receptors, Class A; Schools; Seasons; Seeds; Sequence Analysis, DNA; Severity of Illness Index; Sex Factors; Shock, Cardiogenic; Short Chain Dehydrogenase-Reductases; Signal Transduction; Silver; Singlet Oxygen; Sinusitis; Skin; Skin Absorption; Small Molecule Libraries; Smoke; Socioeconomic Factors; Soil; Soil Microbiology; Solid Phase Extraction; Solubility; Solvents; Spain; Spectrometry, Mass, Electrospray Ionization; Spectroscopy, Fourier Transform Infrared; Speech; Speech Perception; Spindle Poles; Spleen; Sporothrix; Staphylococcal Infections; Staphylococcus aureus; Stereoisomerism; Stomach Neoplasms; Stress, Physiological; Stroke Volume; Structure-Activity Relationship; Substrate Specificity; Sulfonamides; Surface Properties; Surface-Active Agents; Surveys and Questionnaires; Survival Rate; T-Lymphocytes, Cytotoxic; Tandem Mass Spectrometry; Temperature; Tenofovir; Terpenes; Tetracycline; Tetrapleura; Textiles; Thermodynamics; Thiobarbituric Acid Reactive Substances; Thrombin; Thyroid Hormones; Thyroid Neoplasms; Tibial Meniscus Injuries; Time Factors; Tissue Distribution; Titanium; Toluidines; Tomography, X-Ray Computed; Tooth; Tramadol; Transcription Factor AP-1; Transcription, Genetic; Transfection; Transgender Persons; Translations; Treatment Outcome; Triglycerides; Ubiquinone; Ubiquitin-Specific Proteases; United Kingdom; United States; Up-Regulation; Vascular Stiffness; Veins; Ventricular Remodeling; Viral Load; Virulence Factors; Virus Replication; Vitis; Voice; Voice Quality; Wastewater; Water; Water Pollutants, Chemical; Water-Electrolyte Balance; Weather; Wildfires; Wnt Signaling Pathway; Wound Healing; X-Ray Diffraction; Xenograft Model Antitumor Assays; Young Adult; Zoogloea

A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Genome Size; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Normal functioning of phagocytic cells depends upon the integration of chemotaxis, phagocytosis, degranulation and oxidative metabolism. The availability of in vitro assays for the separate quantitative evaluation of each function has permitted the definition of specific congenital and acquired abnormalities of phagocytic cells which are associated with defective mechanisms of host resistance. The appreciation of complex and often adverse effects of certain systemic diseases and pharmacological agents on the phagocytes, as well as the use of new approaches to therapy underline the importance of assessing the role of phagocytic cells in states of impaired host defence. In addition, cellular immune mechanisms involving the interaction of T-cells and macrophages contribute essentially to the proper functioning of intracellular host defence, as indicated by the delayed type hypersensitivity reaction.

Topics: Antigens, Bacterial; Chemotaxis; Cytoplasmic Granules; Granulomatous Disease, Chronic; Humans; Hydrolases; Hypersensitivity, Delayed; Immunity, Cellular; Immunosuppression Therapy; Listeria; Listeriosis; Liver; Macrophages; Oxidation-Reduction; Oxygenases; Phagocytosis; Receptors, Complement; Receptors, Fc; Spleen; T-Lymphocytes; Ubiquinone

Unprecedented community containment measures were taken following the recent outbreak of COVID-19 in Italy. The aim of the study was to explore the self-reported future compliance of citizens with such measures and its relationship with potentially impactful psychological variables.. An online survey was completed by 931 people (18-76 years) distributed across the Italian territory. In addition to demographics, five dimensions were measured: self-reported compliance with containment measures over time (today, at 7, 14, 30, 60, 90, and 180 days from now) at three hypothetical risk levels (10, 50, 90% of likelihood of contracting the COVID-19), perceived risk, generalized anxiety, intolerance of uncertainty, and relevance of several psychological needs whose satisfaction is currently precluded.. The duration of containment measures plays a crucial role in tackling the spread of the disease as people will be less compliant over time. Psychological needs of citizens impacting on the compliance should be taken into account when planning an easing of the lockdown, along with interventions for protecting vulnerable groups from mental distress.. La apendicitis aguda (AA) es la urgencia quirúrgica abdominal más frecuente. No encontramos estudios específicos que evalúen el impacto de la pandemia causada por el coronavirus 2 (SARS-Cov-2) sobre la AA y su tratamiento quirúrgico. Analizamos la influencia de esta nueva patología sobre la AA.. Estudio observacional retrospectivo en pacientes intervenidos por AA desde enero hasta abril de 2020. Fueron clasificados según el momento de la apendicectomía, antes de la declaración del estado de alarma (Pre-COVID19) y después de la declaración del estado de alarma (Post-COVID19) en España. Se evaluaron variables demográficas, duración de la sintomatología, tipo de apendicitis, tiempo quirúrgico, estancia hospitalaria y complicaciones postoperatorias.. La pandemia por SARS-Cov-2 influye en el momento de diagnóstico de la apendicitis, así como en su grado de evolución y estancia hospitalaria. La peritonitis fue lo más frecuentemente observado. Una sospecha y orientación clínica más temprana, es necesaria para evitar un manejo inadecuado de este trastorno quirúrgico común.. The primary outcome is improvement in PaO. Findings will provide timely information on the safety, efficacy, and optimal dosing of t-PA to treat moderate/severe COVID-19-induced ARDS, which can be rapidly adapted to a phase III trial (NCT04357730; FDA IND 149634).. None.. The gut barrier is crucial in cirrhosis in preventing infection-causing bacteria that normally live in the gut from accessing the liver and other organs via the bloodstream. Herein, we characterised gut inflammation by measuring different markers in stool samples from patients at different stages of cirrhosis and comparing this to healthy people. These markers, when compared with equivalent markers usually measured in blood, were found to be very different in pattern and absolute levels, suggesting that there is significant gut inflammation in cirrhosis related to different immune system pathways to that seen outside of the gut. This provides new insights into gut-specific immune disturbances that predispose to complications of cirrhosis, and emphasises that a better understanding of the gut-liver axis is necessary to develop better targeted therapies.. La surveillance de l’intervalle QT a suscité beaucoup d’intérêt durant la pandémie de la COVID-19 en raison de l’utilisation de médicaments prolongeant l’intervalle QT et les préoccupations quant à la transmission virale par les électrocardiogrammes (ECG) en série. Nous avons posé l’hypothèse que la surveillance en continu de l’intervalle QT par télémétrie était associée à une meilleure détection des épisodes de prolongation de l’intervalle QT.. Nous avons introduit la télémétrie cardiaque en continu (TCC) à l’aide d’un algorithme de surveillance automatisée de l’intervalle QT dans nos unités de COVID-19. Les mesures automatisées quotidiennes de l’intervalle QT corrigé (auto-QTc) en fonction de la fréquence cardiaque maximale ont été enregistrées. Nous avons comparé la proportion des épisodes de prolongation marquée de l’intervalle QTc (QTc long), définie par un intervalle QTc ≥ 500 ms, chez les patients montrant une suspicion de COVID-19 ou ayant la COVID-19 qui avaient été admis avant et après la mise en place de la TCC (groupe témoin. La surveillance en continu de l’intervalle QT est supérieure à la norme de soins dans la détection des épisodes de QTc long et exige peu d’ECG. La réponse clinique aux épisodes de QTc long est sous-optimale.. Exposure to a model wildfire air pollution source modifies cardiovascular responses to HC challenge, suggesting air pollution sensitizes the body to systemic triggers.. Though the majority of HIV-infected adults who were on HAART had shown viral suppression, the rate of suppression was sub-optimal according to the UNAIDS 90-90-90 target to help end the AIDS pandemic by 2020. Nonetheless, the rate of immunological recovery in the study cohort was low. Hence, early initiation of HAART should be strengthened to achieve good virological suppression and immunological recovery.. Dust in Egyptian laying hen houses contains high concentrations of microorganisms and endotoxins, which might impair the health of birds and farmers when inhaled. Furthermore, laying hens in Egypt seem to be a reservoir for ESBL-producing Enterobacteriaceae. Thus, farmers are at risk of exposure to ESBL-producing bacteria, and colonized hens might transmit these bacteria into the food chain.. The lack of significant differences in the absolute changes and relative ratios of injury and repair biomarkers by contrast-associated AKI status suggests that the majority of mild contrast-associated AKI cases may be driven by hemodynamic changes at the kidney.. Most comparisons for different outcomes are based on very few studies, mostly low-powered, with an overall low CoE. Thus, the available evidence is considered insufficient to either support or refute CH effectiveness or to recommend one ICM over another. Therefore, further well-designed, larger RCTs are required.. PROSPERO database Identifier: CRD42016041953.. Untouched root canal at cross-section perimeter, the Hero 642 system showed 41.44% ± 5.62% and Reciproc R40 58.67% ± 12.39% without contact with instruments. Regarding the untouched area, Hero 642 system showed 22.78% ± 6.42% and Reciproc R40 34.35% ± 8.52%. Neither instrument achieved complete cross-sectional root canal debridement. Hero 642 system rotary taper 0.02 instruments achieved significant greater wall contact perimeter and area compared to reciprocate the Reciproc R40 taper 0.06 instrument.. Hero 642 achieved higher wall contact perimeter and area but, regardless of instrument size and taper, vital pulp during. The functional properties of the main mechanisms involved in the control of muscle Ca. This study showed that the anti-inflammatory effect of the iron-responsive product DHA in arthritis can be monitored by an iron-like radioactive tracer (. Attenuated vascular reactivity during pregnancy suggests that the systemic vasodilatory state partially depletes nitric oxide bioavailability. Preliminary data support the potential for MRI to identify vascular dysfunction in vivo that underlies PE. Level of Evidence 2 Technical Efficacy Stage 1 J. MAGN. RESON. IMAGING 2021;53:447-455.. La evaluación de riesgo es importante para predecir los resultados postoperatorios en pacientes con cáncer gastroesofágico. Este estudio de cohortes tuvo como objetivo evaluar los cambios en la composición corporal durante la quimioterapia neoadyuvante e investigar su asociación con complicaciones postoperatorias. MÉTODOS: Los pacientes consecutivos con cáncer gastroesofágico sometidos a quimioterapia neoadyuvante y cirugía con intención curativa entre 2016 y 2019, identificados a partir de una base de datos específica, se incluyeron en el estudio. Se utilizaron las imágenes de tomografía computarizada, antes y después de la quimioterapia neoadyuvante, para evaluar el índice de masa muscular esquelética, la sarcopenia y el índice de grasa visceral y subcutánea.. In this in vitro premature infant lung model, HF oscillation of BCPAP was associated with improved CO. Our results showed that HPC significantly promotes neurogenesis after MCAO and ameliorates neuronal injury.. Inflammatory markers are highly related to signs of systemic hypoperfusion in CS. Moreover, high PCT and IL-6 levels are associated with poor prognosis.. These findings indicate that Tetrapleura tetraptera fruit has a protective potential against stroke through modulation of redox and electrolyte imbalances, and attenuation of neurotransmitter dysregulation and other neurochemical dysfunctions. Tetrapleura tetraptera fruit could be a promising source for the discovery of bioactives for stroke therapy.

Topics: 3T3-L1 Cells; A Kinase Anchor Proteins; Acetates; Achilles Tendon; Acute Kidney Injury; Acute Pain; Acyclic Monoterpenes; Adenine Nucleotides; Adhesins, Escherichia coli; Adipocytes; Adipocytes, Brown; Adipogenesis; Administration, Inhalation; Administration, Oral; Adrenal Cortex Hormones; Adsorption; Adult; Aeromonas hydrophila; Africa; Aged; Aged, 80 and over; Agrobacterium tumefaciens; Air; Air Pollutants; Air Pollution; Air Pollution, Indoor; Algorithms; Alkaloids; Alkynes; Allosteric Regulation; Amines; Amino Acid Sequence; Amino Acids; Amino Acids, Branched-Chain; Aminoisobutyric Acids; Aminopyridines; Amyotrophic Lateral Sclerosis; Anaerobic Threshold; Angiography; Angiotensin II Type 1 Receptor Blockers; Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Animal Distribution; Animal Feed; Animal Nutritional Physiological Phenomena; Animals; Ankle Joint; Anti-Bacterial Agents; Anti-HIV Agents; Anti-Inflammatory Agents; Antibodies, Bacterial; Antifungal Agents; Antimalarials; Antineoplastic Agents; Antineoplastic Agents, Phytogenic; Antioxidants; Antiretroviral Therapy, Highly Active; Antiviral Agents; Aotidae; Apelin; Apoptosis; Arabidopsis Proteins; Argentina; Arginine; Artemisinins; Arthritis, Experimental; Arthritis, Rheumatoid; Arthroscopy; Aspergillus; Aspergillus niger; Asteraceae; Asthma; ATP Binding Cassette Transporter, Subfamily B, Member 1; ATP Binding Cassette Transporter, Subfamily G, Member 2; Auditory Cortex; Autoantibodies; Autophagy; Bacteria; Bacterial Infections; Bacterial Proteins; Bacterial Typing Techniques; Base Composition; Base Sequence; Basketball; Beclin-1; Benzhydryl Compounds; Benzimidazoles; Benzo(a)pyrene; Benzofurans; Benzoxazines; Bereavement; beta Catenin; beta-Lactamase Inhibitors; beta-Lactamases; beta-Lactams; Betacoronavirus; Betaine; Binding Sites; Biofilms; Biological Assay; Biological Availability; Biological Evolution; Biomarkers; Biomechanical Phenomena; Biopolymers; Biopsy; Bismuth; Blood Glucose; Blood Platelets; Blood Pressure; Body Composition; Body Weight; Bone Marrow; Bone Marrow Cells; Bone Regeneration; Boron; Botrytis; Brain Ischemia; Brain Neoplasms; Brain-Derived Neurotrophic Factor; Brazil; Breast Neoplasms; Breath Tests; Bronchoalveolar Lavage Fluid; Burkholderia; C-Reactive Protein; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Calcification, Physiologic; Calcium; Calcium Signaling; Calorimetry, Differential Scanning; Cameroon; Camptothecin; Candida; Candida albicans; Capillaries; Carbapenem-Resistant Enterobacteriaceae; Carbapenems; Carbohydrate Conformation; Carbon; Carbon Dioxide; Carbon Isotopes; Carcinoma, Ovarian Epithelial; Cardiac Output; Cardiomyopathy, Hypertrophic; Cardiotonic Agents; Cardiovascular Diseases; Caregivers; Carps; Case-Control Studies; Catalase; Catalysis; Cats; CD4 Lymphocyte Count; Cell Culture Techniques; Cell Differentiation; Cell Line, Tumor; Cell Membrane; Cell Movement; Cell Proliferation; Cell Survival; Cells, Cultured; Cellulose; Centrosome; Ceratopogonidae; Chickens; Child; China; Cholera Toxin; Choline; Cholinesterases; Chromatography, High Pressure Liquid; Chromatography, Liquid; Chromatography, Micellar Electrokinetic Capillary; Chromatography, Reverse-Phase; Chronic Disease; Cinnamates; Cities; Citrates; Climate Change; Clinical Trials, Phase III as Topic; Coal; Coal Mining; Cohort Studies; Coinfection; Colchicine; Colony Count, Microbial; Colorectal Neoplasms; Coloring Agents; Common Cold; Complement Factor H; Computational Biology; Computer Simulation; Continuous Positive Airway Pressure; Contrast Media; Coordination Complexes; Coronary Artery Bypass; Coronavirus 3C Proteases; Coronavirus Infections; Coronavirus Protease Inhibitors; Corynebacterium glutamicum; Cosmetics; COVID-19; Creatinine; Cross-Sectional Studies; Crotonates; Crystallography, X-Ray; Cues; Culicidae; Culture Media; Curcuma; Cyclopentanes; Cyclopropanes; Cymbopogon; Cystine; Cytochrome P-450 CYP2B6; Cytochrome P-450 CYP2C19; Cytochrome P-450 CYP2C19 Inhibitors; Cytokines; Databases, Genetic; Death; Dendritic Cells; Density Functional Theory; Depsides; Diabetes Mellitus, Type 2; Diamond; Diarylheptanoids; Dibenzofurans; Dibenzofurans, Polychlorinated; Diclofenac; Diet; Dietary Carbohydrates; Dietary Supplements; Diffusion Magnetic Resonance Imaging; Dioxins; Diphenylamine; Disease Outbreaks; Disease Susceptibility; Disulfides; Dithiothreitol; Dizocilpine Maleate; DNA Methylation; DNA-Binding Proteins; DNA, Bacterial; Dogs; Dose-Response Relationship, Drug; Double-Blind Method; Doublecortin Protein; Drosophila melanogaster; Droughts; Drug Carriers; Drug Combinations; Drug Delivery Systems; Drug Liberation; Drug Resistance; Drug Resistance, Bacterial; Drug Resistance, Neoplasm; Drug Screening Assays, Antitumor; Dust; Dynactin Complex; Dysferlin; Echo-Planar Imaging; Echocardiography; Edaravone; Egypt; Elasticity; Electrodes; Electrolytes; Emodin; Emtricitabine; Endometriosis; Endothelium, Vascular; Endotoxins; Energy Metabolism; Energy Transfer; Enterobacteriaceae; Enterococcus faecalis; Enterotoxigenic Escherichia coli; Environmental Monitoring; Enzyme Inhibitors; Epidemiologic Factors; Epigenesis, Genetic; Erythrocytes; Escherichia coli; Escherichia coli Infections; Escherichia coli Vaccines; Esophageal Neoplasms; Esophagectomy; Esophagogastric Junction; Esterases; Esterification; Ethanol; Ethiopia; Ethnicity; Eucalyptus; Evidence-Based Practice; Exercise; Exercise Tolerance; Extracorporeal Membrane Oxygenation; Family; Fatty Acids; Feedback; Female; Ferric Compounds; Fibrin Fibrinogen Degradation Products; Filtration; Fish Diseases; Flavonoids; Flavonols; Fluorodeoxyglucose F18; Follow-Up Studies; Food Microbiology; Food Preservation; Forests; Fossils; Free Radical Scavengers; Freund's Adjuvant; Fruit; Fungi; Gallium; Gender Identity; Gene Expression Regulation; Gene Expression Regulation, Neoplastic; Gene Expression Regulation, Plant; Gene Knockdown Techniques; Genes, Bacterial; Genes, Plant; Genetic Predisposition to Disease; Genitalia; Genotype; Glomerulonephritis, IGA; Glottis; Glucocorticoids; Glucose; Glucuronides; Glutathione Transferase; Glycogen Synthase Kinase 3 beta; Gram-Negative Bacterial Infections; Gram-Positive Bacterial Infections; Grassland; Guinea Pigs; Half-Life; Head Kidney; Heart Atria; Heart Rate; Heart Septum; HEK293 Cells; Hematopoietic Stem Cells; Hemodynamics; Hep G2 Cells; Hepacivirus; Hepatitis C; Hepatitis C, Chronic; Hepatocytes; Hesperidin; High-Frequency Ventilation; High-Temperature Requirement A Serine Peptidase 1; Hippocampus; Hirudins; History, 20th Century; History, 21st Century; HIV Infections; Homeostasis; Hominidae; Housing, Animal; Humans; Hydrocarbons, Brominated; Hydrogen Bonding; Hydrogen Peroxide; Hydrogen-Ion Concentration; Hydroxybutyrates; Hydroxyl Radical; Hypertension; Hypothyroidism; Image Interpretation, Computer-Assisted; Immunoconjugates; Immunogenic Cell Death; Indoles; Infant, Newborn; Infant, Premature; Infarction, Middle Cerebral Artery; Inflammation; Inflammation Mediators; Infrared Rays; Inhibitory Concentration 50; Injections, Intravenous; Interferon-gamma; Interleukin-23; Interleukin-4; Interleukin-6; Intermediate Filaments; Intermittent Claudication; Intestine, Small; Iridoid Glucosides; Iridoids; Iron; Isomerism; Isotope Labeling; Isoxazoles; Itraconazole; Kelch-Like ECH-Associated Protein 1; Ketoprofen; Kidney Failure, Chronic; Kinetics; Klebsiella pneumoniae; Lactams, Macrocyclic; Lactobacillus; Lactulose; Lakes; Lamivudine; Laparoscopy; Laparotomy; Laryngoscopy; Leucine; Limit of Detection; Linear Models; Lipid A; Lipopolysaccharides; Listeria monocytogenes; Liver; Liver Cirrhosis; Logistic Models; Longitudinal Studies; Losartan; Low Back Pain; Lung; Lupinus; Lupus Erythematosus, Systemic; Machine Learning; Macular Degeneration; Madin Darby Canine Kidney Cells; Magnetic Phenomena; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Magnetics; Malaria, Falciparum; Male; Mannans; MAP Kinase Signaling System; Mass Spectrometry; Melatonin; Membrane Glycoproteins; Membrane Proteins; Meniscectomy; Menisci, Tibial; Mephenytoin; Mesenchymal Stem Cells; Metal Nanoparticles; Metal-Organic Frameworks; Methionine; Mice; Mice, Inbred C57BL; Mice, Knockout; Mice, Nude; Mice, Obese; Mice, Transgenic; Microbial Sensitivity Tests; Microcirculation; MicroRNAs; Microscopy, Video; Microtubules; Microvascular Density; Microwaves; Middle Aged; Minimally Invasive Surgical Procedures; Models, Animal; Models, Biological; Models, Molecular; Models, Theoretical; Molecular Docking Simulation; Molecular Structure; Molecular Weight; Morus; Mouth Floor; Multicenter Studies as Topic; Multiple Sclerosis; Multiple Sclerosis, Relapsing-Remitting; Muscle, Skeletal; Myocardial Ischemia; Myocardium; NAD; NADP; Nanocomposites; Nanoparticles; Naphthols; Nasal Lavage Fluid; Nasal Mucosa; Neisseria meningitidis; Neoadjuvant Therapy; Neoplasm Invasiveness; Neoplasm Recurrence, Local; Neoplasms, Experimental; Neural Stem Cells; Neuroblastoma; Neurofilament Proteins; Neurogenesis; Neurons; New York; NF-E2-Related Factor 2; NF-kappa B; Nicotine; Nitriles; Nitrogen; Nitrogen Fixation; North America; Observer Variation; Occupational Exposure; Ochrobactrum; Oils, Volatile; Olea; Oligosaccharides; Omeprazole; Open Field Test; Optimism; Oregon; Oryzias; Osmolar Concentration; Osteoarthritis; Osteoblasts; Osteogenesis; Ovarian Neoplasms; Ovariectomy; Oxadiazoles; Oxidation-Reduction; Oxidative Stress; Oxygen; Ozone; p38 Mitogen-Activated Protein Kinases; Pakistan; Pandemics; Particle Size; Particulate Matter; Patient-Centered Care; Pelargonium; Peptides; Perception; Peripheral Arterial Disease; Peroxides; Pets; Pharmaceutical Preparations; Pharmacogenetics; Phenobarbital; Phenols; Phenotype; Phosphates; Phosphatidylethanolamines; Phosphines; Phospholipids; Phosphorus; Phosphorylation; Photoacoustic Techniques; Photochemotherapy; Photosensitizing Agents; Phylogeny; Phytoestrogens; Pilot Projects; Plant Components, Aerial; Plant Extracts; Plant Immunity; Plant Leaves; Plant Oils; Plants, Medicinal; Plasmodium berghei; Plasmodium falciparum; Platelet Activation; Platelet Function Tests; Pneumonia, Viral; Poaceae; Pogostemon; Poloxamer; Poly I; Poly(ADP-ribose) Polymerase Inhibitors; Polychlorinated Biphenyls; Polychlorinated Dibenzodioxins; Polycyclic Compounds; Polyethylene Glycols; Polylysine; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Population Dynamics; Portasystemic Shunt, Transjugular Intrahepatic; Positron Emission Tomography Computed Tomography; Postoperative Complications; Postprandial Period; Potassium Cyanide; Predictive Value of Tests; Prefrontal Cortex; Pregnancy; Prepulse Inhibition; Prevalence; Procalcitonin; Prodrugs; Prognosis; Progression-Free Survival; Proline; Proof of Concept Study; Prospective Studies; Protein Binding; Protein Conformation; Protein Domains; Protein Folding; Protein Multimerization; Protein Sorting Signals; Protein Structure, Secondary; Proton Pump Inhibitors; Protozoan Proteins; Psychometrics; Pulse Wave Analysis; Pyridines; Pyrrolidines; Quality of Life; Quantum Dots; Quinoxalines; Quorum Sensing; Radiopharmaceuticals; Rain; Random Allocation; Randomized Controlled Trials as Topic; Rats; Rats, Sprague-Dawley; Rats, Wistar; RAW 264.7 Cells; Reactive Oxygen Species; Receptor, Angiotensin, Type 1; Receptor, PAR-1; Receptors, CXCR4; Receptors, Estrogen; Receptors, Glucocorticoid; Receptors, Interleukin-1; Receptors, Interleukin-17; Receptors, Notch; Recombinant Fusion Proteins; Recombinant Proteins; Reducing Agents; Reflex, Startle; Regional Blood Flow; Regression Analysis; Reperfusion Injury; Reproducibility of Results; Republic of Korea; Respiratory Tract Diseases; Retrospective Studies; Reverse Transcriptase Inhibitors; Rhinitis, Allergic; Risk Assessment; Risk Factors; Rituximab; RNA, Messenger; RNA, Ribosomal, 16S; ROC Curve; Rosmarinic Acid; Running; Ruthenium; Rutin; Sarcolemma; Sarcoma; Sarcopenia; Sarcoplasmic Reticulum; SARS-CoV-2; Scavenger Receptors, Class A; Schools; Seasons; Seeds; Sequence Analysis, DNA; Severity of Illness Index; Sex Factors; Shock, Cardiogenic; Short Chain Dehydrogenase-Reductases; Signal Transduction; Silver; Singlet Oxygen; Sinusitis; Skin; Skin Absorption; Small Molecule Libraries; Smoke; Socioeconomic Factors; Soil; Soil Microbiology; Solid Phase Extraction; Solubility; Solvents; Spain; Spectrometry, Mass, Electrospray Ionization; Spectroscopy, Fourier Transform Infrared; Speech; Speech Perception; Spindle Poles; Spleen; Sporothrix; Staphylococcal Infections; Staphylococcus aureus; Stereoisomerism; Stomach Neoplasms; Stress, Physiological; Stroke Volume; Structure-Activity Relationship; Substrate Specificity; Sulfonamides; Surface Properties; Surface-Active Agents; Surveys and Questionnaires; Survival Rate; T-Lymphocytes, Cytotoxic; Tandem Mass Spectrometry; Temperature; Tenofovir; Terpenes; Tetracycline; Tetrapleura; Textiles; Thermodynamics; Thiobarbituric Acid Reactive Substances; Thrombin; Thyroid Hormones; Thyroid Neoplasms; Tibial Meniscus Injuries; Time Factors; Tissue Distribution; Titanium; Toluidines; Tomography, X-Ray Computed; Tooth; Tramadol; Transcription Factor AP-1; Transcription, Genetic; Transfection; Transgender Persons; Translations; Treatment Outcome; Triglycerides; Ubiquinone; Ubiquitin-Specific Proteases; United Kingdom; United States; Up-Regulation; Vascular Stiffness; Veins; Ventricular Remodeling; Viral Load; Virulence Factors; Virus Replication; Vitis; Voice; Voice Quality; Wastewater; Water; Water Pollutants, Chemical; Water-Electrolyte Balance; Weather; Wildfires; Wnt Signaling Pathway; Wound Healing; X-Ray Diffraction; Xenograft Model Antitumor Assays; Young Adult; Zoogloea

Im Rahmen der vorliegenden Studie sollte der Einfluss des Weichteilschadens auf das klinische Ergebnis nach offener Ellenbogenluxation untersucht werden.. Von Oktober 2008 bis August 2015 wurden insgesamt 230 Patienten mit Ellenbogenluxation behandelt. Diese retrospektive Studie umfasst 21 Fälle von offenen Ellenbogenluxationen. Das Durchschnittsalter der Patienten betrug 49 Jahre alt (20–83 Jahre), 6 Patienten waren weiblich (29%), 15 männlich (71%). Das Bewegungsausmaß des verletzten und unverletzten Ellenbogens wurde erhoben und das funktionelle Ergebnis u. a. mittels Mayo Elbow Performance Score (MEPS), Mayo Wrist Score (MWS) und dem Disability of Arm, Shoulder and Hand (DASH) Score erfasst. Zusätzlich wurden Komplikationen und Revisionsoperationen aufgezeichnet. Der Einfluss des Weichteilschadens (I°/II° offen vs. III° offen) und des Luxationstyps (einfach vs. komplex) auf das klinische Ergebnis wurde analysiert.. Offene Ellenbogenluxationen können mit einem zufriedenstellenden klinischen Ergebnis einhergehen. Insbesondere komplexe offene Ellenbogenluxationen sind jedoch sehr komplikationsbehaftet, wobei neurovaskuläre Komplikationen am häufigsten auftreten.. The current high rate of multidrug-resistant gram-negative bacteria infections among hospitalised patients with cUTIs in the studied area is alarming. Our predictive model could be useful to avoid inappropriate antibiotic treatment and implement antibiotic stewardship policies that enhance the use of carbapenem-sparing regimens in patients at low risk of multidrug-resistance.. The results indicated differential patterns of Inhibition of Return between the High and Low shape/weight based self-worth groups. The High group displayed increased inhibition of return for the shape/weight stimuli relative to control stimuli, while the Low group displayed reduced inhibition of return for the shape/weight stimuli compared to control stimuli. The ED group displayed a similar pattern of results to the High group, but this did not reach significance.. The current findings indicate that young women without an eating disorder who base their self-worth on shape/weight display a pattern of avoidance of shape/weight stimuli that is in direct contrast to those at low risk of developing eating disorders. The possible implications of these specific patterns of inhibition of return across those at varying levels of risk for an eating disorder are discussed along with their implications for intervention approaches.. These results indicated that Sr. An unusually high HbA

Topics: Activities of Daily Living; Acute Disease; Adalimumab; Adaptation, Physiological; Adenosine Triphosphate; Adipose Tissue; Administration, Intravaginal; Adolescent; Adsorption; Adult; Adverse Childhood Experiences; Age Distribution; Age Factors; Aged; Aged, 80 and over; Air Pollution, Indoor; Aldehyde Oxidase; Alginates; Alloys; alpha-Globins; Aluminum Hydroxide; Alveolar Bone Loss; Anaerobiosis; Anesthesia, General; Anesthetics; Animals; Anovulation; Anti-Bacterial Agents; Anti-Infective Agents; Anti-Inflammatory Agents, Non-Steroidal; Antibodies, Monoclonal, Humanized; Antineoplastic Agents; Apoptosis; Bacillus cereus; Bacterial Typing Techniques; Bacteroidetes; Base Composition; Biocompatible Materials; Biofilms; Biological Availability; Biological Transport; Biosensing Techniques; Bipolar Disorder; Blood Glucose; Body Mass Index; Bone Regeneration; Boranes; Brachial Artery; Butyric Acid; Candida albicans; Carbon; Carcinoembryonic Antigen; Cell Differentiation; Cell Line, Tumor; Cell Respiration; Cell Survival; Cells, Cultured; Cerebrovascular Circulation; Charcoal; Child; Child Health; China; Chloride Channels; Chlorides; CHO Cells; Chromatography, Liquid; Chromatography, Micellar Electrokinetic Capillary; Chromium; Chronic Disease; Chronic Periodontitis; Circular Dichroism; Cities; Cohort Studies; Comamonadaceae; Comorbidity; Coronary Artery Disease; Corrosion; Cricetinae; Cricetulus; Cross Infection; Cross-Sectional Studies; Crowding; Culture Media; Cytokines; Diabetes Mellitus; Diabetes Mellitus, Type 2; Diabetes, Gestational; Diarylheptanoids; Diclofenac; Disability Evaluation; Diterpene Alkaloids; DNA; DNA Mutational Analysis; DNA, Bacterial; Drug Liberation; Drug Resistance, Multiple, Bacterial; Electrochemical Techniques; Electrodes; Electrolytes; Endothelium, Vascular; Enterococcus faecalis; Epithelial Cell Adhesion Molecule; Epithelial Cells; Erbium; Erythropoietin; Ethanol; Ethylenediamines; Fast Foods; Fatty Acids; Female; Fermentation; Ferric Compounds; Fibroblasts; Flavobacteriaceae; Fluorides; Fluorodeoxyglucose F18; Food Microbiology; Formaldehyde; Furaldehyde; Gamma Cameras; Gene Expression; Geologic Sediments; Glucose Tolerance Test; Glycated Hemoglobin; Glycolipids; Glycosylation; Gracilaria; Gram-Negative Bacteria; Gram-Negative Bacterial Infections; Guanine; Health Surveys; HeLa Cells; Hemoglobins, Abnormal; Hexosamines; High Fructose Corn Syrup; High-Intensity Interval Training; Hip Fractures; Hippocampus; HLA-B27 Antigen; Hospitalization; Housing; Humans; Hydrogen-Ion Concentration; Hydrolysis; Hydroxides; Hypercapnia; Hypertension; Hypocreales; Hypromellose Derivatives; Image Processing, Computer-Assisted; Incidence; Indole Alkaloids; Indonesia; Inflammation Mediators; Infrared Rays; Insulin Resistance; Intercalating Agents; Ion Transport; Ionophores; Japan; Kinetics; Kluyveromyces; Letrozole; Linear Models; Lipopolysaccharides; Liposomes; Liver; Lung Diseases; Magnesium Hydroxide; Magnetic Resonance Spectroscopy; Male; Membrane Glycoproteins; Membrane Transport Proteins; Mice, Inbred BALB C; Microbial Sensitivity Tests; Microbial Viability; Microscopy, Electron, Transmission; Middle Aged; Mitochondria; Mitochondria, Muscle; Molecular Docking Simulation; Molecular Structure; Muscle, Skeletal; Mutant Proteins; Mutation; Mutation, Missense; Nanocomposites; Nanoparticles; Neoplasm Recurrence, Local; Neoplastic Cells, Circulating; Nucleic Acid Hybridization; Obesity; Occupational Exposure; Oceans and Seas; Odds Ratio; Organometallic Compounds; Osteogenesis; Ovulation Induction; Oxidation-Reduction; Particle Size; Periodontal Ligament; Permeability; Phaseolus; Phenotype; Philippines; Phosphatidylethanolamines; Phospholipids; Photochemical Processes; Phylogeny; Pichia; Pigmentation; Plant Extracts; Polycystic Ovary Syndrome; Polysaccharides; Postprandial Period; Pregnancy; Pregnancy Rate; Prevalence; Product Surveillance, Postmarketing; Progesterone; Progestins; Protein Engineering; Pseudomonas aeruginosa; Psoriasis; Public Facilities; Rats; Rats, Wistar; Receptors, Thyrotropin; Recombinant Proteins; Reproducibility of Results; Republic of Korea; Retrospective Studies; Rhodobacteraceae; Risk; Risk Assessment; Risk Factors; RNA, Ribosomal, 16S; ROC Curve; Saccharomyces cerevisiae; Salinity; Saliva; Seawater; Seaweed; Sensitivity and Specificity; Sequence Analysis, DNA; Sex Factors; Silver Compounds; Smokers; Social Class; Socioeconomic Factors; Soil Microbiology; Solubility; Soy Foods; Spectrometry, Mass, Electrospray Ionization; Spondylitis, Ankylosing; Staphylococcus aureus; Static Electricity; Steroids; Strontium; Sucrose; Surface Properties; Survival Rate; Sweden; Swine; Synapses; Synchrotrons; Tandem Mass Spectrometry; Tannins; Tea; Temperature; Terpenes; Thalidomide; Thermodynamics; Thiadiazoles; Thyroid Cancer, Papillary; Thyroid Neoplasms; Thyroidectomy; Time Factors; Tissue Distribution; Titanium; Toilet Facilities; Tomography, Emission-Computed, Single-Photon; Treatment Outcome; Ubiquinone; Urinary Tract Infections; Vaginal Creams, Foams, and Jellies; Venezuela; Vitamin K 2; Waist Circumference; Waste Disposal, Fluid; Wastewater; Water Microbiology; Water Pollutants, Chemical; Whole Body Imaging; X-Ray Diffraction; Young Adult; Ytterbium; Yttrium; Yttrium Radioisotopes; Zinc Compounds

Small-molecule tools have enabled mechanistic investigations and therapeutic targeting of the protein kinase-like (PKL) superfamily. However, such tools are still lacking for many PKL members, including the highly conserved and disease-related UbiB family. Here, we sought to develop and characterize an inhibitor for the archetypal UbiB member COQ8, whose function is essential for coenzyme Q (CoQ) biosynthesis. Guided by crystallography, activity assays and cellular CoQ measurements, we repurposed the 4-anilinoquinoline scaffold to selectively inhibit human COQ8A in cells. Our chemical tool promises to lend mechanistic insights into the activities of these widespread and understudied proteins and to offer potential therapeutic strategies for human diseases connected to their dysfunction.

Topics: Humans; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Ubiquinone

Francisella tularensis is the causative agent of tularemia. Because of its extreme infectivity and high mortality rate, this pathogen was classified as a biothreat agent.

Topics: Bacterial Proteins; Biosynthetic Pathways; Francisella; Gene Expression Regulation, Bacterial; Ubiquinone; Virulence

Twelve Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (CY7W

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Cytochrome bd quinol:O

Topics: Bacterial Outer Membrane Proteins; Cytochromes; Electron Transport Chain Complex Proteins; Escherichia coli; Escherichia coli Proteins; Oxidation-Reduction; Oxidoreductases; Quinolones; Ubiquinone

A novel species is proposed for a high-affinity methanotrophic representative of the genus

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Methylocystaceae; Moscow; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Taiga; Ubiquinone

Over a period of 1 year, 270 isolates identified as Taxon 39 of Bisgaard were obtained from the nasopharynx of veal calves at 11 epidemiologically independent Swiss fattening farms. Two isolates from each farm and the Australian Taxon 39 reference strain BNO311 were further characterized by genetic and phenotypic methods. Phylogenetic analysis of 16S rRNA and

Topics: Animals; Bacterial Typing Techniques; Base Composition; Cattle; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Mannheimia; Phylogeny; Respiratory System; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Switzerland; Ubiquinone

Taxonomic positions of six isolates, which were recovered from two different environments in Jeju, Republic of Korea, were examined by a polyphasic analysis. Cells of the isolates were Gram-reaction-negative, facultatively anaerobic, motile and rod-shaped and showed growth at 4-30 °C, pH 4.0-9.0 and with 0-6 (w/v) NaCl. In phylogenomic analysis based on 92 single-copy core genes, it was shown that the isolates belonged to the genus

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Rahnella; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Two independent structures of the proton-pumping, respiratory cytochrome

Topics: Binding Sites; Cryoelectron Microscopy; Cytochrome b Group; Escherichia coli; Escherichia coli Proteins; Heme; Oxidation-Reduction; Phospholipids; Protein Conformation; Proton Pumps; Ubiquinone

Two Gram-negative strains obtained from tank water in a scallop hatchery in Norway, were phenotypically and genotypically characterized in order to clarify their taxonomic position. On the basis of 16S rRNA gene sequence analysis, these isolates, ATF 5.2

Topics: Bacterial Proteins; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Essential; Genome, Bacterial; Halomonas; Norway; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Species Specificity; Ubiquinone

Strain ISS155

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Mediterranean Sea; Phospholipids; Phyllobacteriaceae; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Ubiquinone 8 (coenzyme Q8 or Q8) mediates electron transfer within the aerobic respiratory chain, mitigates oxidative stress, and contributes to gene expression in

Topics: Aerobiosis; Anisotropy; Escherichia coli; Escherichia coli Proteins; Fluorescence; Membrane Fluidity; Membrane Transport Proteins; Mutation; Osmolar Concentration; Osmotic Pressure; Proteolipids; Trehalose; Ubiquinone

The taxonomic position of an unknown bacterial strain designated CNM695-12, isolated from the blood of an immunocompromised subject, was investigated via phenotypic, chemotaxonomic, genotypic and genomic analyses. Bacterial cells were determined to be Gram-stain-negative bacilli, aerobic, non-motile and non-spore-forming. The strain showed catalase activity but no oxidase activity. Optimal growth occurred at 37 °C, pH 7 and with 0-1 % NaCl. C

Topics: Aged, 80 and over; Bacterial Typing Techniques; Base Composition; Betaproteobacteria; Blood; DNA, Bacterial; Fatty Acids; Humans; Male; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spain; Ubiquinone

Four strains assigned the names FT13W

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

To foster trial-readiness of coenzyme Q8A (COQ8A)-ataxia, we map the clinicogenetic, molecular, and neuroimaging spectrum of COQ8A-ataxia in a large worldwide cohort, and provide first progression data, including treatment response to coenzyme Q10 (CoQ10).. Cross-modal analysis of a multicenter cohort of 59 COQ8A patients, including genotype-phenotype correlations, 3D-protein modeling, in vitro mutation analyses, magnetic resonance imaging (MRI) markers, disease progression, and CoQ10 response data.. Fifty-nine patients (39 novel) with 44 pathogenic COQ8A variants (18 novel) were identified. Missense variants demonstrated a pleiotropic range of detrimental effects upon protein modeling and in vitro analysis of purified variants. COQ8A-ataxia presented as variable multisystemic, early-onset cerebellar ataxia, with complicating features ranging from epilepsy (32%) and cognitive impairment (49%) to exercise intolerance (25%) and hyperkinetic movement disorders (41%), including dystonia and myoclonus as presenting symptoms. Multisystemic involvement was more prevalent in missense than biallelic loss-of-function variants (82-93% vs 53%; p = 0.029). Cerebellar atrophy was universal on MRI (100%), with cerebral atrophy or dentate and pontine T2 hyperintensities observed in 28%. Cross-sectional (n = 34) and longitudinal (n = 7) assessments consistently indicated mild-to-moderate progression of ataxia (SARA: 0.45/year). CoQ10 treatment led to improvement by clinical report in 14 of 30 patients, and by quantitative longitudinal assessments in 8 of 11 patients (SARA: -0.81/year). Explorative sample size calculations indicate that ≥48 patients per arm may suffice to demonstrate efficacy for interventions that reduce progression by 50%.. This study provides a deeper understanding of the disease, and paves the way toward large-scale natural history studies and treatment trials in COQ8A-ataxia. ANN NEUROL 2020;88:251-263.

Topics: Adolescent; Adult; Aged; Cerebellar Ataxia; Child; Child, Preschool; Cohort Studies; Cross-Sectional Studies; Female; Genetic Variation; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Mutation; Protein Structure, Secondary; Ubiquinone; Young Adult

Two Gram-stain-negative, catalase- and oxidase-positive, rod-shaped, motile strains (FT29W

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Pseudomonas aeruginosa is a widely found opportunistic pathogen. The emergence of multidrug-resistant strains and persistent chronic infections have increased. The protein encoded by the pa0423 gene in P. aeruginosa is proposed to be critical for pathogenesis and could be a virulence-promoting protease or a bacterial lipocalin that binds a lipid-like antibiotic for drug resistance. Although two functions of proteolysis and antibiotic resistance are mutually related to bacterial survival in the host, it is very unusual for a single-domain protein to target unrelated ligand molecules such as protein substrates and lipid-like antibiotics. To clearly address the biological role of the PA0423 protein, we performed structural and biochemical studies. We found that PA0423 adopts a single-domain β-barrel structure and belongs to the lipocalin family. The PA0423 structure houses an internal tubular cavity, which accommodates a ubiquinone-8 molecule. Furthermore, we reveal that PA0423 can directly interact with the polymyxin B antibiotic using the internal cavity, suggesting that PA0423 has a physiological function in the antibiotic resistance of P. aeruginosa.

Topics: Amino Acid Sequence; Anti-Bacterial Agents; Bacterial Proteins; Crystallography, X-Ray; Hydrophobic and Hydrophilic Interactions; Ligands; Lipocalins; Models, Molecular; Polymyxin B; Protein Structure, Secondary; Pseudomonas aeruginosa; Recombinant Proteins; Solubility; Structural Homology, Protein; Ubiquinone

Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT9W

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-negative, psychrophilic bacterium, designated strain GS1

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Forests; Oxalobacteraceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil; Soil Microbiology; Taiwan; Ubiquinone

An aerobic methane oxidizing bacterium, designated XLMV4

Topics: Alberta; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Methane; Methanol; Methylococcaceae; Nucleic Acid Hybridization; Oil and Gas Fields; Phylogeny; Pigmentation; Ponds; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, aerobic, non-motile and coccoid methanotroph, strain IM1

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hot Springs; Methylococcus; Nucleic Acid Hybridization; Oxygenases; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A novel thermophilic phototrophic purple sulphur bacterium was isolated from microbial mats (56 °C) at Nakabusa hot springs, Nagano prefecture, Japan. Cells were motile, rod-shaped, stain Gram-negative and stored sulphur globules intracellularly. Bacteriochlorophyll

Topics: Bacterial Typing Techniques; Base Composition; Chromatiaceae; DNA, Bacterial; Fatty Acids; Hot Springs; Japan; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sulfides; Sulfur; Thiosulfates; Ubiquinone

Two plant-associated bacterial strains were isolated from Beijing, China. The two strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. The average nucleotide identity (ANI) value and the digital DNA-DNA hybridization (dDDH) value between the two strains were 99.4% and 94.7%, respectively, suggesting that they belonged to the same species. The 16S rRNA gene phylogeny analysis indicated that the two strains belonged to the genus Variovorax and were closely related to V. paradoxus NBRC 15149

Topics: Bacterial Typing Techniques; Base Composition; Beijing; Comamonadaceae; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Solanum lycopersicum; Ubiquinone; Zea mays

A Gram-stain-negative, aerobic and non-motile strain, designated 18x22-1

Topics: Bacterial Typing Techniques; Base Composition; China; Comamonadaceae; DNA, Bacterial; Fatty Acids; Forests; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Tropical Climate; Ubiquinone

Two

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Cytochrome bd-type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of the

Topics: Catalytic Domain; Cryoelectron Microscopy; Cytochrome b Group; Electron Transport Chain Complex Proteins; Escherichia coli; Escherichia coli Proteins; Heme; Models, Molecular; Oxidation-Reduction; Oxidoreductases; Oxygen; Protein Structure, Quaternary; Protein Subunits; Protons; Ubiquinone

Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus contributing to the generation of the protonmotive force. Here, we determine the structure of the Escherichia coli bd oxidase treated with the specific inhibitor aurachin by cryo-electron microscopy (cryo-EM). The major subunits CydA and CydB are related by a pseudo two fold symmetry. The heme b and d cofactors are found in CydA, while ubiquinone-8 is bound at the homologous positions in CydB to stabilize its structure. The architecture of the E. coli enzyme is highly similar to that of Geobacillus thermodenitrificans, however, the positions of heme b

Topics: Cytochrome b Group; Electron Transport Chain Complex Proteins; Escherichia coli; Escherichia coli Proteins; Geobacillus; Heme; Models, Molecular; Oxidoreductases; Oxygen; Protons; Sequence Homology, Amino Acid; Substrate Specificity; Ubiquinone; Water

Two isolates of heterotrophic, facultatively anaerobic, marine bacteria, designated DM1 and DM2

Topics: Aeromonadaceae; Anaerobiosis; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fermentation; Gases; Geologic Sediments; Glucose; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Taiwan; Ubiquinone

Pandoraea species have been isolated from diverse environmental samples and are emerging important respiratory pathogens, particularly in people with cystic fibrosis (CF). In the present study, two bacterial isolates initially recovered from consecutive sputum samples collected from a CF patient and identified as Pandoraea pnomenusa underwent a polyphasic taxonomic analysis. The isolates were found to be Gram-negative, facultative anaerobic motile bacilli and subsequently designated as strains 6399

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; Cystic Fibrosis; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Humans; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sputum; Tasmania; Ubiquinone

A novel aerobic bacterial strain, designated ZS60

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Lysobacter; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Dyella-like bacterium was previously isolated from the planthopper Hyalesthes obsoletus (Hemiptera). Based on its 16S rRNA gene sequence, strain DHo

Topics: Animals; Bacterial Typing Techniques; Base Composition; Disease Vectors; DNA, Bacterial; Fatty Acids; Hemiptera; Israel; Nucleic Acid Hybridization; Phylogeny; Pigmentation; Pseudomonadaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Glycolipids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A slightly beige-pigmented, Gram-stain-negative, rod-shaped bacterium, strain IMT-318

Topics: Alabama; Alcaligenaceae; Bacterial Typing Techniques; Base Composition; Diaminopimelic Acid; DNA, Bacterial; Fatty Acids; Humic Substances; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A white-coloured, Gram-stain-negative, aerobic, rod-shaped bacterium (designated strain SY21

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone; Wastewater; Xanthomonadaceae

A Gram-negative, rod-shaped bacterium, designated KH87

Topics: Bacterial Typing Techniques; Base Composition; Chromatiaceae; DNA, Bacterial; Fatty Acids; Hawaii; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Vitamin K 2

AFrancisella-like bacterium, designated strain SYSU HZH-2

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Lakes; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-staining negative, aerobic, non-motile, rod-shaped bacterial strain, designated YS-37

Topics: Base Composition; Chemical Industry; China; DNA, Bacterial; Fatty Acids; Lysobacter; Manganese; Molecular Typing; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Soil; Soil Microbiology; Soil Pollutants; Ubiquinone

COQ8 proteins are homologs of atypical protein kinases required for the biosynthesis of coenzyme Q (CoQ). In this issue of Cell Chemical Biology, Reidenbach et al. (2018) show that COQ8 has an ATPase activity, required for CoQ biosynthesis, that is strongly activated by cardiolipin and small molecule mimics of early CoQ intermediates.

Topics: Lipids; Mutation; Saccharomyces cerevisiae; Ubiquinone

A Gram-stain-negative, rod-shaped, motile, catalase-positive and cytochrome c oxidase-positive bacterial strain, designated AM20-91

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Forests; Italy; Lysobacter; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacterium, designated strain RPE64

Topics: Animals; Bacterial Typing Techniques; Base Composition; Burkholderia; Digestive System; DNA, Bacterial; Fatty Acids; Heteroptera; Japan; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Symbiosis; Ubiquinone

A novel bacterium, designated strain C3-17

Topics: Bacterial Typing Techniques; Base Composition; Caves; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, rod-shaped, motile, catalase and cytochrome c oxidase-positive bacterial strain, designated S20-91

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Forests; Italy; Oxalobacteraceae; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Clinical studies have identified patients with nephrotic syndrome caused by mutations in genes involved in the biosynthesis of coenzyme Q

Topics: Alkyl and Aryl Transferases; Alleles; Animals; Autophagy; Cell Line; Cells, Cultured; Disease Models, Animal; Gene Silencing; Humans; Mitochondria; Mitophagy; Nephrotic Syndrome; Organisms, Genetically Modified; Oxidative Stress; Reactive Oxygen Species; Signal Transduction; Ubiquinone; Vitamins

A Gram-stain-negative, aerobic, yellow-pigmented, non-spore-forming, non-motile, rod-shaped bacterium, designated strain DHOB07T, was isolated from a soil sample collected from the lower subtropical forest of the Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10' N 112° 31' E). Strain DHOB07T grew at 10-37 °C, pH 4-7 and 0-0.5 % (w/v) NaCl, with an optimum at 28 °C, pH 5-5.5 and 0% (w/v) NaCl on R2A medium. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a clade with Dyella jejuensis JP1T, Dyella nitratireducens DHG59T, Dyella koreensis BB4T, Dyella marensis CS5-B2Tand Dyellasoli JS12-10T, with sequence similarities of 98.9, 98.0, 97.9, 97.9 and 97.8 %, respectively. Multilocus sequence analysis based on the concatenated sequences of partial housekeeping genes gyrB, lepA and recA confirmed that strain DHOB07T belongs to thegenus Dyella but is distinct from all currently known species of the genus Dyella. The G+C content of the genomic DNA was 58.2 mol%. The DNA-DNA relatedness value between strain DHOB07T and D. jejuensis JP1T was 41.8 %. Iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1ω9c were the major fatty acids, and ubiquinone-8 was the only respiratory quinone detected, all of which supported the affiliation of strain DHOB07T to the genus Dyella. On the basis of the polyphasic characterization results presented above, strain DHOB07T represents a novel species of the genus Dyella, for which the name Dyella lipolytica sp. nov. is proposed. The type strain is DHOB07T (=NBRC 111473T=KCTC 52132T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Forests; Genes, Bacterial; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A Gram-staining-negative, rod-shaped, motile bacterium, designated WD12T, was isolated from a rotten tree at Chungbuk National University, South Korea. WD12T grew optimally at 30-37 °C and pH 7.0-7.5 and could assimilate arbutin and potassium-5-ketogluconate. The major cellular fatty acid were iso-C16 : 0, C16 : 0, cyclo C17 : 0, iso-C15 : 0, summed features 3 (comprising C16 : 1ω7c/iso-C15 : 0 2-OH) and anteiso-C15 : 0. The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was ubiquinone-8 (Q-8). The G+C content of the genomic DNA was 69.1 %. The results of phylogenetic and comparative analysis based on the 16S rRNA gene sequence indicated that WD12T formed a tight phylogenetic lineage with Pseudoxanthomonas mexicana AMX 26BT and Pseudoxanthomonas japonensis 12-3T of the the genus Pseudoxanthomonas in the family Xanthomonadaceae. Sequence similarity to other members of the genus Pseudoxanthomonasranged from 98.6 % (P. mexicana AMX 26BT) to 95.1 % (Pseudoxanthomonas taiwanensis CB-226T). DNA-DNA relatedness between WD12T and eight type strains of species of the genus Pseudoxanthomonasshowing more than 97 % 16S rRNA sequence similarity were 6±0-26±1 %. On the basis of the evidence from this polyphasic study, WD12T represents a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas putridarboris sp. nov. is proposed. The type strain is WD12T (=KACC 15045T=LMG 25968T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Wood; Xanthomonadaceae

A Gram-straining-negative, facultatively aerobic, rod-shaped strain, motile by a polar flagellum and designated P03D4T, was isolated from the bottom seawater of the East China Sea. Growth occurred at 10-50 °C (optimum 32 °C), pH 5.0-10.0 (optimum pH 6.0) and in the presence of 1-7 % (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequence placed P03D4T within the genus Photobacterium of the family Vibrionaceae in the class Gammaproteobacteria, and revealed that strain P03D4T was most closely related to Photobacterium frigidiphilum SL13T with 96.9 % sequence similarity and had sequence similarities with other species of the genus Photobacterium in the range 94.6-96.9 %. The dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The polar lipids of strain P03D4T comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and one unknown lipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain P03D4T was 44.3 mol%. On the basis of the evidence from this polyphasic study, strain P03D4T is proposed as representing a novel species of the genus Photobacterium, for which the name Photobacterium alginatilyticum sp. nov. is proposed. The type strain is P03D4T (=KCTC 52365T=MCCC 1K03200T=CGMCC 1.15764T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Phospholipids; Photobacterium; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A bacterial strain, designated RA6T, was isolated from the rhizosphere of Cistus ladanifer. Phylogenetic analyses based on 16S rRNA gene sequence placed the isolate into the genus Delftia within a cluster encompassing the type strains of Delftia lacustris, Delftia tsuruhatensis, Delftia acidovorans and Delftia litopenaei, which presented greater than 97 % sequence similarity with respect to strain RA6T. DNA-DNA hybridization studies showed average relatedness ranging from of 11 to 18 % between these species of the genus Delftia and strain RA6T. Catalase and oxidase were positive. Casein was hydrolysed but gelatin and starch were not. Ubiquinone 8 was the major respiratory quinone detected in strain RA6T together with low amounts of ubiquinones 7 and 9. The major fatty acids were those from summed feature 3 (C16 : 1ω7c/C16 : 1 ω6c) and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RA6T should be considered as a representative of a novel species of genus Delftia, for which the name Delftia rhizosphaerae sp. nov. is proposed. The type strain is RA6T (=LMG 29737T= CECT 9171T).

Topics: Bacterial Typing Techniques; Base Composition; Cistus; Delftia; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spain; Ubiquinone

A Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YM319T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YM319T was related to the genus Oceanisphaera and had highest 16S rRNA gene sequence similarities with the type strains Oceanisphaera profunda SM1222T (97.4 %), Oceanisphaera sediminis TW92T (97.3 %) and Oceanisphaera ostreae T-w6T (97.1 %). The predominant cellular fatty acids were summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C16 : 0 and C18 : 1ω7c. Strain YM319T had Q-8 as the predominant ubiquinone. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content of strain YM319T was 54.8 mol%. On the basis of the evidence presented in this study, strain YM319T represents a novel species of the genus Oceanisphaera, for which we propose the name Oceanisphaera marina sp. nov. (type strain YM319T=KACC 18564T=CGMCC 1.15923T).

Topics: Aeromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Pacific Ocean; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represented a member of the genus Colwellia and exhibited the highest sequence similarity (97.4 %) to Colwellia aestuarii SMK-10T. Average nucleotide identity (ANI) values based on draft genome sequences between strain QM50T and C. aestuarii KCTC 12480T showed a relatedness of 72.0 % (ANIb) and 85.1 % (ANIm). Cells of strain QM50T were approximately 0.3-0.6×0.8-2.5 µm in size and motile by means of a polar flagellum. Growth occurred in the presence of 1.0-6.0 % (w/v) NaCl (optimum, 2.0-3.0 %), at pH 6.5-8.5 (optimum, pH 7.0) and at 4-37 °C (optimum, 28-30 °C). Strain QM50T was found to contain ubiquinone 8 (Q-8) as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C17 : 1ω8c as the main cellular fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were found to be major polar lipids. The DNA G+C content of strain QM50T was determined to be 35.7 mol%. On the basis of phylogenetic and phenotypic data, strain QM50T represents a novel species of the genus Colwellia, for which the name Colwellia agarivorans sp. nov. is proposed. The type strain is QM50T (=KCTC 52273T=MCCC 1H00143T).

Topics: Alteromonadaceae; Aquaculture; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A slightly yellow-pigmented, Gram-stain-negative, rod-shaped bacterium, strain IMT-305T, was isolated from soil in Alabama, USA. Phylogenetic analysis based on the nearly full-length 16S rRNA gene sequence placed the strain in between the genera Pusillimonas, Parapusillimonas and Candidimonas with highest 16S rRNA gene sequence similarity to the type strain of Parapusillimonas granuli (97.5 %) and Candidimonas nitroreducens (97.4 %). The genomic G+C content of strain IMT-305T was 63.9 mol%. The main cellular fatty acids were C18:1ω7c, C17:0 cyclo, C16:0 and C16:1ω7c/iso-C15:0 2-OH (detected as summed feature 3). The polyamine pattern of strain IMT-305T contained the major compound putrescine and the betaproteobacterial diagnostic 2-hydroxyputrescine and the major respiratory quinone was ubiquinone Q-8. Predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified lipid lacking any functional group. Based on phylogenetic, chemotaxonomic and phenotypic analyses a novel species within a new genus, Paracandidimonas soli gen. nov., sp. nov., is proposed. The type strain of Paracandidimonas soli is IMT-305T (=DSM 100048T=CIP 110902T=LMG 28740T=CCM 8599T).

Topics: Alabama; Alcaligenaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A taxonomic study was performed on strain SYSU D3-2T, isolated from coastal seawater near the estuary of Pearl River in southern China. The strain was observed to be Gram-reaction-negative, non-motile and non-spore-forming. Cells were found to be of coccobacilli shape. Chemotaxonomic analysis of the plasma membrane revealed ubiquinone-8 as the respiratory quinone, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified phospholipid as the polar lipids, and anteiso-C15 : 0, C18 : 0 and anteiso-C17 : 0 as the major fatty acids (>10 % of total fatty acids). Comparison of 16S rRNA gene sequences showed that strain SYSU D3-2T shared maximum similarities with Caedibacter taeniospiralis 51T (92.3 %) and Fangia hongkongensis UST040201-002T (90.6 %), while sharing 85.8-90.0 % similarity with species of the genera Allofrancisella and Francisella. Phylogenetic dendrograms based on the 16S rRNA gene sequences showed that the strain clustered within the family Francisellaceae, but formed a separate lineage closely linked to Caedibactertaeniospiralis 51T and F. hongkongensis UST040201-002T. Based on the findings of the polyphasic taxonomic study, strain SYSU D3-2T is proposed to be recognized as a representative of a novel species of a new genus within the order Thiotrichales, with the name Cysteiniphilum litorale gen. nov., sp. nov. The type strain of the type species is SYSU D3-2T (=NBRC 112441T=DSM 101832T=KCTC 52386T=CGMCC 1.15758T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, rod-shaped, non-spore forming, motile and strictly oxidative bacterium, strain CHU3T, was isolated from fresh water in the Daecheong Reservoir, South Korea. A comparison of the 16S rRNA gene sequence showed that the novel bacterium is closely related to Paucibacter toxinivorans 2C20T (=KCTC 42569T) with a sequence similarity value of 97.8 %, Pelomonas saccharophila DSM 654T (=KCTC 52256T) with 97.4 % similarity and Pelomonas aquatica CCUG 52575T (=KCTC 42961T) with 97.3 % similarity, respectively. The major fatty acids (>10 %) of the isolate were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Ubiquinone-8 was detected as the respiratory quinone. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and an unidentified aminolipid. The DNA G+C content was 62.5 mol%. DNA-DNA hybridization experiments with PaucibactertoxinivoransKCTC 42569T (=2C20T), PelomonassaccharophilaKCTC 52256T (=DSM 654T) and PelomonasaquaticaKCTC 42961T (=CCUG 52575T) resulted in relatedness values of 20 % (reciprocal 11 %), 16 % (reciprocal 17 %) and 15 % (reciprocal 19 %), respectively. The phylogenetic analysis, DNA-DNA hybridization value, polar lipids, fatty acid composition and other physiological characteristics confirmed that strain CHU3T represents a novel species in the genus Paucibacter for which the name Paucibacter oligotrophus sp. nov. is proposed. The type strain is CHU3T (=KCTC 42519T=CICC 24092T). An emended description of the genus Paucibacter is also proposed on the basis of new data obtained in this study.

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; DNA, Bacterial; Fatty Acids; Fresh Water; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel bacterial strain, S66T, was isolated from eelgrass collected on the coastline of Zealand, Denmark. Polyphasic analyses involving phenotypic, phylogenetic and genomic methods were used to characterize strain S66T. The strain was Gram-reaction-negative, rod-shaped, aerobic, and displayed growth at 10-25 °C (optimum 20-25 °C) and at pH 7-9 (optimum pH 7.5). Furthermore, strain S66T grew on seaweed polysaccharides agar, agarose, porphyran, κ-carrageenan, alginate and laminarin as sole carbon sources. Major fatty acids were C16 : 0, C16 : 1ω7c and C18 : 1ω7c. The respiratory quinone was determined to be Q-8, and major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was determined to be 42.2 mol%. Phylogenetic analyses based on the 16S rRNA gene and GyrB sequence comparisons showed that the bacterium was affiliated with the genus Paraglaciecola within the family Alteromonadaceae of the class Gammaproteobacteria. The percentage similarity between the 16S rRNA gene and GyrB sequences of strain S66T and other members of the genus Paraglaciecola were 94-95 % and 84-85 %, respectively. Based on the genome sequence of S66T, the average nucleotide identity (ANI) between strain S66T and other members of the genus Paraglaciecola was 77-80 %, and DNA-DNA hybridization prediction showed values of less than 24 % relatedness, respectively, between S66T and other species of the genus Paraglaciecola. The phenotypic, phylogenetic and genomic analyses support the hypothesis that strain S66T represents a novel species of the genus Paraglaciecola, for which the name Paraglaciecola hydrolytica sp. nov. is proposed. The type strain is S66T (=LMG 29457T=NCIMB 15060T=DSM 102834T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; Denmark; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Polysaccharides; RNA, Ribosomal, 16S; Seaweed; Sequence Analysis, DNA; Ubiquinone

A Gram-stain negative, oxidase- and catalase- positive, motile, aerobic, non-pigmented spirillum, designated CPA1T, was isolated from the surface-sterilized tissues of a halophyte, Halimione portulacoides, collected from a salt marsh in Aveiro, Portugal. The isolate was mesophilic, facultatively alkaliphilic and halophilic, and grew between 18 and 42.5 °C (optimum 30 °C), from pH 5.0 to 11.5 (optimum 7.0-7.5), from 0.5 to 5 % NaCl (w/v, optimum 2 %). Analysis of the 16S rRNA gene sequence showed that this strain belongs to the genus Saccharospirillum, as the highest sequence similarities were observed with Saccharospirillum impatiens EL-105T (96.46 %), Saccharospirillum salsuginis YIM-Y25T (96.32 %) and Saccharospirillum aestuariiIMCC 4453T (95.17 %). The next closest matches were with other genera and below 95.0 %. Phylogenetic analyses revealed that the strain forms a robust clade with other species of the genus Saccharospirillum. The main respiratory quinone was Q-8 and the major fatty acids were C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was 55.2 mol%. Molecular, physiological and biochemical differences between strain CPA1T and other type strains of species of the genus Saccharospirillum support the addition of this novel species to the genus, and the name Saccharospirillum correiae sp. nov. is proposed, with CPA1T (=CECT 9131T=LMG 29516T) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; Chenopodiaceae; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Phylogeny; Portugal; RNA, Ribosomal, 16S; Salt-Tolerant Plants; Sequence Analysis, DNA; Ubiquinone; Wetlands

A Gram-staining-negative, aerobic, rod-shaped bacterial strain, designated LPB0090T, was isolated from the Pacific oyster, Crassostreagigas, collected from the Yeongheung Island, Korea (37° 15' 16.1″ N; 126° 29' 46.5″ E). The complete genome sequence of LPB0090T (accession number CP017689) was 3 861 670 bp long with a DNA G+C content of 38.8 mol%. The genome included 3245 protein-coding genes and six copies of rRNA operons. On the basis of the results of 16S rRNA gene sequence analysis, LPB0090T was found to form an independent phyletic line within the genus Thalassotalea, with 94.7-96.0 % sequence similarities to the previously known species of the genus. The isoprenoid quinone (Q-8) and major fatty acids (C16 : 0, C17 : 1 ω8c, and C16 : 1 ω7c and/or C16 : 1 ω6c) of the isolate were similar to those of the other members of the genus Thalassotalea. A number of phenotypic features, however, distinguished LPB0090T from its closest neighbour Thalassotalea ponticola as well as other species of the genus Thalassotalea. On the basis of the phylogenetic, genomic and phenotypic data presented in this study, the strain was classified as representing a novel species of the genus Thalassotalea. Therefore, the name Thalassotalea crassostreae sp. nov. is proposed for the isolate. The type strain is LPB0090T (=KACC 18695T=JCM 31189T).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Crassostrea; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Islands; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel Gram-stain-negative, aerobic and rod-shaped marine bacterium, designated strain HMF4135T, was isolated from a sand sample which was collected from the seashore of the South Sea, Republic of Korea. It required NaCl for growth and exhibited optimal growth at 30 °C, with 2 % (w/v) NaCl and at pH 7-8. Cellular fatty acids were dominated by C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω9c and C12 : 0 3-OH. The predominant isoprenoid quinone was ubiquinone-8 (Q-8). Polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.9 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain HMF4135T formed a distinct species-level lineage within the genus Thalassotalea of the class Gammaproteobacteria and was most closely related to Thalassotalea ponticola GJSW-36T (96.4 % similarity). Based on the distinctive phenotypic characteristics and phylogenetic analysis, it is concluded that strain HMF4135T represents a novel species of the genus Thalassotalea, for which the name Thalassotalea litorea sp. nov. is proposed. The type strain is HMF4135T (=KCTC 52154T=NBRC 112672T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Silicon Dioxide; Ubiquinone

A Gram-staining-negative, non-motile, non-pigmented, strictly aerobic and rod-shape bacterium, designated BK296T, was isolated from stream water originating from a limestone cave in Samcheok, Korea. Optimal growth of strain BK296T was observed at 30 °C, pH 7.0-8.0 and without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BK296T belonged to the genus Perlucidibaca, forming a robust clade with a member of the genus, and was most closely related to Perlucidibaca piscinae (97.8 %). The average nucleotide identity value between strain BK296T and Perlucidibacapiscinae IMCC1704T was 79.8 %, and the genome-to-genome distance was 17.5 % on mean. The G+C content of the DNA of strain BK296T was 55.7 mol%. The major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C12 : 0 3-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was ubiquinone Q-8. On the basis of phenotypic, genotypic and phylogenetic analyses, strain BK296T (=KCTC 52162T=JCM 31377T) represents a novel species of the genus Perlucidibaca, for which the name Perlucidibaca aquatica sp. nov. is proposed.

Topics: Bacterial Typing Techniques; Base Composition; Caves; DNA, Bacterial; Fatty Acids; Fresh Water; Moraxellaceae; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel Gram-stain-negative, aerobic marine bacterial strain, SAB-3T, was isolated from brown macroalgae (Dictyota sp.) growing in the Arabian sea, Goa, India. The strain grew optimally at 30 °C, with 2.0-4.0 % (w/v) NaCl and at pH 7.0 on marine agar medium. Strain SAB-3T was unable to hydrolyse aesculin and did not grow in the presence of rifamycin but showed resistance to antibiotics such as cefadroxil and co-trimoxazole. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 0, and Q-8 was the major ubiquinone. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.0 mol%. 16S rRNA gene sequencing and phylogenetic analysis indicated that the strain was a member of the genus Marinomonas with Marinomonas aquiplantarum IVIA-Po-159T (97.6 % similarity), Marinomonas posidonica IVIA-Po-181T (97.5 %) and Marinomonas dokdonensis DSM 17202T (97.4 %) as the closest relatives. Whole genome relatedness determined through DNA-DNA hybridization revealed values of 40-50 % (below the 70 % threshold recommended for species delineation) with the above three species, thus confirming it as representing a distinct and novel species of the genus Marinomonas for which the name Marinomonas epiphytica sp. nov. is proposed. The type strain is SAB-3T (=JCM 31365T=KCTC 52293T=MTCC 12569T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; India; Marinomonas; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; RNA, Ribosomal, 16S; Seaweed; Sequence Analysis, DNA; Ubiquinone

A light yellow-coloured, Gram-stain-negative, motile and rod-shaped bacterium, designated strain K-3-1T, was isolated from reclaimed grassland soils of Belbari, Morang, Nepal. It was able to grow at 4-45 °C, at pH 5.0-10.0, and at 0-2 % (w/v) NaCl concentrations. This strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain K-3-1T belongs to the genus Massilia and is closely related to Massilia consociata CCUG 58010T (98.3 % sequence similarity), Massilia tieshanensis TS3T (98.1 % sequence similarity), Massilia kyonggiensis TSA1T (98.1 % sequence similarity), Massilia yuzhufengensisY1243-1T (98.1 % sequence similarity), Massilia haematophila CCUG 38318T (98.0 % sequence similarity), Massilia varians CCUG 35299T (97.9 % sequence similarity), Massilia niastensis 5516 S-1T (97.6 % sequence similarity) and Massilia alkalitolerans YIM 31775T (97.5 % sequence similarity). The predominant respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids of strain K-3-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C12 : 0, C10 : 0 3-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The genomic DNA G+C content of this novel strain was 66.8 mol%. The DNA-DNA relatedness between strain K-3-1T and its closest reference strains were significantly lower than the threshold value of 70 %. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-3-1T represents a novel species of the genus Massilia, for which the name Massilia agri sp. nov. is proposed. The type strain is K-3-1T (=KEMB 9005-446T=KACC 19000T=JCM 31661T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Grassland; Nepal; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain negative, rod-shaped, aerobic bacterial strain, BII-R7T, was isolated during a study targeting the culture-dependent microbial diversity occurring in bentonite formations from southern Spain. Comparative 16S rRNA gene sequence analysis showed that BII-R7T represented a member of the genus Stenotrophomonas (class Gammaproteobacteria), and was related most closely to Stenotrophomonas rhizophila e-p10T (99.2 % sequence similarity), followed by Stenotrophomonas pavanii ICB 89T (98.5 %), Stenotrophomonas maltophilia IAM 12423T, Stenotrophomonas chelatiphaga LPM-5T and Stenotrophomonas tumulicola T5916-2-1bT (all 98.3 %). Pairwise sequence similarities to all other type strains of species of the genus Stenotrophomonas were below 98 %. Genome-based calculations (orthologous average nucleotide identity, original average nucleotide identity, genome-to-genome distance and DNA G+C percentage) indicated clearly that the isolate represents a novel species within this genus. Different phenotypic analyses, such as the detection of a quinone system composed of the major compound ubiquinone Q-8 and a fatty acid profile with iso-C15 : 0 and anteiso-C15 : 0 as major components, supported this finding at the same time as contributing to a comprehensive characterization of BII-R7T. Based on this polyphasic approach comprising phenotypic and genotypic/molecular characterization, BII-R7T can be differentiated clearly from its phylogenetic neighbours, establishing a novel species for which the name Stenotrophomonas bentonitica sp. nov. is proposed with BII-R7T as the type strain (=LMG 29893T=CECT 9180T=DSM 103927T).

Topics: Bacterial Typing Techniques; Base Composition; Bentonite; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spain; Stenotrophomonas; Ubiquinone

A Gram-stain-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, JDTF-113T, was isolated from a tidal flat in Jindo, an island of South Korea. Strain JDTF-113T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, revealed that strain JDTF-113T fell within the clade enclosing the type strains of species of the genus Alteromonas. Strain JDTF-113T exhibited 16S rRNA gene sequence similarity values of 97.1-98.1 % to the type strains of Alteromonaslipolytica, Alteromonaslitorea, Alteromonasmediterranea, Alteromonasconfluentis, Alteromonas hispanica, Alteromonasgenovensis and Alteromonasmarina, and of 94.8-96.9 % to those of the other species of the genus Alteromonas. Strain JDTF-113T contained Q-8 as the predominant ubiquinone and C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 1ω7c as the major fatty acids. The major polar lipids of strain JDTF-113T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified glycolipid. The DNA G+C content of strain JDTF-113T was 51.1 mol% and its mean DNA-DNA relatedness values with the type strains of seven closely phylogenetically related species of the genus Alteromonaswere was 10-23 %. The differential phenotypic properties and phylogenetic and genetic distinctiveness support strain JDTF-113T being separated from species of the genus Alteromonaswith validly publishednames. On the basis of the data presented, strain JDTF-113T is considered to represent a novel species of the genus Alteromonas, for which the name Alteromonas aestuariivivens sp. nov. is proposed. The type strain is JDTF-113T (=KCTC 52655T=NBRC 112708T).

Topics: Alteromonas; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Using a newly developed culture method for not yet cultured soil bacteria, three Gram-stain-negative, aerobic, non-spore-forming, motile, and rod-shaped bacteria (strain designated J18T, J11T and J9T) were isolated from forest soil at Kyonggi University, South Korea. Isolates were subjected to a taxonomic study by using a polyphasic approach. According to a phylogenetic tree based on 16S rRNA gene sequences, strains J18T, J11T and J9T belonged to the genus Massilia and clustered with Massilia haematophila CCUG 38318T (similarity range: 97.6~98.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, and the genomic DNA G+C contents of strains J18T, J11T and J9T were 63.4, 68.7 and 64.5 mol%, respectively. The major polyamines were putrescine and 2-hydroxyputescine, which were detected in all three strains. DNA-DNA between the three tested strains and the reference strains much lower than 70 %, the recommended threshold value for the delineation of genomic species. The predominant respiratory quinine was ubiquinone-8 (Q-8) and the major cellular fatty acids were Summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C16 : 0. On the basis of phenotypic and genotypic data and DNA-DNA hybridization results, the three isolates are considered to represent three novel species of the genus Massilia, for which the names Massilia solisilvae sp. nov. for type strain J18T (=KEMB 9005-366T=JCM 31607T), Massilia terrae sp. nov. for type strain J11T (=KEMB 9005-360T=JCM 31606T) and Massilia agilis sp. nov. for type strain J9T (=KEMB 9005-359T=JCM 31605T) are proposed.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Forests; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; Putrescine; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated M23T, was isolated from a laboratory culture of a bloom-forming cyanobacterium, Microcystis, which was isolated from a eutrophic lake in Korea. The strain grew optimally without NaCl and at 25-30 °C on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the genus Silanimonas, with the highest similarity to Silanimonas lenta DSM 16282T (98.5 %). DNA-DNA relatedness between strain M23T and the closely related species in the genus Silanimonas was <30 %. Strain M23T contained iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C16 : 0 as major fatty acids and ubiquinone-8 (Q-8) as the major quinone. Strain M23T contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmethylethanolamine as major polar lipids. The DNA G+C content of strain M23T was 69.6 mol%. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain M23T represents a novel species in the genus Silanimonas, for which the name Silanimonas algicola sp. nov. is proposed. The type strain is M23T (=KCTC 52219T=JCM 31889T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Eutrophication; Fatty Acids; Lakes; Microcystis; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Xanthomonadaceae

Three strains, DHOB09T, DHOC52T and DHON07T, were isolated from the forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. They were all Gram-stain-negative, aerobic, rod-shaped cells. The ranges (optimum) for the temperature, pH and NaCl concentration for growth of DHOB09T, DHOC52T and DHON07T were 10-42 (25-28) °C, pH 5.5-9.0 (7.0-7.5) and 0-4.0 (0-0.5) % (w/v); 10-42 (28) °C, pH 4.0-7.0 (4.5-6.5) and 0-2.0 (0) % (w/v) and 10-37 (25-28) °C, pH 4.0-7.5 (5.5-6.0) and 0-2.5 (0)  % (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that DHOB09T, DHOC52T and DHON07T formed a phyletic cluster with seven species of the genus Dyella within the major clade of Dyella with sequence similarities ranged from 96.9 to 98.6 %. This indicated that the three strains may represent three novel species of the genus Dyella. This result was also strongly supported by the concatenated analysis of partial gyrB, lepA and recA gene sequences. DNA-DNA hybridization between strains DHON07T and DHOB09T, as well as DHON07T and Dyella koreensis BB4T was much lower than 70 %. The G+C content of strains DHOB09T, DHOC52T and DHON07T were 59.4, 60.7 and 59.5 %, respectively. The major fatty acids of the three strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 and the predominant respiratory lipoquinone was ubiquinone-8. All of the physiological, phylogenetic and chemotaxonomic data showed that strains DHOB09T, DHOC52T and DHON07T are distinctive from each other and from all species of the genus Dyellawith validly published names. Therefore, we suggest that they represent three novel species of the genus, for which the names Dyella caseinilytica sp. nov. (type strain DHOB09T=CGMCC 1.15434T=LMG 29202T), Dyella flava sp. nov. (type strain DHOC52T=NBRC 111979T=KCTC 52128T) and Dyella mobilis sp. nov. (type strain DHON07T=CGMCC 1.15400T=NBRC 111475T) are proposed.

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Forests; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

Two Gram-stain-negative bacterial strains, SAP-32T and SAP-36, were isolated from sap drawn from the Acer pictum from Mount Halla in Jeju, Republic of Korea. The organisms were strictly aerobic, non-sporulating, motile rods and showed growth at 10-30 °C, pH 7-8 and with 0-2 % NaCl. The major isoprenoid quinone was Q-8. The predominant fatty acids were C16 : 0, cyclo-C17 : 0, summed feature 3 and C18 : 0. The polar lipids contained phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unknown aminophosphoglycolipid, an unknown glycolipid, an unknown phospholipid and two unknown lipids. The DNA G+C content was 64.4 mol%. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that SAP-32T and SAP-36 formed a distinct cluster with members of the genus Pigmentiphaga within the family Alcaligenaceae. Both strains showed 16S rRNA gene sequence similarity of 100 % to each other. The closest relatives of the isolates were Pigmentiphaga daeguensis (97.08 % sequence similarity), Pigmentiphaga kullae (97.01 %) and Pigmentiphaga litoralis (96.73 %). On the basis of data from phenotypic, chemotaxonomic and phylogenetic analyses, SAP-32T (=KCTC 52619T=DSM 104039T) and SAP-36 (=KCTC 52620=DSM 104072) represent members of a novel species of the genus Pigmentiphaga, for which the name Pigmentiphaga aceris sp. nov. is proposed.

Topics: Acer; Alcaligenaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative and rod-shaped bacterial strain, 12-OD1T, with rock phosphate solubilizing ability was isolated from agricultural soil in Hailun, Heilongjiang, PR China. The isolate was affiliated to the genus Massilia, based on 16S rRNA gene sequence alignments, having the highest similarities with Massilia putida6 NM-7T (98.67 %), Massilia kyonggiensis TSA1T (98.28 %), and Massilia norwichensis NS9T (98.07 %), respectively. The DNA G+C content was 67.72 mol% and DNA-DNA hybridization showed low relatedness values (less than 47 %) between strain 12-OD1T and other phylogenetically related species of the genus Massilia. The predominant isoprenoid quinone was Q-8 and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C17 : 0 cyclo (25.4 %), C16 : 0 (23.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c) (22.5 %), which differentiates it from close relatives within the genus Massilia. Combined genetic, physiological and biochemical properties indicate that strain 12-OD1T is a novel species of the genus Massilia, for which the name Massilia phosphatilytica sp. nov., is proposed, with the type strain 12-OD1T (=CCTCC AB 2016251T=LMG 29956T=KCTC 52513T).

Topics: Agriculture; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Fertilizers; Nucleic Acid Hybridization; Oxalobacteraceae; Phosphates; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-staining-negative, non-motile, aerobic bacterial strain, designated Y3L17T, was isolated from the saline-alkaline soil of a farmland, Hangjin Banner, Inner Mongolia, northern China. Y3L17T could grow at 15-45 °C (optimum 35 °C), pH 6.0-10.0 (optimum pH 8.0) and with 0-4 % (w/v) NaCl (optimum 0 %). The results of phylogenetic analysis based on the 16S rRNA gene and gyrB gene sequences revealed that Y3L17T tightly clustered with strains of members of the genus Arenimonas, sharing the highest 16S rRNA gene similarities with Arenimonas aestuarii S2-21T (99.5 %) and Arenimonas donghaensis HO3-R19T (98.2 %), and lower similarities (<97 %) with all the other type strains of species of this genus. However, Y3L17T shared only 92.62 % gyrB gene similarities with A. aestuarii S2-21T. The DNA-DNA hybridization values of Y3L17T with A. aestuariiS2-21T and A. donghaensis HO3-R19T were 20.1±2.5 and 18.2±3.2 %, respectively. Y3L17T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, five unknown phospholipids and one unknown lipid as the major polar lipids. Ubiquinone-8 (Q-8) was the predominant respiratory quinone, while iso-C15 : 0, iso-C17 : 0ω9c and iso-C11 : 0 3-OH were the major cellular fatty acids. Its genomic DNA G+C content was 65.4 mol%. On the basis of its phenotypic, phylogenetic and genotypic characteristics, Y3L17T represents a novel species within the genus Arenimonas, for which the name Arenimonas soli sp. nov. is proposed, the type strain is Y3L17T (=CGMCC 1.15905T =KCTC 52420T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A new betaproteobacterium, CGI-09

Topics: Alcaligenaceae; Bacterial Typing Techniques; Base Composition; Bioreactors; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Romania; Sequence Analysis, DNA; Sewage; Ubiquinone

A novel Marinomonas-like, aerobic, Gram-reaction-negative, moderately halophilic, acidophilic, motile by a single polar flagellum, non-spore-forming, rod-shaped bacterium that showed algalytic activity, designated strain Yeongu 1-4

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Marinomonas; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Three alkaliphilic and halotolerant bacterial strains, designated ZV-19

Topics: Alkalies; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hungary; Nucleic Acid Hybridization; Oceanospirillaceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

A polyphasic approach was used to characterize a novel bacterium, designated strain TPP412T, isolated from a paddy soil in Taiwan. Strain TPP412T was Gram-stain-negative, facultatively anaerobic, rod-shaped, motile with a single polar flagellum and lacked bacteriochlorophyll. Growth was observed at 24-45 °C (optimal 25 °C), at pH 5.0-10.0 (optimal pH 7.0) and with 0-0.75 % (w/v) NaCl. Strain TPP412T showed highest 16S rRNA gene sequence similarity to members of the genera Rhodocyclus (94.1-94.5 %), Azospira (93.9-94.5 %) and Propionivibrio (93.4-94.4 %) and established a discrete taxonomic lineage in phylogenetic analysis. The major fatty acids found in strain TPP412T were C12 : 0, C12 : 0 3-OH, iso-C15 : 0 3-OH, C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids consisted of phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified lipid. The polyamine pattern showed a predominance of putrescine and a minor amount of spermidine. The DNA G+C content was 58.4 mol% and the predominant quinone system was ubiquinone-8 (Q-8). The low 16S rRNA gene sequence similarity values (≤94.5%) and distinct phylogenetic clustering clearly distinguished strain TPP412T from other representatives of the family Rhodocyclaceae. Based on the discrete phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain TPP412T is considered to represent a novel species of a new genus in the family Rhodocyclaceae, for which the name Oryzomicrobium terrae gen. nov., sp. nov. is proposed. The type strain of Oryzomicrobium terrae is TPP412T (=BCRC 80905T=JCM 30814T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Polyamines; Rhodocyclaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Taiwan; Ubiquinone

A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated RA2-7T, was isolated from a mussel (Mytilus edulis) collected from the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain RA2-7T grew optimally at 20 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain RA2-7T belonged to the genus Colwellia. Strain RA2-7T exhibited 16S rRNA gene sequence similarity values of 98.3, 98.0 and 97.5 % to the type strains of Colwellia sediminilitoris, Colwellia aestuarii and Colwellia polaris, respectively, and of 94.5-96.5 % to the type strains of the other species of the genus Colwellia. Strain RA2-7T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids detected in strain RA2-7T were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain RA2-7T was 39.0±0.04 mol% and its DNA-DNA relatedness values with the type strains of C. sediminilitoris, C. aestuarii and C. polaris were 14-19 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RA2-7T is separated from recognized species of the genus Colwellia. On the basis of the data presented, strain RA2-7T is considered to represent a novel species of the genus Colwellia, for which the name Colwellia mytili sp. nov. is proposed. The type strain is RA2-7T (=KCTC 52417T=NBRC 112381T).

Topics: Alteromonadaceae; Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Mytilus edulis; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Strain AHQ-12T, isolated from a freshwater lake in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain AHQ-12T were Gram-staining-negative, aerobic, non-motile, non-spore forming, straight rods and formed translucent white-coloured colonies. Optimal growth occurred at 20 °C, pH 6.0 and with 0 % NaCl. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-8, and the DNA G+C content was 50.4 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and lipids. The major polyamine was cadaverine. 16S rRNA gene sequence analysis demonstrated that this isolate was unique, showing less than 91 % sequence similarity to its closest relatives, including members of the genera Ralstonia (89.7-90.8 %), Cupriavidus (88.8-90.3 %), Polynucleobacter (88.2-89.5 %), Burkholderia (86.6-90.3 %) and Pandoraea (89.2-90.1 %). Phylogenetic analyses demonstrated that strain AHQ-12T formed a distinct clade closely related to species of the family Burkholderiaceae. On the basis of the phylogenetic inference and phenotypic data, strain AHQ-12T should be classified as a novel species of a new genus in the family Burkholderiaceae, for which the name Formosimonas limnophila gen. nov., sp. nov. is proposed. The type strain is AHQ-12T (=BCRC 80690T=LMG 27847T=KCTC 32501T).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; Cadaverine; DNA, Bacterial; Fatty Acids; Lakes; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone

Two Gram-staining-negative, strictly aerobic, rod-shaped bacteria, designated strains AVA-1T and AVA-2, were isolated from the root of Aloe vera (L.) Brum.f. derived from Chachoengsao Province, Thailand. The strains contained cytochrome oxidase and catalase activities. They grew in 4 % (w/v) NaCl, at a pH range of 6.0-9.0 (optimally at pH 7) and at 20-42 °C (optimally at 30-37 °C). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). The major fatty acids were C16 : 0 and C17 : 0 cyclo. On the basis of 16S rRNA gene sequence analysis, the strains represent a species belonging to the genus Achromobacter and are closely related to Achromobacter xylosoxidans NBRC 15126T (98.80 %), Achromobacter insolitus LMG 6003T (98.64 %), Achromobacter aminicus LMG 26690T (98.59 %), Achromobacter pulmonis LMG 26696T (98.58 %) and Achromobacter insuavis LMG 26845T (98.58 %). The DNA G+C content of strain AVA-1T was 66.5 mol%. The novel strains had low DNA-DNA relatedness values with related type strains. On the basis of the phenotypic and genotypic data obtained, the strains clearly represent a novel species, for which the name Achromobacter aloeverae sp. nov. is proposed. The type strain is strain AVA-1T (=LMG 29108T=NBRC 111463T=PCU 352T=TISTR 2383T).

Topics: Achromobacter; Aloe; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Thailand; Ubiquinone

A novel Gram-stain-negative, non-spore-forming, facultatively anaerobic bacterium, designated YH6T, was isolated from marine sediment in Weihai, China. Cells of starin YH6T were motile, straight rods that formed ivory-white colonies on 2216E agar. Optimal growth occurred at 28-33 °C (range 15-37 °C), in the presence of 2-4 % (w/v) NaCl (range 1-8 %) and at pH 7.5-8.5 (range pH 6.5-9.0). The sole respiratory lipoquinone was Q-8, and the major fatty acids (>10 %) were C16 : 0 and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). The polar lipids profile of the novel strain consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and several other unknown lipids (phospholipids, lipid and phosphoaminolipid). The G+C content of the genomic DNA was 46.5 mol%. The closest type strain phylogenetically to strain YH6T was Vibrio variabilis (92.99 % 16S rRNA gene sequence similarity) followed by Paramoritella alkaliphila (92.55 %), Pseudoalteromonas aurantia (92.20 %) and Pseudoalteromonas citrea (92.20 %). Phylogenetic analysis of the 16S rRNA gene sequence placed the novel strain in the order Alteromonadales, class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence data as well as physiological and biochemical characteristics, we concluded that strain YH6T represents a novel species of a new genus. We propose the name of Motilimonas eburnea gen. nov., sp. nov. for this novel species. The type strain of the novel species is YH6T (=KCTC 42594T=MCCC 1H00122T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Cephalotes 'turtle' ants host a core group of gut-associated symbionts, but their potential contributions to ant nutrition and disease resistance remain uncharacterized in vitro. To gain a better understanding of the metabolic capability of core symbionts belonging to the Burkholderiales, we cultivated and characterized strain CAG32T from the guts of Cephalotes rohweri ants. Strain CAG32T was rod-shaped, Gram-stain-negative, motile and formed pale-white colonies on trypticase soy agar. Optimum growth occurred under an atmosphere of 20 % O2 supplemented with 1 % CO2. Strain CAG32T grew under NaCl concentrations of 0-2.0 %, temperatures of 23-47 °C and pH values of 4.0-8.0, and was capable of producing n-butyric acid and degrading carbohydrates for growth. The G+C content of the genomic DNA was 59.2±0.6 mol% and the major fatty acids were C16 : 0, C16 : 1ω7c/C16 : 1ω6c, C17 : 0 cylcopropane, C12 : 0 and C14 : 0 3-OH/C16 : 1 iso I. The only respiratory quinone detected was ubiquinone-8 (Q-8) and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on phylogenetic analysis of the 16S rRNA gene sequence, strain CAG32T shared 96.9 % nucleotide similarity with its closest cultivated neighbours Bordetella petrii Se-1111RT and Bordetella bronchiseptica ATCC 19395T. This, combined with differences in the phenotypic and biochemical profile from neighbouring strains, warrants the classification of strain CAG32T as representing a novel species of a new genus within the Burkholderiales family Alcaligenaceae. The name Saccharedens versatilis gen. nov., sp. nov. is proposed. The type strain of Saccharedens versatilis is CAG32T (=NCIMB 15010T=DSM 100909T).

Topics: Alcaligenaceae; Animals; Ants; Arizona; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Symbiosis; Ubiquinone

Three strains of obligately methylotrophic Betaproteobacteria (ZT, SP and M3) with the ribulose monophosphate pathway of C1 assimilation are described. The isolates were strictly aerobic, Gram-stain-negative, asporogenous, motile (strains ZT and M3) or non-motile (strain SP) rods that multiplied by binary fisson, and were mesophilic and neutrophilic. All three strains utilized methanol but only strains SP and M3 utilized methylamine as carbon and energy sources. The prevailing cellular fatty acids were straight-chain saturated C16 : 0 and unsaturated C16 : 1ω7c acids. The major ubiquinone was Q-8. The predominant phospholipids were phosphatidylethanolamine, phosphatidylglycerol and cardiolipin. Ammonia was assimilated by glutamate dehydrogenase. The DNA G+C contents of strains ZT, SP and M3 were 51.0, 52.0 and 52.0 mol% (Tm), respectively. Levels of 16S rRNA gene sequence similarity between the three strains were very high (99.9-100 %), and they shared high levels of DNA-DNA relatedness (88-98 %). Based on 16S rRNA gene sequence analysis and DNA-DNA relatedness (19-30 %) with the type strains of the genus Methylobacillus, the novel isolates ZT, SP and M3 are classified as representing a novel species of this genus, for which the name Methylobacillus methanolivorans sp. nov. is proposed. The type strain is ZT (=VKM B-3037T=JCM 31401T=CCUG 68999T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Methanol; Methylobacillus; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Russia; Sequence Analysis, DNA; Sewage; Ubiquinone

An obligately piezophilic strain was isolated from an amphipod crustacean obtained in the Challenger Deep region of the Mariana Trench during the DEEPSEA CHALLENGE expedition. The strain, MTCD1T, grew at extremely high hydrostatic pressures, with a growth range of 80-140 MPa (optimum, 120 MPa) at 6 °C. Phylogenetic analyses based on the 16S rRNA gene sequence indicate that it is closely affiliated with the genus Colwellia. Comparative 16S rRNA gene sequence analyses revealed 95.7, 95.5 and 95.2 % similarity to Colwellia maris ABE-1T, Colwellia piezophila Y233GT and Colwellia psychrerythraea ATCC 27364T, respectively. The major cellular fatty acids were C16 : 1, C16 : 0 and C22 : 6 (docosahexaenoic acid), and the sole isoprenoid quinone produced was ubiqinone-8. DNA G+C content was 48.6 mol%. The strain was positive for oxidase and catalase activities. Based on the results from this study, strain MTCD1T is a novel Gram-negative species of the genus Colwellia, and the name Colwellia marinimaniae sp. nov. (type strain MTCD1T=ATCC TSD-5T=JCM 30270T) is proposed. It is the most piezophilic organism yet described.

Topics: Alteromonadaceae; Amphipoda; Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Hydrostatic Pressure; Nucleic Acid Hybridization; Pacific Ocean; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A new betaproteobacterium, CGII-59m2T, was isolated from an activated sludge bioreactor which treated landfill leachate. The 16S rRNA gene sequence analysis revealed that strain CGII-59m2T belonged to the family Alcaligenaceae and shared the highest pairwise similarity values with Parapusillimonas granuli LMG 24012T (97.7 %), various species of the genus Bordetella (97.3-97.0 %) and Candidimonas nitroreducens LMG 24812T (97.0 %). Cells of strain CGII-59m2T were rod-shaped, non-motile, and oxidase- and catalase-positive. The predominant fatty acids were C16 : 1ω7c, C16 : 0, cyclo C17 : 0 and C18 : 1ω7c, the major respiratory quinone was Q-8, and the main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown phospholipid. The G+C content of the genomic DNA of strain CGII-59m2T was 62.3 mol%. The new bacterium can be distinguished from the closely related type strains based on its non-motile cells and its high C16 : 1ω7c fatty acid content. On the basis of the phenotypic, chemotaxonomic and molecular data, strain CGII-59m2T is considered to represent a novel species of a new genus, for which the name Caenimicrobium hargitense gen. nov., sp. nov. is proposed. The type strain is CGII-59m2T (=DSM 29806T=NCAIM B.02615T).

Topics: Alcaligenaceae; Bacterial Typing Techniques; Base Composition; Bioreactors; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Romania; Sequence Analysis, DNA; Sewage; Ubiquinone

A Gram-stain-negative, motile, non-spore-forming bacterium, designated strain Y4G10-17T, was isolated from the saline-alkali farmland top soil, Inner Mongolia, northern China. Strain Y4G10-17T could grow at 4-45 °C (with 30 °C as the optimal temperature), pH 6.0-12.0 (optimal at pH 9.0) and in the presence of 1.0-12.0 % (w/v) NaCl (optimal at 4.0-6.0 %). Phylogenetic analysis based on the eight different copies of the 16S rRNA gene sequences revealed that strain Y4G10-17T shared the highest sequence similarity with Aliidiomarina maris CF12-14T, 97.93-98.66 %, and lower than 97.0 % sequence similarity with all other type strains. Its major cellular fatty acids contained iso-C15 : 0, iso-C17 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 1 F, iso-C11 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Q-8 was the predominantubiquinone. The major polar lipids of strain Y4G10-17T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unknown lipids and one unknown aminolipid. The genomic DNA G+C content was 49.3 mol%. DNA-DNA hybridization revealed that strain Y4G10-17T showed 20.2±5 % genomic DNA relatedness with its close relative A. maris CF12-14T. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y4G10-17T represents a novel species within the genus Aliidiomarina, for which the name Aliidiomarina soli sp. nov. is proposed. The type strain is Y4G10-17T (=CGMCC 1.15759T=KCTC 52381T).

Topics: Alkalies; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A yellow-pigmented and strictly aerobic bacterial strain, designated FJY8T, was isolated from the soil of Goyang, South Korea. The cells of FJY8T were Gram-reaction-negative, non-motile rods. Colonies were circular, convex and transparent. Strain FJY8T grew optimally at 30 °C, with 0 % (w/v) NaCl and at pH 8. Phylogenetic analysis of the 16S rRNA gene sequence of FJY8T revealed a clear affiliation of this bacterium to the family Lysobacteraceae, and it was related to members of the genus Lysobacter, with Lysobacter xinjiangensis KCTC 22558T being its closest relative (98.7 % sequence similarity). The DNA G+C content was 68.0±0.4 mol%. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids, and an unidentified phospholipid and two unidentified aminophospholipids were also detected as the minor polar lipids. The major fatty acids were iso-C16 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. Only ubiquinone-8 (Q-8) was detected as the isoprenoid quinone. DNA-DNA hybridization values of strain FJY8T with Lysobacter xinjiangensisRCML-52T and Lysobacter mobilis9NM-14T were 55.8±2.0 and 45.2±4.8 %, respectively. On the basis of DNA-DNA hybridization, phylogenetic distinctiveness, and some physiological and biochemical tests, strain FJY8T (=KCTC 42810T=JCM 31019T) represents a novel species of the genus Lysobacter, for which the name Lysobacter humi sp. nov. is proposed.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Lysobacter; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, oxidase-negative, catalase-positive, facultative anaerobe, designated XJ16T, was isolated from a marine solar saltern on the coast of Weihai, China. Cells of strain XJ16T were long and rod-shaped. The colonies were ochre in colour and were able to reduce nitrate to nitrite. Optimal growth occurred at 33-37 °C (range, 20-45 °C) and in the presence of 8-10 % (w/v) NaCl (range, 2-20 %). The pH range for growth was found to be 6.5-9.5, with optimum growth at pH 7.5-8.0. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain XJ16T was related to the phylum Proteobacteria. The most closely related neighbours were species of the genus Thioalkalivibrio, and the 16S rRNA gene sequence of strain XJ16T shared 93.1 % similarity with that of Thioalkalivibrio sulfidiphilus HL-EbGr7T and 93.0 % similarity with that of Thioalkalivibrio denitrificans ALJDT. The G+C content of the genomic DNA was 65.9 mol% (HPLC). The sole respiratory quinone was Q-8, and the predominant cellular fatty acids (>10 %) were iso-C15 : 0 2-OH/C16 : 1ω7c, C18 : 0 and C16 : 0 10-CH3. The predominant polar lipids in strain XJ16T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on these phylogenetic, physiological and biochemical characteristics, strain XJ16T should be classified representing a novel species of a new genus within the family Ectothiorhodospiraceae, for which the name Halofilum ochraceum gen. nov., sp. nov. is proposed. The type strain of the type species is XJ16T (=KCTC 42259T=MCCC 1H00120T=CICC 23817T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Seawater; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

Bacterial strains 4M-Z03

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Forests; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A novel bacterium, designated as strain AM134T, was isolated from the gut of a purple sea urchin (Heliocidaris crassispina) gathered from the coastal waters of Dokdo, Korea. Strain AM134T was Gram-stain-negative, both catalase- and oxidase-positive, strictly aerobic and showed a rod-coccus cell cycle. Optimum growth occurred at 30 °C, in the presence of 2 % (w/v) NaCl and at pH 7. The 16S rRNA gene sequence analysis showed that strain AM134T belonged to the genus Microbulbifer in the family Alteromonadaceae and had high 16S rRNA gene sequence similarity (>97 %) with Microbulbifer epialgicus F-104T (98.9 % similarity) and Microbulbifer variabilis Ni-2088T (98.6 % similarity). The polar lipid profile of strain AM134T was composed of phosphatidylethanolamine, phosphatidylserine, three unidentified aminophospholipids, two unidentified phospholipids, an unidentified amino lipid and six unidentified lipids. The major respiratory quinone was identified as ubiquinone-8 (Q-8). The major cellular fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. The DNA-DNA hybridization analysis showed that the strain shared less than 28 % genomic relatedness with Microbulbifer epialgicus DSM 18651T (27±3 %) and Microbulbifer variabilis ATCC 700307T (15±1 %). The G+C content of the genomic DNA was 56.1 mol%. The results of the phylogenetic, phenotypic and genotypic analyses suggest that strain AM134T represents a novel species in the genus Microbulbifer, for which the name Microbulbifer echini is proposed. The type strain is AM134T (=KACC 18258T=JCM 30400T).

Topics: Alteromonadaceae; Animals; Anthocidaris; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gastrointestinal Tract; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A bacterial strain designated K7T was isolated from the South China Sea and characterized using a polyphasic taxonomic approach. Cells of strain K7T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore forming rods surrounded by a thick capsule and forming yellow colonies. Growth occurred at 4-35 °C (optimum, 25-30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0.5-10 % (w/v) NaCl [optimum, 1-4 % (w/v)]. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8 and the DNA G+C content was 46.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, one uncharacterized phospholipid, two uncharacterized aminophospholipids and five uncharacterized lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain K7T formed a distinct lineage with respect to closely related genera in the family Alteromonadaceae. Strain K7T was most closely related to Aestuariibacter, Aliiglaciecola, Paraglaciecola and Glaciecola, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 95 %. On the basis of the genotypic and phenotypic data, strain K7T represents a novel species of a new genus of the family Alteromonadaceae, for which the name Planctobacterium marinum gen. nov., sp. nov. is proposed. The type strain of Planctobacterium marinum is K7T (=BCRC 80901T=LMG 28835T=KCTC 42657T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Phospholipids; Phylogeny; Pigmentation; Polyesters; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A bacterial strain, designated T20R-70T, was isolated from tomato rhizosphere soil collected in Yecheon-gun, Gyeongsangbuk-do in South Korea. Growth was observed within the ranges 10-40 °C (optimally at 28-30 °C), pH 7.0-8.0 (optimally at pH 7.0) and 0-1 % NaCl (optimally at 0 %). The 16S rRNA gene sequence showed the highest similarities with those of Lysobacter hankyongensis KTCe-2T (98.7 %), Lysobacter brunescens KCTC 12130T (98.0 %), 'Lysobacter daecheongensis' Dae08 (97.2 %) and Lysobacter oligotrophicus 107-E2T (97.1 %). The phylogenetic tree showed that strain T20R-70T formed a clade with Lysobacterhankyongensis KTCe-2T and Lysobacterbrunescens KCTC 12130T. The dominant fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0, iso-C17 : 1ω9c and summed feature 3 (including iso-C15 : 0 2-OH and/or iso-C16 : 1ω7c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was Q-8. DNA-DNA hybridization data revealed that strain T20R-70T had a hybridization value of 42±4 % (mean±sd) to the most closely related species of the genus Lysobacter. The DNA G+C content was 63.0 mol%. The physiological, biochemical and chemotaxonomic data allowed the discrimination of the new isolate from its phylogenetic relatives. Strain T20R-70T is thus considered to be a representative of a novel species of the genus Lysobacter, for which the name Lysobactersolanacearum sp. nov. is proposed. The type strain is T20R-70T (=KACC 18656T=NBRC 111881T).

Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Lysobacter; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Solanum lycopersicum; Ubiquinone

A Gram-stain-negative, rod-shaped, motile bacterium, designated AER10T, was isolated from the roots of Ammodendron bifolium collected from Takeermohuer desert in Xinjiang Uygur Autonomous Region, northwestern China. Growth was found to occur from 10 to 45 °C, at pH 5.0-9.0, and could tolerate up to 10 % (w/v) NaCl. 16S rRNA gene sequence result indicated that the strain AER10T belongs to the genus Alcaligenes and was closely related to Alcaligenes aquatilis (98.4 %), Alcaligenes faecalissubsp. parafaecalis (98.4 %), Alcaligenes faecalissubsp. faecalis (98.1 %) and Alcaligenes faecalissubsp. phenolicus (97.9 %). However, the DNA-DNA hybridization values between the strain AER10T and the above strains were less than the threshold value (below 70 %) for the delineation of genomic species. The DNA G+C content was 53.3 mol%. Ubiquinone-8 (Q-8) was the only quinone system present. The major fatty acids were summed feature 8 (C18 : 1ω7c, 25 %), C16 : 0 (24.2 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 19.3 %) and cyclo-C17 : 0 (10.5 %). The polar lipid profile of the strain AER10T consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, two unidentified aminolipids and five unknown polar lipids. On the basis of the evidence presented in this study, strain AER10T is a representative of a novel species in the genus Alcaligenes, for which the name Alcaligenes endophyticus sp. nov. is proposed. The type strain is AER10T (=DSM 100498T=KCTC 42688T).

Topics: Alcaligenes; Bacterial Typing Techniques; Base Composition; China; Desert Climate; DNA, Bacterial; Fabaceae; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A straw-coloured, Gram-staining-negative, aerobic, motile and rod-shaped bacterium, designated strain K-1-15T, was isolated from reclaimed grassland soil from Biratnagar, Morang, Nepal. This strain was non-spore-forming, catalase-negative and oxidase-positive. It was able to grow at 10-45 °C, pH 6.5-9.5 and 0-1.5 % (w/v) NaCl concentration. This strain was taxonomically characterized by a polyphasic approach. Based on the results of 16S rRNA gene sequence analysis, K-1-15T formed a distinct lineage within the family Oxalobacteraceae and was most closely related to members of the genera Herbaspirillum(96.99-95.34 % sequence similarity), Noviherbaspirillum(96.72-95.45 % sequence similarity) and Paraherbaspirillum (95.85 % sequence similarity). The only respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major fatty acids of K-1-15T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16  :   0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C10 : 0 3-OH, and iso-C16 : 0. The genomic DNA G+C content of this novel strain was 65.2 mol %. The DNA-DNA relatedness between K-1-15T and Herbaspirillum massiliense DSM 25712T and Noviherbaspirillum soli LMG 26149T were 18.3 and 13.7 % repectively. On the basis of the results of morphological, physiological, chemotaxonomic and phylogenetic analyses, K-1-15T represents a novel species of the genus Noviherbaspirillum in the family Oxalobacteraceae, for which the name Noviherbaspirillum agri sp. nov. is proposed. The type strain is K-1-15T (=KEMB 9005-422T=KACC 18909T=JCM 31463T). Based on new data obtained in this study, we also propose the reclassification of Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov. (type strain JC206T=CSUR P159T=DSM 25712T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Grassland; Herbaspirillum; Nepal; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A novel Gram-staining-negative straight or curved rod-shaped, moderately halophilic and alkaliphilic bacterium, designated strain GBSy1T, was isolated from a sediment sample from the coastal-marine wetland Gomishan in Iran. GBSy1T was motile, and formed non-pigmented, mucoid colonies. Growth occurred with between 1 and 15 % (w/v) NaCl and the isolate grew optimally with 5 % (w/v) NaCl. The optimum pH and temperature for growth were 8.5 and 34 °C, while the strain was able to grow at pH 7.0-10 and 4-40 °C. On the basis of the results of 16S rRNA gene sequence analysis, GBSy1T was shown to represent a member of the genus Aliidiomarina within the class Gammaproteobacteria, family Idiomarinaceae and showed closest phylogenetic similarity to Aliidiomarina marisCF12-14T (97.7 %). The DNA G+C content of GBSy1T was 51.2 mol%. The cells of GBSy1T contained the isoprenoid ubiquinones Q-8, Q-9 and Q-10 (92, 2 and 2 %, respectively). The major cellular fatty acids of the isolate were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and three unknown phospholipids. The level of DNA-DNA relatedness between GBSy1T and Aliidiomarina marisDSM 22154T was 31 %. All these features confirmed the placement of GBSy1T within the genus Aliidiomarina. On the basis of evidence from this study, a novel species of the genus Aliidiomarina, Aliidiomarina sedimenti sp. nov., is proposed, with GBSy1T (=IBRC-M 10764T=CECT 8340T) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Iran; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Wetlands

Two closely related thermophilic bacterial strains, designated YIM 73013T and YIM 73008, were isolated from a sediment sample collected from a hot spring in Tibet, western Tibet province, China. The taxonomic positions of the two isolates were investigated using a polyphasic approach. The novel isolates were Gram-stain-negative, aerobic, short-rod-shaped and motile by means of a polar flagellum. They were oxidase- and catalase-positive and were able to grow at 30-55 °C (optimum, 37-45 °C), at pH 6.0-8.0 (optimum, pH 7.0) and with NaCl tolerance up to 1 % (w/v). Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 73013T and YIM 73008 formed a distinct lineage with respect to closely related genera in the family Comamonadaceae and shared highest 16S rRNA gene sequences similarities with Acidovorax caeni R-24608T (96.3 and 96.4 %, respectively). The respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids observed were C17 : 1ω6c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The genomic DNA G+C contents of strains YIM 73013T and YIM 73008 were 68.7 and 68.3 mol%, respectively. Based on the morphological, phylogenetic and chemotaxonomic results, the two isolates represent a novel species in a new genus, for which the name Tibeticola sediminis gen. nov., sp. nov. is proposed. The type strain of Tibeticola sediminis is YIM 73013T (=DSM 101684T=KCTC 42873T).

Topics: Bacterial Typing Techniques; Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Hot Springs; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Tibet; Ubiquinone

A novel acid-tolerant and alkalitolerant gammaproteobacterium designated strain RS22T was isolated from Kyonggi University forest soil. Cells were aerobic, Gram-stain-negative, catalase- and oxidase-positive, non-motile, non-spore-forming, rod-shaped and yellow-pigmented. Flexirubin-type pigments were absent. Strain RS22T was able to assimilate lactic acid, l-proline and 3-hydroxybenzoic acid; it tolerated 4 % (w/v) NaCl, fermented glucose and was able to grow at pH 11.0. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RS22T formed a lineage within the class Gammaproteobacteria of the phylum Proteobacteria that was distinct from various species of the genus Rhodanobacter, including Rhodanobacter denitrificans 2APBS1T (97.7 % sequence similarity), Rhodanobacter thiooxydans LCS2T (97.5 %), Rhodanobacter terrae GP18-1T (97.5 %) and Rhodanobacter soli DCY45T (97.2 %). The predominant respiratory quinone was Q-8. The major polar lipids of strain RS22T were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0, iso-C17 : 0, iso-C16 : 0, anteiso-C15 : 0 and C16 : 0. The DNA G+C content of strain RS22T was 63.2 mol%. DNA-DNA hybridization between strain RS22T and other closest members of the genus Rhodanobacterrevealed relatedness values from 28 to 51 %. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strain RS22T represents a novel species of the genus Rhodanobacter, for which the name Rhodanobacter humi sp. nov. is proposed. The type strain is RS22T (=KEMB 9005-480T=KACC 19048T=NBRC 112473T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Forests; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A Gram-stain-negative, smooth, opaque, white-pigmented, helical-shaped, catalase- and oxidase-positive bacterium that was motile by means of bipolar tufts of flagella and grew under microaerophilic conditions, was isolated from a soil sample of a reed pond in Shangqiu, Henan province, PR China. The strain, designated THG-SQE6T, grows well at 25-42 °C, pH 6.5-7.5 and in the presence of 0-1 % (w/v) NaCl. hylogenetic analysis based on 16S rRNA gene sequences showed that strain THG-SQE6T was most closely related to Aquaspirillum serpens IAM 13944T (97.23 % 16S rRNA gene sequence similarity). The DNA G+C content of strain THG-SQE6T was 53.10 mol%. In DNA-DNA hybridization experiments, the DNA-DNA relatedness between strain THG-SQE6T and its closest phylogenetic neighbour was below 62.6 %. The predominant isoprenoid quinone detected in strain THG-SQE6T was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. The major fatty acids were identified as C12 : 0 3-OH, C16 : 0, C18 : 0, summed feature 3 and summed feature 8. These data support the affiliation of strain THG-SQE6T to the genus Aquaspirillum. Based on findings from the phenotypic, genotypic and phylogenetic characterization of strain THG-SQE6T, a novel species of the genus AquaspirillumnamedAquaspirillum soli sp. nov. is proposed. The type strain is THG-SQE6T (=KACC 18846T=CCTCC AB 2016081T).

Topics: Bacterial Typing Techniques; Base Composition; Betaproteobacteria; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, aerobic, non-motile, non-spore-forming, yellow and rod-shaped bacterium, designated strain CR164T, was isolated from the rhizosphere soil of a ginseng field at Geumsan in Korea. CR164T grew at between 15 and 37 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.0) and at salinities of 0-1.0 % (w/v) NaCl, growing optimally in the absence of NaCl. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that CR164T represents a member of the genus Rhodanobacter, showing the highest sequence similarity to Rhodanobactercaeni MJ01T (98.5 %), Rhodanobacter ginsenosidimutans Gsoil 3054T (98.4 %), Rhodanobacter thiooxydans LCS2T (98.3 %), Rhodanobacter lindaniclasticus RP5557T (98.1 %), Rhodanobacter denitrificans 2APBS1T (98.0 %), Rhodanobacter fulvus Jip2T (97.6 %), Rhodanobacter soli DCY45T (97.3 %) and 'Rhodanobacterxiangquanii' BJQ-6 (97.0 %). The major fatty acids were iso-C17 : 1ω9c (21.8 %), iso-C15 : 0 (12.1 %), iso-C11 : 0 (11.9 %) and iso-C16 : 0 (11.1 %). The predominant ubiquinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The G+C content of the genomic DNA was 62.3 mol%. DNA-DNA relatedness between CR164T and the type strains of eight other species of the genus ranged from 51 to 9 %. On the basis of the polyphasic analysis, CR164T represents a novel species of the genus Rhodanobacter, for which the name Rhodanobacter rhizosphaerae sp. nov. is proposed. The type strain is CR164T (=KACC 18699T=NBRC 111845T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Panax; Phospholipids; Phylogeny; Republic of Korea; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A Gram-stain-negative, strictly aerobic and moderate halotolerant bacterial strain, designated S2-26T, was isolated from sediment of the Asan Bay estuary in South Korea. Cells were motile rods with two polar flagella showing oxidase and catalase activities. Growth of S2-26T was observed at 15-45 °C (optimum, 25 °C) and pH 5.5-10.0 (optimum, pH 7.0-8.5) and in the presence of 0-8.0 % (w/v) NaCl (optimum, 2.0 %). S2-26T contained C17 : 1ω8c, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (comprising C16:1ω7c/C16:1ω6c) and C17 : 0 as the major fatty acids and ubiquinone-8 as the sole isoprenoid quinone. The polar lipids of S2-26T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid, an unknown aminolipid, an unknown glycolipid and an unknown lipid. The G+C content of the genomic DNA was 62.2 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that S2-26T formed a tight phylogenetic lineage with Parahaliea mediterranea 7SM29T with a 100 % bootstrap value. S2-26T was most closely related to the type strain of Parahaliea mediterranea, with a 97.8 % 16S rRNA gene sequence similarity, and its DNA-DNA relatedness level was 45.2±2.2 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that S2-26T represents a novel species of the genus Parahaliea, for which the name Parahaliea aestuarii sp. nov. is proposed. The type strain is S2-26T (=KACC 18801T=JCM 31547T).

Topics: Bacterial Typing Techniques; Base Composition; Bays; DNA, Bacterial; Estuaries; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, rod-shaped bacterium, designated DCY83T, was isolated from soil of a ginseng field in Gwangju Province, Republic of Korea. Cells were motile by means of flagella. Growth occurred at 4-40 °C (optimum 30 °C), at pH 6-8 (optimum pH 7.0) and with ≤ 0.4 % NaCl. Strain DCY83T was able to produce siderophore and was positive for phosphate solubilization. Indole-3-acetic acid production was 12.9 μg ml- 1 after 3 days in culture. 16S rRNA gene sequence analysis showed that strain DCY83T belonged to the genus Duganella and was related most closely to Duganella sacchari Sac-22T (97.4 % similarity), Duganella zoogloeoides IAM 12670T (97.1 %) and Duganella radicis Sac-41T (97.1 %). The major fatty acids were C16 : 0 and summed feature 3 (containing C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The only quinone was ubiquinone 8. The genomic DNA G+C content was 55.3 mol%. DNA-DNA relatedness between strain DCY83T and D. sacchari KCTC 22381T, D. zoogloeoides JCM 20729T and D. radicis KCTC 22382T was 27.7, 22.4 and 35.5 %, respectively. On the basis of the phenotypic and genotypic analysis, DCY83T is classified as representing a novel species in the genus Duganella, for which the name Duganella ginsengisoli sp. nov. is proposed. The type strain is DCY83T ( = KCTC 42409T = JCM 30745T).

Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Panax; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A heavy metal-resistant and dimethyl disulfide-producing bacterial strain, designated 6NM-7T, was isolated from wolfram mine tailing, Dayu County, Jiangxi Province, PR China. Strain 6NM-7T was aerobic, Gram-stain-negative and motile by means of a single polar flagellum. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain 6NM-7T was affiliated with the genus Massilia and was closely related to Massilia norwichensis LMG 28164T (98.8 % 16S rRNA gene sequence similarity), Massilia kyonggiensis KACC 17471T (98.4 %), Massilia niastensis KACC 12599T (97.8 %), Massilia tieshanensis KACC 14940T (97.3 %), Massilia haematophila KACC 13771T (97.2 %), Massilia namucuonensis CGMCC 1.11014T (97.1 %) and Massilia aerilata KACC 12505T (97.1 %). The DNA-DNA relatedness values between strain 6NM-7T and its closely related type strains were all below 70 %. The major respiratory quinone was unbiquinone 8 (Q-8) and the major cellular fatty acids consisted of C16 : 0 (33.2 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 21.8 %), C17 : 0 cyclo (20.8 %), C18 : 1ω7c (7.4 %) and C10 : 0 3-OH (5.8 %). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain 6NM-7T was 66.8 ± 0.6 mol%. On the basis of the results of this polyphasic taxonomic study, strain 6NM-7T should be assigned to a novel species of the genus Massilia, for which the name Massilia putida sp. nov. is proposed. The type strain is 6NM-7T ( = DSM 27523T = KCTC 42761T).

Topics: Bacterial Typing Techniques; China; Disulfides; DNA, Bacterial; Fatty Acids; Mining; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Tungsten; Ubiquinone

A novel Gram-stain-negative, rods or bent rods, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated XK5T, was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Optimal growth occurred at 28-35 °C (range 8-42 °C) and pH 7.0-8.0 (range pH 6.0-9.0) with 1-3 % (w/v) NaCl (range 0.5-8 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain XK5T was 92.1 % similar to the type strain of Thioalkalivibrio thiocyanodenitrificans, 91.9 % to the type strain of Thioalkalivibrio sulfidiphilus and 91.8 % to the type strain of Thioalkalivibrio denitrificans; similarity to other species was less than 91 %. The isolate and closely related environmental clones formed a novel family level clade in the order Chromatiales. The polar lipid profile of the novel isolate consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown phospholipids, aminolipids and lipids. Major cellular fatty acids were iso-C17 : 1ω9c and iso-C15 : 0 and the main respiratory lipoquinone was Q-8. The DNA G+C content of strain XK5T was 59.3 mol%. Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain XK5T represents a novel species of a new genus within a novel family of the order Chromatiales, for which the name Woeseia oceani gen. nov., sp. nov. is proposed. The type strain of Woeseia oceani is XK5T ( = ATCC BAA-2615T = CICC 10905T). In addition, a novel family name, Woeseiaceae fam. nov., is proposed to accommodate the genus Woeseia.

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Islands; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Two novel strains, designated KTCe-2T and 7C-9T, isolated from an activated sludge and freshwater sediment, respectively in South Korea, were characterized by a polyphasic approach to clarify their taxonomic positions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Lysobacter and are most closely related to 'Lysobacter daecheongensis' Dae 08 (98.5 % and 97.6 % similarity for strains KTCe-2T and 7C-9T, respectively), Lysobacter brunescens KCTC 12130T (98.4 % and 97.2 %), and Lysobacter oligotrophicus JCM 18257T (97.1 % and 96.8 %). The G+C content of the genomic DNA of strains KTCe-2T and 7C-9T was 68.6 % and 71.5 mol%, respectively. Strains KTCe-2T and 7C-9T possessed ubiquinone-8 as the sole respiratory quinone, and a fatty acid profile with iso-C15 : 0 and iso-C16 : 0 as the major fatty acids supported the affiliation of the two strains to the genus Lysobacter. Moreover, the physiological and biochemical results and low DNA-DNA relatedness values allowed the phenotypic and genotypic differentiation of strains KTCe-2T and 7C-9T from other species of the genus Lysobacter with validly published names. Therefore, the two isolates represent two novel species of the genus Lysobacter, for which the name Lysobacter hankyongensis sp. nov. (type strain KTCe-2T = JCM 18204T = KACC 16618T) and Lysobacter sediminicola sp. nov. (type strain 7C-9T = JCM 18205T = KACC 16617T) are proposed.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fresh Water; Geologic Sediments; Lysobacter; Molecular Sequence Data; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone

A Gram-stain-negative, elliptical and facultatively anaerobic strain, designated SW014T, motile by means of a single polar flagellum and positive for poly-β-hydroxybutyrate accumulation, was isolated from surface seawater of the South Pacific Gyre, during the Integrated Ocean Drilling Program Expedition 329. The strain was able to grow at 10-37 °C (optimum 28 °C). Growth was observed at NaCl concentrations (w/v) of 1-7 % (optimum 3-4 %). The pH range for growth was 7.0-9.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences and multilocus sequence analysis indicated that strain SW014T belongs to the genus Enterovibrio within the family Vibrionaceae and is related most closely to Enterovibrio coralii LMG 22228T with 96.3, 83.7, 95.0, 77.1, 84.1 and 85.8 % sequence similarity based on 16S rRNA, recA, rpoA, rpoD, pyrH and ftsZ genes, respectively. The predominant cellular fatty acids were C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0, and C18 : 1ω7c and/or C18 : 1ω6c. The respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain SW014T comprised phosphatidylethanolamine, glycolipid, two unidentified aminolipids, two unidentified phospholipids and two unidentified polar lipids. The DNA G+C content was 44.8 mol%. Combining phylogenetic analysis, phenotypic characteristics and chemotaxonomic studies, strain SW014T represents a novel species of the genus Enterovibrio, for which the name Enterovibrio pacificus sp. nov. is proposed. The type strain is SW014T ( = KCTC 42425T = MCCC 1K00500T). Emended descriptions of Enterovibrio coralii and of the genus Enterovibrio are also provided.

Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Hydroxybutyrates; Molecular Sequence Data; Pacific Ocean; Phospholipids; Phylogeny; Polyesters; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Vibrionaceae

A Gram-stain-negative, curved rod-shaped and non-pigmented strain, HME8277T, was isolated from surface seawater of the Yellow Sea in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Reinekea blandensis MED297T (96.4 % 16S rRNA gene sequence similarity), Reinekea aestuarii IMCC4489T (96.3 %) and Reinekea marinisedimentorum KMM 3655T (95.8 %). The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c; 43.0 %), C16 : 0 (19.0 %) and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 15.0 %). The DNA G+C content was 46.1 mol%. The predominant respiratory quinone was Q-8. The major polar lipids of strain HME8277T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified phospholipids and four unidentified lipids. On the basis of polyphasic analyses, strain HME8277T represents a novel species of the genus Reinekea, for which the name Reinekea marina sp. nov. is proposed. The type strain HME8277T ( = KACC 17315T = CECT 8288T). An emended description of the genus Reinekea is also provided.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, facultatively aerobic bacterium, strain X13M-12T, was isolated from a salt lake (Lake Xiaochaidan) in the Qaidam basin, Qinghai Province, PR China. Cells of strain X13M-12T were slightly curved, rod-shaped, 0.5-0.8 μm wide and 1.2-2.3 μm long, and motile by means of a polar flagellum. Strain X13M-12T was catalase- and oxidase-positive. Growth was observed in the presence of 0-15.0 % (w/v) NaCl (optimum 3.0-5.0 %), and at 4-40 °C (optimum 25-30 °C) and pH 6.0-11.0 (optimum pH 8.5). Strain X13M-12T contained Q-8 as the sole respiratory quinone, and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The major cellular fatty acids (>10 % of totals) were C16 : 0, C16 : 1ω7c and/or C16 : 1ω6c, and C18 : 1ω7c and/or C18 : 1ω6c. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain X13M-12T belonged to the family Alteromonadaceae and formed a distinct lineage, showing low gene sequence similarities to closely related genera: Bowmanella, Aestuariibacter and Salinimonas (16S rRNA gene sequence similarities, 93.0-93.1 %, 92.3-93.1 % and 92.6-92.7 %, respectively). In addition, strain X13M-12T showed < 92.7 % gene sequence similarities to other species of the family Alteromonadaceae. The DNA G+C content of strain X13M-12T was 49 mol% (Tm). Based on the data presented above, strain X13M-12T is considered to represent a novel genus and species of the family Alteromonadaceae, for which the name Lacimicrobium alkaliphilum gen. nov., sp. nov. is proposed. The type strain is X13M-12T ( = CGMCC 1.12923T = KCTC 42674T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Lakes; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Saline Waters; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, facultatively anaerobic, non-pigmented, non-sporulating, rod-shaped bacterial strain (WYH 22-41T) was isolated from a phosphate mine in Yunnan Province, China. The cells were motile with a single polar flagellum. The 16S rRNA gene of strain WYH 22-41T was phylogenetically related to the corresponding gene of Comamonas terrae DSM 27221T (98.4 % 16S rRNA gene sequence similarity), Comamonas odontotermitis LMG 23579T (97.6 %) and Comamonas aquatica LMG 2370T (97.4 %). DNA-DNA hybridizations of strain WYH 22-41T with these three strains showed relatedness values of 33.2 %, 20.5 % and 27.7 %, respectively. The DNA G+C content of strain WYH 22-41T was 62.4 mol%. The predominant respiratory quinone was ubiquinone-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major fatty acids of strain WYH 22-41T were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). On the basis of phenotypic properties, phylogenetic characteristics, DNA-DNA hybridization, as well as whole-cell fatty acid composition, strain WYH 22-41T represents a novel species of the genus Comamonas, for which the name Comamonas phosphati sp. nov. is proposed. The type strain is WYH 22-41T ( = CGMCC 1.12294T = DSM 26017T).

Topics: Bacterial Typing Techniques; Base Composition; China; Comamonas; DNA, Bacterial; Fatty Acids; Mining; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphates; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A total of 13 Pasteurellaceae isolates from healthy freshwater turtles were characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group. The closest related species based on 16S rRNA gene sequencing was Chelonobacter oris CCUG 55632T with 94.4 % similarity and the closest related species based on rpoB gene sequence comparison was [Pasteurella] testudinis CCUG 19802T with 91.5 % similarity. All the investigated isolates exhibited phenotypic characteristics of the family Pasteurellaceae. However, they could be separated from existing genera of the Pasteurellaceae by the following test results: indole, ornithine decarboxylase and Voges-Proskauer positive; and methyl red, urease and PNPG (α-glucosidase) negative. No X- or V-factor requirement was observed. A zone of β-haemolysis surrounded the colonies after 24 h of incubation on bovine blood agar at 37 °C. Acid was produced from l-arabinose, dulcitol, d-mannitol, sucrose and trehalose. Representative strain ELNT2xT had a fatty acid profile that was characteristic for members of the Pasteurellaceae. ELNT2xT expressed only one respiratory quinone, ubiquinone-8 (100 %). The DNA G+C content of strain ELNT2xT was 42.8 mol%. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the strains should be classified as representatives of a novel species of a new genus, Testudinibacter aquarius gen. nov., sp. nov. The type strain of Testudinibacter aquarius is ELNT2xT ( = CCUG 65146T = DSM 28140T), which was isolated from the oral cavity of a captive eastern long-necked turtle (Chelodina longicollis) in Denmark in 2012.

Topics: Animals; Bacterial Typing Techniques; Base Composition; Denmark; DNA, Bacterial; Fatty Acids; Fresh Water; Mouth; Pasteurellaceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Turtles; Ubiquinone

A bacterial strain, designated TTM-24T, was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TTM-24T were Gram-stain-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by a single polar flagellum, rod-shaped, with rods surrounded by a thick capsule and forming white-coloured colonies. Growth occurred at 15-37 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, pH 7.0) and with 0-1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TTM-24T belonged to the genus Vogesella and was most closely related to 'Vogesella amnigena' Npb-02 with sequence similarity of 97.1 %. Strain TTM-24T contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major respiratory quinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The genomic DNA G+C content of strain TTM-24T was 67.4 mol%. The DNA-DNA hybridization value for strain TTM-24T with 'V. amnigena' Npb-02 was less than 45 %. On the basis of the phylogenetic inference and phenotypic data, strain TTM-24T should be classified as a novel species, for which the name Vogesella facilis sp. nov. is proposed. The type strain is TTM-24T ( = BCRC 80912T = KCTC 42742T = LMG 29003T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Neisseriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Polyesters; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone; Water Microbiology

A Gram-stain-negative, non-pigmented, non-spore-forming, non-motile, strictly aerobic bacterial strain, designated CAU 1038T, was isolated from a sea sand sample in Modo, Republic of Korea, and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1038T grew optimally at 30 °C, pH 7.5 in 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1038T formed a distinct lineage within the class Gammaproteobacteria as a separate deep branch, with 95.2 % or lower sequence similarity to representatives of the genera Haliea, Halioglobus and Chromatocurvus, and 92.3 % or lower with Luminiphilus, Pseudohaliea and Congregibacter. The major cellular fatty acids of strain CAU 1038T were C16 : 0, C16 : 1ω7c and C18 : 1ω7c. The polar lipid pattern of the isolate consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The strain contained lipoquinone (Q-8) as the sole respiratory quinone. The G+C content of the genomic DNA was 65 mol%. On the basis of phenotypic and chemotaxonomic data, and phylogenetic inference, strain CAU 1038T represents a novel species of a new genus in the family Halieaceae, for which the name Marimicrobium arenosum gen. nov., sp. nov. is proposed. The type strain of the type species is CAU 1038T ( = KCTC 42300T = NBRC 110727T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Silicon Dioxide; Ubiquinone; Water Microbiology

A bacterial strain designated CAVIOT was isolated during the course of a study of culturable bacteria in a riverbank soil sample from Tlaxcala, Mexico. The strain was subjected to a polyphasic taxonomic characterization. Strain CAVIOT was aerobic, Gram-stain-negative, non-spore-forming and rod-shaped. Colonies grown on R2A agar at 28 °C were pale violet, mucoid, rounded, smooth and glossy. The strain was motile and catalase- and oxidase-positive, and maximum growth temperature was 35 °C. Strain CAVIOT was classified within the genus Massilia as its 16S rRNA gene sequence was closely related to those of Massilia umbonata LP01T (97.5 % similarity), Massilia dura 16T (97.2 %) and Massilia plicata 76T (97.1 %). The predominant respiratory quinone was Q8. The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c). The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and an unknown phospholipid. The DNA G+C content was 65.0 mol% (Tm). DNA-DNA hybridization results showed values below 25 % with respect to the type strains of the closest related species. Therefore, strain CAVIOT can be differentiated from previously described species of the genus Massilia and represents a novel species, for which the name Massilia violacea sp. nov. is proposed. The type strain is CAVIOT ( = CECT 8897T = LMG 28941T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Mexico; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-staining-negative, strictly aerobic, rod-shaped and bright-yellow-pigmented bacterium, motile by means of a single polar flagellum, designated THG-MD21T, was isolated from rhizosphere soil of Radix ophiopogonis in Henan province, PR China. On the basis of 16S rRNA gene sequence similarity, strain THG-MD21T belongs to the genus Luteimonas and was most closely related to Luteimonas aestuarii B9T (98.2 % sequence similarity), Lysobacter panaciterrae Gsoil 068T (97.2 %) and Luteimonas marina FR1330T (97.0 %). The DNA G+C content was 64.4 mol%. The DNA-DNA relatedness between strain THG-MD21T and its closest phylogenetic neighbours was below 30.0 %. The only isoprenoid quinone detected in strain THG-MD21T was ubiquinone-8.The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, and the predominant fatty acids were iso-C11 : 0, iso-C15 : 0, iso-C16 : 0, C16 : 0 and iso-C17 : 1ω9c. The DNA-DNA hybridization result and characteristics revealed by a polyphasic study showed that strain THG-MD21T represents a novel species, for which the name Luteimonas terrae sp. nov. is proposed. The type strain is THG-MD21T ( = KACC 18131T = JCM 30122T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Roots; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A Gram-stain-negative, motile, aerobic, rod- or ovoid-shaped bacterium, designated DB-1T, was isolated from a tidal flat on the Yellow Sea in South Korea and subjected to a taxonomic study using a polyphasic approach. Strain DB-1T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 0.5-2.0% (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain DB-1T falls within the clade comprising species of the genus Marinobacterium, clustering coherently with the type strain of Marinobacterium nitratireducens and showing a sequence similarity value of 98.4 %. The novel strain exhibited 16S rRNA gene sequence similarities of 91.5-94.4 % to the type strains of other species of the genus Marinobacterium. Strain DB-1T contained Q-8 as the predominant ubiquinone and C18:1ω7c, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0 as the major fatty acids. The major polar lipids detected in strain DB-1T were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid, one unidentified glycolipid, one unidentified phospholipid and two unidentified lipids. The DNA G+C content of strain DB-1T was 62.3 mol% and the mean DNA-DNA relatedness value with the type strain of M. nitratireducens was 21±4.6%. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain DB-1T is separated from recognized species of the genus Marinobacterium. On the basis of the data presented, strain DB-1T is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium aestuariivivens sp. nov. is proposed. The type strain is DB-1T (=KCTC 42778T=NBRC 111756T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, non-motile, non-spore-forming, non-pigmented, oxidase- and catalase-positive bacterial strain, designated BIc20019T, was isolated from the ice core of Austre Lovénbreen in Ny-Ålesund, Svalbard. The temperature and NaCl ranges for growth were 4-34 °C (optimum, 25-29 °C) and 0-8% (w/v) (optimum, 2-4%). Analysis of the 16S rRNA gene sequence indicated that strain BIc20019T belonged to the genus Psychrobacter and was closely related to Psychrobacter arcticus 273-4T, Psychrobacter cryohalolentis K5T, 'Psychrobacter fjordensis' BSw21516B, Psychrobacter fozii LMG 21280T, Psychrobacter luti LMG 21276T and Pyschrobacter okhotskensis MD17T at greater than 99% similarity. Phylogenetic analysis based on gyrB gene sequences revealed highest similarity (93.6%) to P. okhotskensis MD17T. However, DNA hybridization experiments revealed a low level of DNA-DNA relatedness (<59%) between strain BIc20019T and its closest relatives. Strain BIc20019T contained ubiquinone-8 (Q-8) as the predominant respiratory quinone, and C18:1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) as the major fatty acids. It had a DNA G+C content of 46.3 mol%. The polar lipid profile of strain BIc20019T was mainly composed of phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Owing to the differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on 16S rRNA gene and gyrB gene sequences, and DNA-DNA relatedness data, the isolate merits classification within a novel species for which the name Psychrobacter glaciei sp. nov. is proposed. The type strain is BIc20019T (=KCTC 42280T = CCTCC AB 2014019T).

Topics: Arctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Ice Cover; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Psychrobacter; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Svalbard; Ubiquinone

A Gram-negative, strictly aerobic, non-motile, rod-shaped bacterium, designated THG-S6.8(T), was isolated from soil in Incheon, South Korea. Based on 16S rRNA gene sequence, strain THG-S6.8(T) was moderately related to Massilia plicata 76(T) (97.3 %), Massilia dura 16(T) (97.2 %) and Massilia albidiflava 45(T) (96.9 %). Chemotaxonomic data revealed that strain THG-S6.8(T) possesses ubiquinone-8 as the predominant respiratory quinone, and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and C16:0 as the major fatty acids. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA-DNA relatedness between strain THG-S6.8(T) and Massilia plicata KCTC 12344(T) and Massilia dura KACC 12342(T) was 38.7 and 40.5 %, respectively. The DNA G+C content was 66.8 %. These data, together with phenotypic characterization, suggest the isolate represents a novel species, for which the name Massilia humi sp. nov. is proposed, with THG-S6.8(T) as the type strain (=KCTC 42737(T) = CCTCC AB 2015296(T)).

Topics: Bacterial Typing Techniques; Base Composition; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Species Specificity; Ubiquinone

Three bacterial strains, designated DS48-6-5T, DS48-6-7 and DS48-6-9, were isolated from a sediment sample taken from Daechung Reservoir (Republic of Korea) at a water depth of 48 m. Cells of the strains were Gram-stain-negative, aerobic, rod-shaped and motile with a single polar flagellum. Comparative 16S rRNA gene sequence studies showed that the three isolates had clear affiliation with Betaproteobacteria and the closest relatives were Rhizobacter bergeniae KCTC 32299T, Rhizobacter dauci DSM 11587T and Rhizobacter fulvus KCTC 12591T with 97.2-97.9 % 16S rRNA gene sequence similarities; the 16S rRNA gene sequence similarities between the three strains were 99.5-100 %. The only isoprenoid quinone of the three strains was ubiquinone-8, and the major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0. The G+C content of the genomic DNA of strains DS48-6-5T, DS48-6-7 and DS48-6-9 was 66.7, 67.0 and 66.8 mol%, respectively. DNA-DNA hybridization values of the novel strains with R. bergeniae KCTC 32299T, R. dauci DSM 11587T and R. fulvus KCTC 12591T were 19.3-48.5 %. Based on the evidence from this taxonomic study using a polyphasic approach, it is proposed that strains, DS48-6-5T, DS48-6-7 and DS48-6-9, represent a novel species of the genus Rhizobacter, for which the name Rhizobacter profundi sp. nov. is proposed. The type strain is DS48-6-5T ( = KCTC 42645T = NBRC 111169T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fresh Water; Geologic Sediments; Nucleic Acid Hybridization; Phylogeny; Pseudomonadaceae; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

A novel, salt-dependent, non-motile, rod-shaped, Gram-stain-negative and non-endospore-forming bacterium, designated strain Cs16bT, was isolated from the rhizosphere of Arthrocnemum macrostachyum, a halophytic plant at the Lebrija marshes (Seville, Spain). Strain Cs16bT was catalase- and oxidase-positive, and able to hydrolyse casein. Growth occurred from 15-40 °C, at pH 6.0-10.0 and with 1-6% (w/v) NaCl. Q-8 was identified as the major ubiquinone and the predominant cellular fatty acids were iso-C15:0, iso-C17:1cis8, iso-C11:0 3-OH, iso-C17:0, C17:0 cyclo and iso-C11:0. The polar lipids profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unknown glycophospholipids, an unknown aminoglycophospholipid, an unknown aminophospholipid and an unknown phospholipid. The 16S rRNA gene of strain Cs16bT showed 98.1%, 97.8%, and 97.6% sequence similarity with Microbulbifer maritimus CIP 108504T, Microbulbifer taiwanensis DSM 24146T and Microbulbifer gwangyangensis JCM 17800T, respectively. Based on the phenotypic and genotypic features, it is concluded that strain Cs16bT represents a novel species of the genus Microbulbifer, for which the name Microbulbifer rhizosphaerae sp. nov. is proposed. The type strain is Cs16bT (=DSM 28920T=CECT 8799T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; Chenopodiaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phospholipids; Phylogeny; Rhizosphere; RNA, Ribosomal, 16S; Salt-Tolerant Plants; Sequence Analysis, DNA; Soil Microbiology; Spain; Ubiquinone

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming, yellow pigmented bacterial strain (UM1T) was isolated from the hexachlorocyclohexane (HCH)-contaminated dumpsite located at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain UM1T belongs to the genus Luteimonas with Luteimonas aestuarii B9T as the closest neighbour (97.2% 16S rRNA gene sequence similarity). The DNA G+C content of strain UM1T was 64.3 mol%. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Main fatty acids were iso-C15:0, iso-C11:0, iso-C11:0 3-OH, iso-C17:0 and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). Ubiquinone (Q-8) was the only respiratory quinone. Spermidine was detected as the major polyamine. The DNA-DNA relatedness value of strain UM1T with respect to its closest neighbour Luteimonas aestuarii B9T was well below 70 % (∼49%). Thus, data obtained from phylogenetic analysis, DNA-DNA hybridization, and chemotaxonomical and biochemical analyses supports classification of strain UM1T as representative of a novel species of the genus Luteimonas, for which the name Luteimonas tolerans sp. nov. is proposed. The type strain is UM1T (=DSM 28473T=MCC 2572T=KCTC 42936T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hexachlorocyclohexane; India; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants; Spermidine; Ubiquinone; Xanthomonadaceae

A moderately halophilic, aerobic bacterium, strain BZ-SZ-XJ27T, belonging to the genus Halomonas, was isolated from a saline-alkaline lake in the Xinjiang Uyghur Autonomous Region of China. Phylogenetic analysis based on 16S rRNA gene sequences and a multilocus sequence analysis using the 16S rRNA, gyrB and rpoD genes demonstrated that strain BZ-SZ-XJ27T represents a member of the genus Halomonas. On the basis of 16S rRNA gene sequence similarity, the closest relatives were Halomonas campaniensis 5AGT, H. fontilapidosi 5CRT, H. korlensis XK1T and H. sinaiensis ALO SharmT, with similarities of 96.2-97.2 %. DNA-DNA hybridization with H. korlensis CGMCC 1.6981T (the nearest phylogenetic neighbour) and H. campaniensis DSM 15293T (the highest 16S rRNA gene sequence similarity) showed relatedness values of 53 and 38 %, respectively, demonstrating the separateness of the three taxa. The bacterium stained Gram-negative and the cells were motile and rod-shaped. The strain formed creamy-white colonies and grew under optimal conditions of 1.42 M Na+ (range 0.22-4.32 M Na+), pH 8.0-8.5 (range pH 6.0-10.0) and 39 °C (range 4-43 °C). The dominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 36.6 %), C16 : 0 (25.9 %) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 21.2 %). The dominant polar lipids were two unknown phospholipids, phosphatidylethanolamine and phosphatidylglycerol, and the main respiratory quinones were ubiquinone 9 (Q-9; 89 %) and ubiquinone 8 (Q-8; 10 %). The genomic DNA G+C content was 61.7 ± 0.8 mol% (Tm). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BZ-SZ-XJ27T is proposed to represent a novel species, Halomonas urumqiensis sp. nov., within the genus Halomonas of the family Halomonadaceae. The type strain is BZ-SZ-XJ27T ( = JCM 30202T = CGMCC 1.12917T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Halomonadaceae; Halomonas; Hydrogen-Ion Concentration; Lakes; Multilocus Sequence Typing; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

An endohyphal bacterium (strain B1-EBT) living in association with the fungus Mortierella elongata FMR23-6 I-B1 was isolated from a fungal cell homogenate and studied for its taxonomic allocation. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, non-motile, and negative for oxidase and catalase. Strain B1-EBT required cysteine for growth and grew at temperatures between 4 and 35 °C. A comparative analysis of 16S rRNA gene sequences revealed that strain B1-EBT forms a distinct clade in the family Burkholderiaceae, encompassing a group of endosymbionts associated with several soil isolates of M. elongata. The most closely related genus is 'Candidatus Glomeribacter gigasporarum', an endosymbiont of the arbuscular mycorrhizal fungus Gigaspora margarita. The major cellular fatty acids of strain B1-EBT were C16 : 0, summed feature 3 (C16 : 1ω7c and C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c or C18 : 1ω6c). Ubiquinone Q-8 was the only quinone detected. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid and two unknown aminolipids. The DNA G+C content was 49.8 mol%. On the basis of phenotypic, chemotaxonomic, and phylogenetic characteristics, strain B1-EBT represents a novel genus and novel species in the family Burkholderiaceae, for which the name Mycoavidus cysteinexigens gen. nov., sp. nov. is proposed. The type strain is B1-EBT ( = JCM 30646T = LMG 28693T = NBRC 110909T).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; DNA, Bacterial; Fatty Acids; Japan; Mortierella; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, aerobic, motile, rod-shaped or ovoid bacterial strain, designated DB-2T, was isolated from a tidal flat of the Yellow Sea in South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain DB-2T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain DB-2T belonged to the genus Pseudoalteromonas. Strain DB-2T exhibited 16S rRNA gene sequence similarities of 97.17-97.36 % to the type strains of Pseudoalteromonas mariniglutinosa, Pseudoalteromonas spongiae and Pseudoalteromonas tetraodonis and of 93.79-96.99 % to the type strains of the other species of the genus Pseudoalteromonas. Strain DB-2T contained Q-8 as the predominant ubiquinone and C16 : 0, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C12 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DB-2T were phosphatidylglycerol, phosphatidylethanolamine, two unidentified glycolipids, an unidentified phospholipid and an unidentified aminolipid. The DNA G+C content of strain DB-2T was 54.9 ± 0.2 mol% and mean DNA-DNA relatedness values with the type strains of P. mariniglutinosa, P. spongiae and P. tetraodonis were 10-17 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain DB-2T is separated from recognized species of the genus Pseudoalteromonas. On the basis of these data, strain DB-2T is considered to represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas aestuariivivens sp. nov. is proposed. The type strain is DB-2T ( = KCTC 42779T = CECT 8945T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pseudoalteromonas; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel Gram-stain-negative, straight rod-shaped, non-pigmented, slightly halophilic and alkaliphilic bacterium, designated strain GBPy7T, was isolated from a sample of the coastal-marine wetland Gomishan in Iran. Cells of strain GBPy7T were motile. Growth occurred on media with 1-15 % (w/v) NaCl (optimum 3 %), at pH 7-10 (optimum pH 8.5) and at 4-45 °C (optimum 37 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparison indicated that strain GBPy7T belonged to the family Idiomarinaceae. Its closest relatives were Aliidiomarina shirensis AIST (98.1 % 16S rRNA gene sequence similarity) and other Aliidiomarina species (95.9-94.2 %), together with Idiomarina seosinensis CL-SP19T (94.3 %) and Idiomarina fontislapidosi F23T (94.3 %). The major cellular fatty acids of the isolate were iso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c and C18 : 1ω7c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and one unknown aminophospholipid. Cells of strain GBPy7T contained ubiquinone Q-8. The G+C content of the genomic DNA of this strain was 51.6 mol%. The level of DNA-DNA relatedness between strain GBPy7T and A. shirensis IBRC-M 10414T was 21 %. The physiological, biochemical, genotypic and phylogenetic differences between strain GBPy7T and other previously described taxa indicate that the strain represents a novel species of the genus Aliidiomarina within the family Idiomarinaceae, for which the name Aliidiomarina iranensis sp. nov. is proposed. The type strain is GBPy7T ( = IBRC-M 10763T = CECT 8339T).

Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Iran; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spiro Compounds; Ubiquinone; Wetlands

A novel Proteus-like, Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated strain JS9T, was isolated from Korean fermented seafood, Jeotgal. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain JS9T belonged to the genus Proteus in the family Enterobacteriaceae. The highest 16S rRNA gene sequence similarity of strain JS9T was to Proteus vulgaris KCTC 2579T (98.98 %) and the genomic DNA G+C content is 39.0 mol%. DNA-DNA hybridization values were measured and strain JS9T showed <20.8 % genomic relatedness with closely-related members of the genus Proteus. The isolate showed bacterial motility and swarming activity similar to those of pathogenic Proteus mirabilis but distinct from those of other species of the genus Proteus. The isolate grows optimally at 30 °C, at pH 7, and in the presence of 2 % (w/v) NaCl. The main respiratory quinones are ubiquinone Q-8 and Q-10, and the major cellular fatty acids are C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprise phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified amino lipid, two unidentified amino-phospholipids, and three unidentified lipids. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain JS9T represents a novel species of the genus Proteus, for which the name Proteus cibarius sp. nov. is proposed. The type strain is JS9T (=KACC 18404T=JCM 30699T). An emended description of the genus Proteus is also provided.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fermentation; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Proteus; RNA, Ribosomal, 16S; Seafood; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, aerobic, rod-shaped bacterium motile by means of a single polar flagella, strain ST-6T, was isolated from a brown alga (Sargassum thunbergii) collected in Jeju, Republic of Korea. Strain ST-6T was psychrotolerant, growing at 4-30 °C (optimum 20 °C). Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that strain ST-6T belonged to a distinct lineage in the genus Shewanella. Strain ST-6T was related most closely to Shewanella basaltis J83T, S. gaetbuli TF-27T, S. arctica IT12T, S. vesiculosa M7T and S. aestuarii SC18T, showing 96-97 % and 85-70 % 16S rRNA and gyrB gene sequences similarities, respectively. DNA-DNA relatedness values between strain ST-6T and the type strains of two species of the genus Shewanella were <22.6 %. The major cellular fatty acids (>5 %) were summed feature 3 (comprising C16:1ω7c and/ or iso-C15:0 2-OH), C16:0, iso-C13:0 and C17:1ω8c. The DNA G+C content of strain ST-6Twas 42.4 mol%, and the predominant isoprenoid quinones were menaquinone MK-7 and ubiquinones Q-7 and Q-8. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain ST-6T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella algicola sp. nov. is proposed. The type strain is ST-6T (= KCTC 23253T = JCM 31091T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Nucleic Acid Hybridization; Phaeophyceae; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Shewanella; Ubiquinone; Vitamin K 2

A Gram-stain-negative, rod-shaped bacterium that formed yellow and viscous colonies was isolated from arsenic-contaminated soil of the Jianghan plain, Hubei Province, China, and it was designated 26-35T. This strain was capable of resisting arsenate and arsenite with MICs of 40 and 20 mM, respectively. The 16S rRNA gene of the novel isolate displayed 96.7-94.2 % sequence similarities to those of other known species of the genus Luteimonas. The respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content was 71.4 mol%. The predominant cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, iso-C11 : 0, iso-C11 : 0 3-OH and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic and physiological analysis indicated that the isolate represents a novel species of the genus Luteimonas, for which the name Luteimonas arsenica sp. nov. is proposed. The type strain is 26-35T (=KCTC 42824T=CCTCC AB 2014326T).

Topics: Arsenic; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants; Ubiquinone; Xanthomonadaceae

Phylogenetic and taxonomic characterization was performed for bacterium RB-25T, which was isolated from a soil sample collected in a former municipal landfill site in Puchong, Malaysia. Growth occurred at 20-37 °C at pH 5-8 but not in the presence of 9 % (w/v) NaCl or higher. The principal fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). Ubiquinone-8 was the only isoprenoid quinone detected. Polar lipid analysis revealed the presence of phospholipid, phosphoaminolipid, phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. DNA G+C content was 50.9 mol% phylogenetic analysis based on 16S rRNA gene sequence showed that strain RB-25T formed a distinct lineage within the family Enterobacteriaceae of the class Gammaproteobacteria. It exhibited a low level of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pantoea rwandensis LMG 26275T (96.6 %), Rahnella aquatilis CIP 78.65T (96.5 %), Pectobacterium betavasculorum ATCC 43762T (96.4 %), Pantoea rodasii LMG 26273T (96.3 %), Gibbsiella dentisursi NUM 1720T (96.3 %) and Serratia glossinae C1T (96.2 %). Multilocus sequence analyses based on fusA, pyrG, rplB, rpoB and sucA sequences showed a clear distinction of strain RB-25T from the most closely related genera. Isolate RB-25T could also be distinguished from members of these genera by a combination of the DNA G+C content, respiratory quinone system, fatty acid profile, polar lipid composition and other phenotypic features. Strain RB-25T represents a novel species of a new genus, for which the name Chaniamultitudinisentens gen. nov., sp. nov. is proposed. The type strain is RB-25T (=DSM 28811T=LMG 28304T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Enterobacteriaceae; Fatty Acids; Genes, Bacterial; Homoserine; Lactones; Malaysia; Multilocus Sequence Typing; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Waste Disposal Facilities

A Gram-stain-negative, strictly aerobic, non-motile, non-gliding, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain sw153T, was isolated from surface seawater of the South Pacific Gyre (39° 19' S 139° 48' W) during Integrated Ocean Drilling Program Expedition 329. Growth occurred at 10-42 °C (optimum 28 °C), in the presence of 1-8 % (w/v) NaCl (optimum 2 %) and at pH 6.0-10.0 (optimum pH 7.5-8.5). The major fatty acids (>10 %) were iso-C15:0 and summed feature 3 (C16:1ω6c and/or C16:1ω7c). The major polar lipids comprised phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified polar lipid and an unidentified phospholipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain sw153T was 44.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain sw153T within the genus Marinicella, class Gammaproteobacteria. The most closely related species was Marinicella litoralis KMM 3900T (96.6 % 16S rRNA gene sequence similarity). Based on the polyphasic analyses in this study, strain sw153T is considered to represent a novel species of the genus Marinicella, for which the name Marinicella pacifica sp. nov. is proposed. The type strain is sw153T (=JCM 18208T=CGMCC 1.12181T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Pacific Ocean; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, aerobic, coccoid to small rod-shaped bacterium, designated X1T, was isolated from sludge collected from the vicinity of a pesticide manufacturer in Nantong, Jiangsu Province, China. Based on 16S rRNA gene sequence analysis, strain X1T belonged to the genus Cupriavidus, and was most closely related to Cupriavidus taiwanensis LMG 19424T (99.1 % 16S rRNA gene sequence similarity) and Cupriavidus alkaliphilus LMG 26294T (98.9 %). Strain X1T showed 16S rRNA gene sequence similarities of 97.2-98.2 % with other species of the genus Cupriavidus. The major cellular fatty acids of strain X1T were C16 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3), C18 : 1ω7c and C17 : 0 cyclo, and the major respiratory quinone was ubiquinone Q-8. The major polar lipids of strain X1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phospholipid and hydroxyphosphatidylethanolamine. The DNA G+C content was 66.6 mol%. The DNA-DNA relatedness values of strain X1T with the five reference strains C. taiwanensis LMG 19424T, C. alkaliphilus LMG 26294T, Cupriavidus necator LMG 8453T, Cupriavidus gilardii LMG 5886T and 'Cupriavidus yeoncheonense' KCTC 42053 were lower than 70 %. The results obtained from phylogenetic analysis, phenotypic characterization and DNA-DNA hybridization indicated that strain X1T should be proposed to represent a novel species of the genus Cupriavidus, for which the name Cupriavidus nantongensis sp. nov. is proposed. The type strain is X1T (=KCTC 42909T=LMG 29218T).

Topics: Bacterial Typing Techniques; Base Composition; China; Chlorpyrifos; Cupriavidus; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone

A Gram-stain-negative, aerobic, motile rod-shaped bacterium, designated 6-67T, was isolated from a soil sample collected from Longyearbyen, Svalbard. Its taxonomic position was investigated by genotypic, phenotypic and chemotaxonomic analyses. This isolate grew at 4-28 °C (optimum, 20 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0-0.2 % (w/v) NaCl. Strain 6-67T contained Q-8 as a major respiratory quinone and MK-7 as a minor component; the major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified phospholipids and one unidentified aminophospholipid. The polyamines were putrescine and 2-hydroxyputrescine. 16S rRNA gene sequence analysis indicated that the novel strain 6-67T belonged to the family Oxalobacteraceae within the class Betaproteobacteria. The DNA G+C content of strain 6-67T was 56.21 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain 6-67T is considered to represent a novel species of the genus Undibacterium, for which the name Undibacterium arcticum sp. nov. is proposed. The type strain is 6-67T (=CCTCC AB 2015162T=KCTC 42986T).

Topics: Arctic Regions; Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Oxalobacteraceae; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Svalbard; Ubiquinone

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterium, designed strain 201-F6T, was isolated from a microbial consortium that degrades poly(ethylene terephthalate) (PET) collected in Sakai city, Japan, and was characterized on the basis of a polyphasic taxonomic study. The cells were motile with a polar flagellum. The strain contained cytochrome oxidase and catalase. It grew within the pH range 5.5-9.0 (optimally at pH 7-7.5) and at 15-42 ºC (optimally at 30-37 ºC). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). C16 : 0, C17 : 0 cyclo, C18 :1ω7c and C12 : 0 2-OH were the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of genomic DNA was 70.4 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that strain 201-F6T was affiliated to the genus Ideonella, and was closely related to Ideonella dechloratans LMG 28178T (97.7 %) and Ideonella azotifigens JCM 15503T (96.6 %). Strain 201-F6T could be clearly distinguished from the related species of the genus Ideonella by its physiological and biochemical characteristics as well as by its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Ideonella, for which the name Ideonella sakaiensis sp. nov. (type strain 201-F6T=NBRC 110686T=TISTR 2288T) is proposed.

Topics: Bacterial Typing Techniques; Base Composition; Betaproteobacteria; DNA, Bacterial; Fatty Acids; Japan; Microbial Consortia; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Polyethylene Terephthalates; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel Gram-stain-negative, straight or slightly curved rod-shaped, non-spore-forming, facultatively anaerobic bacterium with a single polar flagellum, designated RZB5-4T, was isolated from a sample of the red algae Gelidium amansii collected from the coastal region of Rizhao, PR China (119.625° E 35.517° N). The organism grew optimally between 24 and 28 °C, at pH 7.0 and in the presence of 2-3 % (w/v) NaCl. The strain required seawater or artificial seawater for growth, and NaCl alone did not support growth. Strain RZB5-4T contained C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0 and iso-C15 : 0 as the dominant fatty acids. The respiratory quinones detected in strain RZB5-4T were ubiquinone 7, ubiquinone 8, menaquinone 7 and methylmenaquinone 7. The polar lipids of strain RZB5-4T comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, one unidentified glycolipid, one unidentified phospholipid and one unknown lipid. The DNA G+C content of strain RZB5-4T was 47 mol %. Phylogenetic analysis based on 16S rRNA and gyrase B (gyrB) gene sequences showed that strain RZB5-4T belonged to the genus Shewanella, clustering with Shewanella waksmanii ATCC BAA-643T. Strain RZB5-4T exhibited the highest 16S rRNA gene sequence similarity value (96.6 %) and the highest gyrB gene sequence similarity value (80.7 %), respectively, to S. waksmanii ATCC BAA-643T. On the basis of polyphasic analyses, strain RZB5-4T represents a novel species of the genus Shewanella, for which the name Shewanella gelidii sp. nov. is proposed. The type strain is RZB5-4T (=JCM 30804T=KCTC 42663T=MCCC 1K00697T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA Gyrase; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Rhodophyta; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Shewanella; Ubiquinone; Vitamin K 2

Bdellovibrio bacteriovorus 109J, a predatory bacterium with potential as a bacterial control agent, can exist in several lifestyles that differ both in predatory capacity and color. We determined that levels of ubiquinone-8 contribute to the distinctive but variable yellow color of different types of Bdellovibrio cells. Steady-state ubiquinone-8 concentrations did not differ markedly between conventional predatory and host-independent B. bacteriovorus despite upregulation of a suite of ubiquinone-8 synthesis genes in host-independent cells. In contrast, in spatially organized B. bacteriovorus films, the yellow inner regions contain significantly higher ubiquinone-8 concentrations than the off-white outer regions. Correspondingly, RT-PCR analysis reveals that the inner region, previously shown to consist primarily of active predators, clearly expresses two ubiquinone biosynthesis genes, while the outer region, composed mainly of quiescent or stalled bdelloplasts, expresses those genes weakly or not at all. Moreover, B. bacteriovorus cells in the inner region of week-old interfacial films, which are phenotypically attack-phase, have much higher UQ8 levels than regular attack-phase bdellovibrios, most likely because their "trapped" state prevents a high expenditure of energy to power flagellar motion.

Topics: Bdellovibrio bacteriovorus; Biosynthetic Pathways; Gene Expression Profiling; Real-Time Polymerase Chain Reaction; Ubiquinone

A denitrifying bacterium, designated strain E4-1(T), was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1(T), a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1(T) forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1(T) is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1(T) (=KACC 17565(T) = NCAIM B 025327(T)).

Topics: Bioreactors; Denitrification; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Phospholipids; Phylogeny; Quinones; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sodium Chloride; Ubiquinone; Wastewater; Xanthomonadaceae

A microcystin-degrading strain, designated CPCC 100154(T), was isolated from a forest soil sample collected from Hainan Island, South China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CPCC 100154(T) is affiliated to the family Sinobacteraceae in Gammaproteobacteria, with high 16S rRNA gene sequence similarities of 98.1, 96.6 and 96.6 % to Steroidobacter agariperforans JCM 18477(T), S. denitrificansis DSM 18526(T), and Povalibacter uvarum JCM 18749(T), respectively. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 100154(T) formed a stable phylogenetic subclade with S. agariperforans JCM 18477(T), which indicated that strain CPCC 100154(T) should be identified as a member of the genus Steroidobacter. The phylogenetic analysis based on partial gyrB gene sequences confirmed the affiliation of strain CPCC 100154(T) to the genus Steroidobacter. While the DNA-DNA hybridization value (47.0 ± 1.7 %) between the new isolate and its near phylogenetic neighbor S. agariperforans JCM 18477(T) was far below 70 %, which demonstrated that strain CPCC 100154(T) represents a different genomic species from S. agariperforans. The strain CPCC 100154(T) was found to be a Gram-stain negative, rod-shaped, motile with a polar flagellum, non-endospore-forming bacterium. Good growth was observed at 28-32 °C and pH 7.0-7.5. Polar lipids were identified to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, a unidentified phospholipid, an aminophospholipid and an unidentified aminolipid. The polyamine pattern was determined to contain spermidine as the predominant polyamine, moderate amounts of putrescine as well as traces of sym-homospermidine and spermine. The respiratory quinone was identified as ubiquinone-8. The major cellular fatty acids were found to include summed feature 3 (C16: 1 ω7C/C16: 1 ω6C) (46.1 %) and C16: 0 (29.6 %). The genomic DNA G+C content was determined to be 64.4 mol%. On the basis of the above polyphasic taxonomy evidence, a novel species, Steroidobacter flavus sp. nov. is proposed. The type strain is CPCC 100154(T) (=DSM 23339(T) =CGMCC 1.10759(T)).

Topics: Base Sequence; China; Fatty Acids; Forests; Gammaproteobacteria; Lipids; Microcystins; Nucleic Acid Hybridization; Phospholipids; Quinones; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil; Soil Microbiology; Ubiquinone

A novel Gram-stain-negative bacterium, named strain NSCS20N07DT, was isolated from surface seawater of the South China Sea. Cells of this strain contained poly-β-hydroxybutyrate granules. Growth was observed at 15-35 °C with optimum of 30 °C, at a salinity range of 1-6 % (w/v) NaCl with optimum of 3 % and at pH 5-8 with optimum of pH 5. The full-length 16S rRNA gene sequence of strain NSCS20N07DT showed highest similarity to Photobacterium iliopiscarium ATCC 51760T of 96.0 %, followed by Photobacterium kishitanii pjapo.1.1T, Photobacterium phosphoreum ATCC 11040T and Photobacterium aquimaris LC2-065T of 96.0, 95.8 and 95.7 %, respectively. Phylogenetic analysis showed that strain NSCS20N07DT formed a separate clade distinct from species of the genus Photobacterium and other genera within the family Vibrionaceae, indicating that strain NSCS20N07DT represented a novel genus affiliated with this family. The genome size of strain NSCS20N07DT was 2.5 Mb, which was much smaller than those of related species in the family Vibrionaceae. The predominant fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, C18 : 0 and summed feature 2 (C14 : 0 3-OH/iso-C16 : 1 I). The respiratory quinone was Q-8. The polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and four unidentified lipids. The DNA G+C content was 30.7 mol%. Combined, these results suggest that strain NSCS20N07DT represents a novel species of a new genus, for which the name Paraphotobacterium marinum gen. nov., sp. nov. is proposed. The type strain of Paraphotobacterium marinum is NSCS20N07DT (=KCTC 52126T=MCCC 1A01886T=CIP 111031T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Phospholipids; Phylogeny; Polyesters; RNA, Ribosomal, 16S; Salinity; Seawater; Sequence Analysis, DNA; Ubiquinone; Vibrionaceae

A Gram-reaction-negative, aerobic, non-spore forming, rod-shaped bacterium motile with a single polar flagellum, designated strain hydD622T, was isolated from the sediment of a tidal flat at Asan Bay, Korea. Strain hydD622T exhibited an agarolytic activity. Comparison of 16S rRNA gene sequences revealed that strain hydD622T was closely related to Agarivorans litoreus KCTC 42116T, Agarivorans albus KCTC 22256T and Agarivorans gilvus KCTC 32555T with similarities of 98.4, 98.0 and 96.5 %, respectively. Strain hydD622T was clustered distantly from the other genera in the family Alteromonadaceae but formed a unique clade within the genus Agarivorans based on the 16S rRNA gene sequence. The DNA-DNA relatedness with Agarivorans litoreus KCTC 42116T and Agarivorans. albus KCTC 22256T was 39.0 and 37.8 %, respectively. The major fatty acids (>10 %) were C16 : 0,C16 : 1ω6c/C16 : 1ω7c and C18 : 1ω6c/C18 : 1ω7c. The respiratory quinone was ubiquinone-8, and the polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified lipid. The DNA G+C content was 44 mol%. On the basis of physiological, chemotaxonomic and phylogenetic analyses, strain hydD622T represents a novel species within the genus Agarivorans, for which the name Agarivorans aestuarii sp. nov. is proposed. The type strain of Agarivorans aestuarii sp. nov. is hydD622T (=KCTC 32543T=CGMCC 1.12692T).

Topics: Agar; Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

An agarose- and alginate-assimilating, Gram-reaction-negative, non-motile, rod-shaped bacterium, designated strain SA2T, was isolated from the gut of a turban shell sea snail (Turbo cornutus) collected near Noto Peninsula, Ishikawa Prefecture, Japan. The 16S rRNA gene sequence of strain SA2T was 99.59 % identical to that of Vibrio rumoiensis DSM 19141T and 98.19 % identical to that of Vibrio litoralis DSM 17657T. This suggested that strain SA2T could be a subspecies of V. rumoiensis or V. litoralis. However, DNA-DNA hybridization results showed only 37.5 % relatedness to DSM 19141T and 44.7 % relatedness to DSM 17657T, which was far lower than the 70 % widely accepted to define common species. Strain SA2T could assimilate agarose as a sole carbon source, whereas strains DSM 19141T and DSM 17657T could not assimilate it at all. Furthermore, results using API 20NE and API ZYM kits indicated that their enzymic and physiological phenotypes were also different. These results suggested that strain SA2T represented a novel species within the genus Vibrio. The major isoprenoid quinone in SA2T was Q-8, and its major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major fatty acids were summed feature 3, (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, and summed feature 8 (comprising C18 : 1ω6c and/or C18 : 1ω7c). The DNA G+C content of SA2T was 40.7 mol%. The name proposed for this novel species of the genus Vibrio is Vibrio algivorus sp. nov., with the type strain designated SA2T (=DSM 29824T=NBRC 111146T).

Topics: Alginates; Animals; Aquatic Organisms; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gastrointestinal Microbiome; Glucuronic Acid; Hexuronic Acids; Japan; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sepharose; Sequence Analysis, DNA; Snails; Ubiquinone; Vibrio

A Gram-stain-negative, aerobic, motile and rod-shaped or ovoid bacterial strain, designated YSM-23T, was isolated from a tidal flat on the South Sea in South Korea, and subjected to a polyphasic taxonomic study. Strain YSM-23T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain YSM-23T represented a member of the genus Colwellia. Strain YSM-23T exhibited 16S rRNA gene sequence similarity values of 98.0, 97.4 and 97.3 % to the type strains of Colwellia aestuarii, Colwellia polaris and Colwellia chukchiensis, respectively, and of 94.5-96.8 % to the type strains of the other species of the genus Colwellia. Strain YSM-23T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acid. The major polar lipids detected in strain YSM-23T were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain YSM-23T was 43.8±0.08 mol% and its DNA-DNA relatedness values with the type strain of C. aestuarii, C. polaris and C. chukchiensis were 10±3.5-22±4.9 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain YSM-23T is separated from species of the genus Colwelliawith validly published names. On the basis of the data presented, strain YSM-23T is considered to represent a novel species of the genus Colwellia, for which the name Colwellia sediminilitoris sp. nov. is proposed. The type strain is YSM-23T (=KCTC 52213T=NBRC 111994T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, facultatively anaerobic bacterium, designated WM3T, was isolated from surface seawater collected from the East China Sea. Cells were catalase- and oxidase-positive, short rods and motile by means of a single polar flagellum. Growth occurred at 15-43 °C (optimum 37-40 C), pH 5.5-9.5 (optimum pH 6.5-7.5) and with 0.25-9.0 % (w/v) NaCl (optimum 1.0-1.5 %). Chemotaxonomic analysis showed that the respiratory quinone was ubiquinone-8, the major fatty acids included C16 : 0 (23.6 %), C18 : 1ω7c (26.2 %) and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH, 22.1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WM3T was most closely related to the genus Marinobacterium, sharing the highest 16S rRNA gene sequence similarity of 95.5 % with both Marinobacterium litorale KCTC 12756T and Marinobacterium mangrovicola DSM 27697T. The genomic DNA G+C content of the strain WM3T was 55.8 mol%. On the basis of phenotypic, chemotaxonomic and genotypic characteristics presented in this study, strain WM3T is suggested to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium zhoushanense sp. nov. is proposed. The type strain is WM3T (=KCTC 42782T=CGMCC 1.15341T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-staining-negative, facultatively aerobic, white-colony-forming bacterium, designated strain SE-S21T, was isolated from forest soil of Jeju Island in Korea. Cells were motile rods with a single polar flagellum, showing catalase- and oxidase-positive reactions. Growth was observed at 10-40 °C (optimum, 30 °C), pH 4.0-10.0 (optimum, pH 7.0-7.5) and with 0-4.0 % (w/v) NaCl (optimum, 0-2 %). Only ubiquinone-8 was detected as the isoprenoid quinone, and C16 : 0, C17 : 0 cyclo, C19 : 1ω8c cyclo and summed feature 2 (comprising C12 : 0 aldehyde and/or unknown) were found to be the major fatty acids. Phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. Putrescine and 2-hydroxyputrescine were the predominant polyamines. The DNA G+C content was 61.0 mol%. Phylogenetic analyses based on 16S rRNA and DNA gyrase B gene sequences revealed that strain SE-S21T formed a phyletic lineage within the genus Pandoraea. Strain SE-S21T was most closely related to Pandoraea faecigallinarum KOxT and Pandoraea pnomenusa CCUG 38742T with 98.8 % and 98.7 % 16S rRNA gene sequence similarities, respectively. However, the DNA-DNA relatedness values between strain SE-S21T and the type strains of P. faecigallinarum and P. pnomenusa were 26.6±5.7 % and 20.5±3.7 %, respectively. On the basis of phenotypic, chemotaxonomic and molecular features, strain SE-S21T clearly represents a novel species of the genus Pandoraea, for which the name Pandoraea terrae sp. nov. is proposed. The type strain is SE-S21T (=KACC 18127T=JCM 30137T). An emended description of the genus Pandoraea is also proposed.

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; DNA, Bacterial; Fatty Acids; Forests; Islands; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Putrescine; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Three Gram-stain-negative, rod-shaped bacteria, designated strains NH153T, F-2-11 and M-1-78, were isolated from surface seawater of the South China Sea and the East China Sea. The three isolates were able to grow at 15-45 °C (optimum 28-37 °C), but no growth occurred at 4 or 50 °C. The pH range for growth was pH 5.5-9.5 (optimum pH 7.5-8.5). The isolates required sea salts for growth and growth occurred in the presence of 0-10 % (w/v) NaCl (optimum 3-5 %); no growth occurred in the presence of 12.0, 15.0 or 20.0 % (w/v) NaCl. They were positive for hydrolysis of gelatin and Tween 80. The sole respiratory quinone was ubiquinone-8 (Q-8). The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipid components were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain NH153T was 41.4 mol%. Based on 16S rRNA gene sequence analysis, the isolates were closely related to the type strain of Pseudoalteromonas shioyasakiensis (98.0-98.6 % sequence similarity). The 16S rRNA gene sequence similarities between the three isolates were 98.8-99.7 %. Phylogenetic analysis indicated that they formed a distinct lineage and clustered with P. shioyasakiensis and Pseudoalteromonas arabiensis. The level of DNA-DNA relatedness among the three isolates was 78.0-85.5 %. Strain NH153T exhibited average nucleotide identity values of 93.4 and 84.2 % with respect to P. shioyasakiensisJCM 18891T and P. arabiensisJCM 17292T, respectively. The genome-to-genome distance analysis revealed that strain NH153T shared 52.4 % DNA relatedness with P. shioyasakiensisJCM 18891T and 28.1 % with P. arabiensisJCM 17292T. On the basis of the phenotypic, genotypic and chemotaxonomic characterizations, as well as phylogenetic inference obtained in this study, strains NH153T, F-2-11 and M-1-78 represent a novel species within the genus Pseudoalteromonas, for which the name Pseudoalteromonasgelatinilytica sp. nov. is proposed. The type strain is NH153T (=CGMCC 1.15370T=DSM 100951T), and F-2-11 (=CGMCC 1.15364=DSM 100953) and M-1-78 (=CGMCC 1.15365=DSM 100952), are additional strains of the species.

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Pseudoalteromonas; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

One beige-pigmented, Gram-stain-negative, rod-shaped bacterium, strain E3/4T, was isolated from a zebrafish, Danio rerio. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the isolate shared 98.5 % 16S rRNA gene sequence identity to the type strain of Undibacterium macrobrachii and 97.8 % to the type strain of Undibacterium seohonense. Lower 16S rRNA gene sequence similarities (<97.0 %) could be found in comparison with all other species of the genus Undibacterium. DNA-DNA hybridization with Undibacterium macrobrachiiLMG 26891T showed a low level of relatedness, <35 %. The main cellular fatty acids of the strain were summed feature 3 fatty acids (C16 : 1ω7c/C16 : 1ω8c), C10 : 0 3-OH and C16 : 0. The polyamine pattern of strain E3/4T contained predominantly putrescine and 2-hydroxyputrescine. The major quinone was ubiquinone Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of phylogenetic, chemotaxonomic, genomic and phenotypic analyses we propose a novel species of the genus Undibacterium, Undibacterium danionis, with strain E3/4T (=DSM 102221T=CCM 8677T=CIP 111017T) as the type strain.

Topics: Animals; Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Zebrafish

A Gram-stain-negative, aerobic, motile with a single polar flagellum, non-spore-forming and rod-shaped bacterial strain named T33T was isolated from forest soil collected at Kyonggi University, South Korea. The strain was catalase- and oxidase-positive, colonies grew on R2A agar at 32 °C. Sequencing of the 16S rRNA gene and phylogenetic analysis revealed that T33T represented a member of the genus Massilia and is closely related to Massilia niastensis KACC 12599T (98.7 % sequence similarity), Massilia aerilata KACC 12505T (98.5 %), Massilia tieshanensis KACC 14940T (98.4 %), Massilia kyonggiensis KACC 17471T (98.1 %), Massilia norwichensis LMG 28164T (97.7 %), Massilia haematophila CCUG 38318T (97.4 %), Massilia consociata CCUG 58010T (97.3 %), and Massilia niabensis KACC 12632T (97.0 %). Ubiquinone Q-8 is the predominant respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol are the major polar lipids. The major fatty acids are summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), and C16 : 0. DNA-DNA hybridization revealed <70 % relatedness between strain T33T and the most closely related type strains. The DNA G+C content of strain T33Tis 69.4 mol%. Based on physiological and biochemical test results, Massilia pinisoli T33T is proposed as a novel species of the genus Massilia. The type strain is T33T (=KACC 18748T=KEMB 9005-368T=JCM 31316T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Forests; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-negative, aerobic, coccoid bacterium, strain O30(T), was isolated from a deep-sea sediment sample collected from the west Pacific. 16S rRNA gene sequence analysis revealed that this strain is affiliated with the family Erythrobacteraceae in the class Alphaproteobacteria, and is closely related to the members of the genera Erythromicrobium (96.6 %), Porphyrobacter (95.5-96.3 %), Altererythrobacter (94.1-96.2 %) and Erythrobacter (94.2-96.2 %). Phylogenetic analysis including all described species of the family Erythrobacteraceae revealed that the isolate forms a clade in the cluster of the genus Altererythrobacter. Strain O30(T) was found to grow at 4-40 °C, pH 6.0-10.0 and in the presence of 0.5-7.0 % (w/v) NaCl. Chemotaxonomic analysis revealed ubiquinones Q-8, Q-9 and Q-10 as the predominant respiratory quinones, summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C17:1 ω6c and C16:0 as major fatty acids, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as the major polar lipids. The DNA G + C content was determined to be 56.9 mol %. On the basis of phenotypic and genotypic data presented in this study, strain O30(T) represents a novel species within the genus Altererythrobacter, for which the name Altererythrobacter aurantiacus sp. nov. is proposed; the type strain is O30(T) (= CGMCC 1.12762(T) = JCM 19853(T) = LMG 28110(T) = MCCC 1A09962(T)).

Topics: Aerobiosis; Alphaproteobacteria; Base Composition; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Geologic Sediments; Phospholipids; Phylogeny; Quinones; RNA, Bacterial; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Sodium Chloride; Ubiquinone

A novel bacterial strain THG-PC4

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Lysobacter; Nucleic Acid Hybridization; Oryza; Phospholipids; Phylogeny; Quinones; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A novel facultatively anaerobic, rod-shaped bacterium, designated LAM1188T, was isolated from the roots of rice (Oryzasativa) in Hubei Province. Cells of LAM1188T were Gram-stain-negative and motile. The temperature and pH ranges for growth were 15-40 °C (optimum: 30 °C) and pH 5-10 (optimum: pH 7), respectively. The strain did not require NaCl for growth but tolerated up to 3.5 % NaCl (w/v). Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Chromobacterium, and was most closely related to Chromobacterium haemolyticum MDA0585T and Chromobacterium aquaticum CC-SEYA-1T with 98.7 % and 97.3 % sequence similarity, respectively. The values of DNA-DNA hybridization between LAM1188T and C. haemolyticum JCM 14163T and C. aquaticum CCUG 55175T were 54.0±2.1 % and 44.0±1.2 %, respectively. The major cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and four unidentified lipids. The respiratory quinone was ubiquinone Q-8. The DNA G+C content was 64.1 mol% as determined by the Tm method. On the basis of its phenotypic, chemotaxonomic and phylogenetic characteristics, strain LAM1188T is suggested to represent a novel species of the genus Chromobacterium, for which the name Chromobacte riumrhizoryzae sp. nov. is proposed. The type strain is LAM1188T (=ACCC 19900T=JCM 31180T).

Topics: Bacterial Typing Techniques; Base Composition; China; Chromobacterium; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oryza; Phospholipids; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A bacterial strain, RS-LYSO-3T, was isolated from tobacco-cultivated soil, collected near Chuxiong, Yunnan province, southwestern China. RS-LYSO-3T could effectively inhibit the invasion of powdery mildew on tobacco. The colonies of RS-LYSO-3T were pale yellow, and its cells were Gram-stain-negative and rod-shaped, with 68 mol% DNA G+C content. Gene sequence analysis for its 16S rRNA gene revealed the highest similarity (97.78 %) with that of Lysobacter spongiicolaKMM 329T. Chemotaxonomic data showed that RS-LYSO-3T possesses a quinone system with Q-8, and iso-C16 : 0, summed feature 9 and iso-C15 : 0 as the predominant fatty acids, all of which support the affiliation of RS-LYSO-3T to the genus Lysobacter. The results of DNA-DNA hybridization, physiological and biochemical tests clearly proved that RS-LYSO-3T is a representative of a novel species of the genus Lysobacter, for which the name Lysobacter erysipheresistens sp. nov. is proposed. The type strain is RS-LYSO-3T (=CCIC 23922T=JCM 31042T).

Topics: Antibiosis; Ascomycota; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Lysobacter; Nicotiana; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-reaction-negative, heterotrophic, marine bacterium, designated strain SPT1T, was isolated from an aged seawater sample which was collected from the shallow coastal region of Nanya, Keelung, Taiwan and stored at room temperature for more than 7 years. Strain SPT1T was a motile rod which exhibited monotrichous flagellation. It required NaCl for growth and exhibited optimal growth at 30-35 °C, 1-3 % NaCl and pH 7-8. The strain was a strictly aerobic bacterium, incapable of anaerobic growth by nitrate reduction or denitrification, or by fermenting glucose or other carbohydrates. Cellular fatty acids were dominated by C16 : 1ω7c and/or C16 : 1ω6c (23.4 %), C17 : 1ω8c (18.1 %), C16 : 0 (8.5 %), C18 : 1ω7c (8.4 %) and C10 : 0 3-OH (6.3 %). The predominant isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and phosphatidic acid. The DNA G+C content was 57.9 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain SPT1T formed a distinct species-level lineage within the genus Spongiibacter of the class Gammaproteobacteria and shared sequence similarities of 94.4-96.2 % with Spongiibacter marinusand Spongiibacter tropicus, the only two species of the genus Spongiibacterwith validly published names. The 16S rRNA gene sequence similarities between strain SPT1T and other species were less than 93.1 %. Polyphasic taxonomic data obtained in this study indicated that strain SPT1T could be classified as a novel species of the genus Spongiibacter, for which the name Spongiibacter taiwanensis sp. nov. is proposed. The type strain is SPT1T (=JCM 31012T=BCRC 80916T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Taiwan; Ubiquinone

A bacterial strain, designated STM-7T, was isolated from a spring in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain STM-7T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by a single polar flagellum, rod-shaped, surrounded by a thick capsule and formed milky-white colonies. Growth occurred at 15-37 °C (optimum, 25-30 °C), at pH 6-8 (optimum, pH 6-7) and with 0-2 % NaCl (optimum, 0-1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain STM-7T belonged to the genus Chitinibacter and was most closely related to Chitinibacter tainanensis S1T with a sequence similarity of 97.3 %. Strain STM-7T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the predominant fatty acids. The major hydroxyl fatty acids were C12 : 0 3-OH and C16 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized phospholipid. The major isoprenoid quinone was Q-8. The DNA G+C content of the genomic DNA was 52.4 mol%. The DNA-DNA hybridization value for strain STM-7T with Chitinibacter tainanensis BCRC 17254T was less than 47 %. On the basis of the phylogenetic inference and phenotypic data, strain STM-7T should be classified as a representative of a novel species, for which the name Chitinibacter fontanus sp. nov. is proposed. The type strain is STM-7T (=BCRC 80923T=LMG 29289T=KCTC 42982T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Natural Springs; Neisseriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Polyesters; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone; Water Microbiology

A novel bacterium, designated strain CF1T, was isolated from a soil sample of a tea plantation and its taxonomic position was determined using a polyphasic approach. Strain CF1T was a Gram-stain-negative, facultatively anaerobic, non-sporulating, non-motile and rod-shaped bacterium. Optimum growth occurred at 25 °C and pH 6.0. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Paraburkholderia, showing highest levels of similarity with respect to Paraburkholderia sediminicola LMG 24238T (98.44 %). Additionally, strain CF1T, P. sediminicola LMG 24238T and Paraburkholderia aspalathi LMG 27731 formed a distinct group in the phylogenetic tree based on 16S rRNA gene sequences. The predominant ubiquinone was Q-8, and the polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid, two unidentified aminolipids and two unidentified polar lipids. The DNA G+C content was 60.2 mol%, and the major fatty acids were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The DNA-DNA relatedness values between strain CF1T and its close relatives including P. sediminicola LMG 24238T and P. aspalathi LMG 27731 49.3±0.4 % and 38.3±0.5 %, respectively. On the basis of phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia caffeinilytica sp. nov. is proposed. The type strain is CF1T (=LMG 28690T=CGMCC 1.15103T).

Topics: Bacterial Typing Techniques; Base Composition; Camellia; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, aerobic, motile, rod-shaped, yellow-pigmented bacterium, designated as DHG40T, was isolated from a soil sample collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, China. Strain DHG40T grew at pH 4.0-8.0 and 10-37 °C (optimum at pH 6.0-7.0 and 25-28 °C). NaCl inhibited growth at concentrations above 2.5 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate fell within the cluster of the genus Dyella. Strain DHG40T was closely related to Dyella ginsengisoli Gsoil 3046T (97.6 % 16S rRNA gene sequence similarity), Dyella marensis CS5-B2T (97.5 %), Dyella koreensis BB4T (97.4 %) and Dyella jejuensis JP1T (97.4 %). The DNA-DNA relatedness values between strain DHG40T and its phylogenetically closest relatives were all below 40 %. The DNA G+C content was 60.3 mol%. In addition, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c were the major fatty acids (>10 %) and ubiquinone-8 was the respiratory quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminolipid and an unidentified phospholipid. On the basis of phylogenetic, phenotypic, physiological and chemotaxonomic distinctiveness, strain DHG40T should be placed in the genus Dyella as a representative of a novel species, for which the name Dyella humi sp. nov. is proposed. The type strain is DHG40T (=KCTC 42629T=LMG 28842T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Forests; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A Gram-stain-negative, rod-shaped, aerobic and motile bacterial strain, DHOK13T, was isolated from the forest soils of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E, 23° 10' N). It grew optimally at 28-33 °C and pH 7.0-7.5. The main fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cycloω8c, summed feature 2 (C12 : 0 aldehyde and/or unknown 10.9525) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The organism contained ubiquinone Q-8 as the predominant isoprenoid quinone. The total DNA G+C content of strain DHOK13T was 62.0 mol%. Phylogenetic analysis of the 16S rRNA gene, as well as the sequence of the partial housekeeping genes, gyrB and recA, showed consistently that strain DHOK13T formed an independent cluster with Paraburkholderia phenazinium LMG 2247T. DNA-DNA hybridization studies showed relatively low relatedness values (39 %) of strain DHOK13T with P. phenazinium LMG 2247T. The phenotypic, chemotaxonomic and phylogenetic data showed that strain DHOK13T represents a novel species of the genus Paraburkholderia for which the name Paraburkholderia pallidirosea sp. nov. is proposed. The type strain is DHOK13T (=KCTC 42626T=LMG 28846T).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; China; DNA, Bacterial; Fatty Acids; Forests; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

The UbiB protein kinase-like (PKL) family is widespread, comprising one-quarter of microbial PKLs and five human homologs, yet its biochemical activities remain obscure. COQ8A (ADCK3) is a mammalian UbiB protein associated with ubiquinone (CoQ) biosynthesis and an ataxia (ARCA2) through unclear means. We show that mice lacking COQ8A develop a slowly progressive cerebellar ataxia linked to Purkinje cell dysfunction and mild exercise intolerance, recapitulating ARCA2. Interspecies biochemical analyses show that COQ8A and yeast Coq8p specifically stabilize a CoQ biosynthesis complex through unorthodox PKL functions. Although COQ8 was predicted to be a protein kinase, we demonstrate that it lacks canonical protein kinase activity in trans. Instead, COQ8 has ATPase activity and interacts with lipid CoQ intermediates, functions that are likely conserved across all domains of life. Collectively, our results lend insight into the molecular activities of the ancient UbiB family and elucidate the biochemical underpinnings of a human disease.

Topics: Animals; Behavior, Animal; Cerebellar Ataxia; Cerebellum; Chlorocebus aethiops; COS Cells; Disease Models, Animal; Exercise Tolerance; Female; Genetic Predisposition to Disease; HEK293 Cells; Humans; Lipid Metabolism; Male; Maze Learning; Mice, Inbred C57BL; Mice, Knockout; Mitochondrial Proteins; Models, Molecular; Motor Activity; Muscle Strength; Muscle, Skeletal; Phenotype; Protein Binding; Protein Conformation; Proteomics; Recognition, Psychology; Rotarod Performance Test; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Seizures; Structure-Activity Relationship; Time Factors; Transfection; Ubiquinone

One beige-pigmented, Gram-staining-negative, rod-shaped bacterium, strain E3/2T, was isolated from a zebrafish, Daniorerio. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the isolate shared 97.7 % 16S rRNA gene sequence similarity to the species Pseudoduganella violaceinigra and between 97.4 to 97.0 % to some species of the genera Duganella and Massilia, including Duganella radicis, Duganella phyllosphaerae, Massilia dura, Massilia lutea, Duganella sacchari, Duganella zoogloeoides, Massiliaalbidiflava and Massilia umbonata. Sequence similarities to all other species were below 97 %. The main cellular fatty acids of the strain were summed feature 3 fatty acids (C16 : 1ω7c/iso-C15 : 0 2-OH), C10 : 0 3-OH, C16 : 0 and C12 : 0. The polyamine pattern of strain E3/2T contained predominantly putrescine and 2-hydroxyputrescine. The major quinone was ubiquinone Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on phylogenetic, chemotaxonomic, genomic and phenotypic analyses we propose a novel species of the genus Pseudoduganella named Pseudoduganella danionis sp. nov., with strain E3/2T (=LMG 29678T=CCM 8698T) as the type strain.

Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Zebrafish

A Gram-staining-negative, aerobic, motile, rod-shaped, catalase- and oxidase-negative strain with one polar flagellum, designated THG-YS3.6T, was isolated from rhizosphere soil of a mugunghwa flower collected from Kyung Hee University, Yongin, South Korea. Growth occurred at 10-37 °C (optimum 25-30 °C), at pH 6-8 (optimum 7.0) and with 0-2.0 % NaCl (optimum 1 %). The isoprenoid quinone was ubiquinone-8 (Q-8). The major cellular fatty acids were iso-C11  : 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C16 : 0, C16 : 1ω7c alcohol, C16 : 0, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unknown phospholipid, one unknown lipid and three unknown aminolipids. The DNA G+C content of strain THG-YS3.6T was 65.3 mol%. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-YS3.6T were identified as Lysobacter yangpyeongensis KACC 11407T (98.7 %), Lysobacter oryzae KCTC 22249T (98.0 %), Lysobacter niabensis KACC 11587T (97.6 %) and Lysobacter terrae KACC 17646T (97.1 %). The DNA-DNA relatedness values between strain THG-YS3.6T and L. yangpyeongensis KACC 11407T, L. oryzae KCTC 22249T, L. niabensis KACC 11587T and L. terrae KACC 17646T were 53.8±1.0 %, 12.9±1.2 %, 10.9±0.6 % and 7.0±1.9 %, respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain THG-YS3.6T represents a novel species of the genus Lysobacter, for which the name Lysobacter rhizophilus sp. nov. is proposed. The type strain is THG-YS3.6T (=KCTC 52082T=CCTCC AB 2015358T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hibiscus; Lysobacter; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Five bacterial strains (SYSU YG23T, SYSU 10HL1970T, 10HP82-10, 10HL1938, 10HP457) isolated from water reservoirs of cooling systems were characterized using a polyphasic taxonomic approach. The isolates were Gram-stain-negative, strictly aerobic and non-motile. Growth was enhanced in the presence of l-cysteine. The major fatty acids (>5 %) for the five strains were C10 : 0, C16 : 0, C16 : 0 3-OH, C18 : 0 3-OH and C18 : 1ω9c. Ubiquinone-8 was detected as the respiratory quinone while the polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, three unidentified phospholipids, two unidentified aminophospholipids and three unidentified glycolipids. The strains shared 16S rRNA gene sequence similarities of 99.0-99.2 % with Francisella guangzhouensis 08HL01032T but less than 95.2 % with other members of the family Francisellaceae. The phylogenetic dendrogram based on 16S rRNA gene sequences showed that these strains form a separate cluster along with Francisella guangzhouensis. This cluster was also confirmed from multilocus-sequence typing based on sequences of the mdhA, rpoB and sdhA genes. Matrix-assisted laser desorption ionization time-of-flight MS analyses of the strains along with closely and distantly related Francisella strains also showed a distinct cluster for these strains. Based on the findings from the polyphasic taxonomy studies, the strains were considered to represent two novel species of a new genus for which the names Allofrancisella inopinata gen. nov., sp. nov. (type strain SYSU YG23T=KCTC 42968T=DSM 101834T) and Allofrancisella frigidaquae sp. nov. (type strain SYSU 10HL1970T=KCTC 42969T=DSM 101835T) are proposed. In addition, Francisella guangzhouensisQu et al. 2013 is proposed to be transferred to this new genus as Allofrancisella guangzhouensis comb. nov.

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Francisella; Gammaproteobacteria; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Microbiology; Water Supply

A Gram-staining-negative, strictly aerobic bacterium, designated SH-1T, was isolated from activated sludge in Korea. Cells were motile rods with a single polar flagellum, showing oxidase-positive and catalase-negative activities. Growth was observed at 25-40 °C (optimum, 37 °C), pH 6.0-9.5 (optimum, pH 7.0) and with 0-0.5 % (w/v) NaCl (optimum, 0 %). Strain SH-1T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C12 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C10 : 0 3-OH as the major fatty acids and ubiquinone-8 as the sole isoprenoid quinone. Phosphatidylethanolamine was the major polar lipid, and diphosphatidylglycerol, phosphatidylglycerol, one aminophospholipid, one phospholipid, five unidentified aminolipids and two unidentified lipids were also detected as the minor polar lipids. The predominant polyamines were 2-hydroxyputrescine, cadaverine and putrescine. The DNA G+C content was 69.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SH-1T formed a tight phyletic lineage with Piscinibacter aquaticus IMCC1728T with a 98.3 % sequence similarity. However, the DNA-DNA relatedness value between strain SH-1T and the type strain of P. aquaticus was 38.0±1.8 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that strain SH-1T represents a novel species of the genus Piscinibacter, for which the name Piscinibacter defluvii sp. nov. is proposed. The type strain is SH-1T (=KACC 18594T=JCM 31230T). An emended description of the genus Piscinibacter is also proposed.

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Putrescine; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone

A bacterium designated as strain roo10T was isolated from roots of Jerusalem artichoke (Helianthus tuberosus). Cells were Gram-stain-negative and non-motile rods. The phylogenetic analysis of the 16S rRNA gene indicated that it represented a member of the genus Pseudoxanthomonas, and its close relatives included Pseudoxanthomonas kalamensis JA40T (97.8 % 16S rRNA gene sequence similarity), Pseudoxanthomonas sangjuensis 5GH38-5T (97.7 %) and Pseudoxanthomonas daejeonensis TR6-08T (97.1 %). Growth of roo10T occurred at pH 7-9. The temperature for growth ranged from 20 to 37 °C. Tolerance to NaCl was observed from 0.005 to 5 % (w/v) concentration. Predominant fatty acids were iso-C15 : 0 (23.5 %), iso-C16 : 0 (18.9 %) and anteiso-C15 : 0 (11.5 %). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidyl-N-methylethanolamine were the major polar lipids. The predominant quinone was ubiquinone 8 (Q-8). The DNA G+C content was 65.7 mol% [from melting temperature (Tm)]. Comparison of phenotypic and chemotaxonomic characteristics indicated that roo10T was distinguishable from its close relatives. Additionally, the DNA-DNA relatedness levels between roo10T and P. kalamensis DSM 18571T (22±0.5 %), P. sangjuensis 5GH38-5T (21±0.2 %) and P. daejeonensis DSM 17801T (3±1 %) were lower than 70 %. These results indicated that roo10T represented a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas helianthi sp. nov. is proposed. The type strain is roo10T (=BCC 70700T=NBRC 110414T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Helianthus; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Thailand; Ubiquinone; Xanthomonadaceae

Strain Eup-16T, isolated from the torch coral Euphyllia glabrescens, was characterized using a polyphasic taxonomy approach. Cells of strain Eup-16T were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, contained poly-β-hydroxybutyrate, rod-shaped and formed pale yellow colonies. Optimal growth occurred at 25-30 °C, pH 7.5-9 and in the presence of 1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Eup-16T belonged to the genus Thalassotalea and was most closely related to Thalassotalea montiporae CL-22T with sequence similarity of 98.4 %. Strain Eup-16T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C16 : 0 and C17 : 1ω8c as the predominant fatty acids. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of strain Eup-16T was 43.2 mol%. The DNA-DNA hybridization value for strain Eup-16T with T. montiporae CL-22T was less than 34 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain Eup-16T should be classified as a representative of a novel species of the genus Thalassotalea, for which the name Thalassotalea euphylliae sp. nov. is presented. The type strain is Eup-16T (=BCRC 80910T=LMG 29001T=KCTC 42743T).

Topics: Animals; Anthozoa; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Hydroxybutyrates; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Polyesters; Sequence Analysis, DNA; Ubiquinone

Two Gram-stain-negative, aerobic, motile by a single polar flagellum and rod-shaped strains, designated SCS-49T and SCS-111, were isolated from seawater of the South China Sea. The two strains grew at 4-35 °C, with 0.5-7.5 % (w/v) NaCl and at pH 6.5-9.0 and were able to reduce nitrate. Q-8 was the sole ubiquinone. The major fatty acids of the two strains were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospoglycolipid, three unidentified glycolipids, five unidentified phospholipids and two to three unidentified lipids. The isolates formed a stable clade with Pseudohongiella acticola and Pseudohongiella spirulinae based on phylogenetic analysis of 16S rRNA gene sequences. Strains SCS-49T and SCS-111 exhibited 16S rRNA gene sequence similarity values of 97.2 and 96.0 % with respect to the type strains of P. acticola and P. spirulinae, respectively. The average nucleotide diversity and in silico DNA-DNA hybridization values between strain SCS-49T and P. acticola KCTC 42131T were 71.4 and 25.1 %, respectively and the values between strain SCS-49T and SCS-111 were 99.9 and 99.2 %, respectively. Based upon the phenotypic, chemotaxonomic and genetic data, strains SCS-49T and SCS-111 represent a novel species in the genus Pseudohongiella, for which the name Pseudohongiella nitratireducens sp. nov. is proposed. The type strain is SCS-49T (=CGMCC 1.15425T=KCTC 52155T=MCCC 1K03186T).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

The taxonomic position of a Gram-stain negative, non-violaceinpigmented bacterium isolated from an insecticide-contaminated site was characterized by a polyphasic approach. The bacterium was able to grow on three different halogenated compounds namely 1-hlorobutane, 1-hloropropane and 1,2-ichloroethane. As a critical step in the degradation of these haloalkanes, stoichiometric amounts of dechlorination were estimated. Based on selective enrichment method for three months, using a highly contaminated mixed chemical soil, a bacterium was obtained and designated as IITR-71T. Its versatility and novelty led us to further characterize it by polyphasic taxonomy. The 16S rRNA gene sequence (1446 bases) comparison showed highest similarity with those of members of the genus Chromobacterium with the most closely related species to strain IITR-71T being Chromobacterium aquaticum (99.3 %) followed by Chromobacterium haemolyticum (98.6 %) and Chromobacterium piscinae (97.1 %). The major ubiquinone was Q-8. Predominant polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The DNA G+C content of IITR-71T was estimated to be 61.2 mol%. The genotypic and phenotypic distinctiveness of IITR-71T and its phylogenetic relationships indicate that IITR-71T represents a novel species, for which the name Chromobacterium alkanivorans sp. nov. is proposed. The type strain is IITR-71T (=MTCC 11059T=JCM 30068T=KCTC 52433T).

Topics: Alkanes; Bacterial Typing Techniques; Base Composition; Chromobacterium; DNA, Bacterial; Fatty Acids; Geologic Sediments; Halogenation; India; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A novel bacterial strain, designated KBP-13T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain KBP-13T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile rods that formed light yellow colonies. Growth occurred at 15-40 °C (optimum, 30-40 °C), at pH 6.0-8.0 (optimum, pH 6.0) and with 0-2 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-13T belonged to the genus Uliginosibacterium within the family Rhodocyclaceae of the class Betaproteobacteria and its most closely related neighbour was Uliginosibacterium gangwonense 5YN10-9T with sequence similarity of 96.0 %. Strain KBP-13T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C14 : 0 as predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid, one uncharacterized aminolipid, two uncharacterized phospholipids and three uncharacterized glycolipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-13T represents a novel species in the genus Uliginosibacterium, for which the name Uliginosibacterium paludis sp. nov. is proposed. The type strain is KBP-13T (=BCRC 80903T=LMG 28837T=KCTC 42655T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Polyesters; Rhodocyclaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone; Water Microbiology; Wetlands

A Gram-stain-negative, rod-shaped strain, Braz8T, isolated from larvae of Anopheles darlingi was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Braz8T was related most closely to species of the genus Thorsellia, with 95.6, 96.5 and 96.6 % similarity to the type strains of Thorsellia anophelis, Thorsellia kandunguensis and Thorsellia kenyensis, respectively, and formed a separate branch in the phylogenetic tree next to the monophyletic cluster of the genus Thorsellia. Chemotaxonomic data supported the allocation of the strain to the family Thorselliaceae. The major fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0. The quinone system was composed of ubiquinones Q-8 and Q-7 (1 : 0.3), the predominant polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and the polyamine pattern showed the major compound putrescine. However, qualitative and quantitative differences in the major polyamine, polar lipid profile and fatty acid patterns distinguished strain Braz8T from species of the genus Thorsellia. Phylogenetic analysis based on 16S rRNA gene sequences, average nucleotide identity, DNA-DNA hybridization, multilocus sequence analysis as well as physiological and biochemical tests distinguished strain Braz8T both genotypically and phenotypically from the three Thorsellia species but also showed its placement in the family Thorselliaceae. Thus, strain Braz8T is considered to represent a novel species of a new genus most closely related to the genus Thorsellia, for which the name Coetzeea brasiliensis gen. nov., sp. nov. is proposed. The type strain of Coetzeea brasiliensis is Braz8T (=LMG 29552T=CIP 111088T).

Topics: Animals; Anopheles; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Enterobacteriaceae; Fatty Acids; Larva; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel Gram-stain-negative, small curved-rod-shaped, motile strain, designated L6T, was isolated from hydrocarbon-contaminated soils collected from Kuwait. Strain L6T was able to grow at 10-40 °C (optimum, 27-32 °C), pH 6.1-8.8 (optimum, 6.5-7.5) and 0-4.5 % (w/v) NaCl (optimum, 0-0.5). C18 : 1ω6c/C18 : 1ω7c, C16 : 0, C16 : 1ω6c/C16 : 1ω7c, C12 : 0 and C12 : 0 3-OH were predominant fatty acids with minor amounts of C14 : 0 and C17 : 0 cyclo. Phosphatidylglycerol and phosphatidylethanolamine were major polar lipids. The genomic G+C content was 61.2 mol%. 16S rRNA gene sequence comparisons indicated that strain L6T represents a member of the genus Microvirgula within the family Neisseriaceae of the class Betaproteobacteria. Strain L6T has a sequence similarity of 99.2 % with Microvirgula aerodenitrificans SGLY2T and <93.8 % with other members of the family Neisseriaceae. However, strain L6T showed only 56.5±2 % relatedness (based on DNA-DNA hybridization) with M. aerodenitrificans KACC 12055T (=SGLY2T). Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain L6T as a representative of a novel species in the genus Microvirgula, for which the name Microvirgula curvata sp. nov. is proposed. The type strain is L6T (=KEMB 2255-471T=JCM 31223T). An emended description of the genus Microvirgula is also proposed.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Environmental Pollution; Fatty Acids; Hydrocarbons; Kuwait; Neisseriaceae; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A tyrosine-metabolizing, Gram-stain-negative, strictly aerobic, non-spore-forming, curved-rod-shaped, motile (due to monopolar flagellum) marine bacterium, designated strain CC-PW-9T, was isolated from estuarine water off Pingtung, Taiwan. Strain CC-PW-9T not only shared highest 16S rRNA gene sequence similarities with Idiomarina representatives (96.4-93.4 %, n=26), but also formed a distinct phyletic lineage and coherent phylogenetic cluster associated with those species. Cells of strain CC-PW-9T grew with 6-12 % (w/v) NaCl, at 20-40 °C and at pH 6-9. It produced predominant amounts of phosphatidylethanolamine, plus diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, two unidentified phospholipids, an unidentified phosphoglycolipid, two unidentified lipids and an unidentified aminolipid in moderate to trace amounts. Fatty acids such as iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and/or C16 : 010-methyl (summed feature 9) were found in major amounts. The DNA G+C content was 51.1 mol%. Ubiquinone-8 (Q-8) was the sole respiratory quinone. Based on evidence from this polyphasic taxonomic study, strain CC-PW-9T is considered to represent a novel species of the genus Idiomarina, affiliated to the family Idiomarinaceae, for which the name Idiomarina tyrosinivorans sp. nov. is proposed. The type strain is CC-PW-9T (=JCM 19757T=BCRC 80745T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Estuaries; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Taiwan; Ubiquinone

A cellulolytic and agarolytic bacterial strain, designated 12-2T, was isolated from a piece of cotton rope fragment washed ashore on a beach and was studied phenotypically, genotypically and phylogenetically. Analyses of 16S rRNA and gyrB gene sequences and DNA base composition suggested that the strain is a member of the genus Gilvimarinus. However, levels of 16S rRNA and gyrB gene sequence similarity between it and the type strains of Gilvimarinus species were no higher than 97.9 and 78.7 %, respectively, suggesting that the strain is distinct. Moreover, the results of DNA-DNA hybridization experiments and physiological characterization clearly differentiated the strain from its closest neighbours. The strain is therefore considered to represent a novel species of the genus Gilvimarinus, for which the name Gilvimarinus japonicus sp. nov. is proposed. The type strain is 12-2T (=NBRC 111987T=KCTC 52141T).

Topics: Bacterial Typing Techniques; Base Composition; DNA Gyrase; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Japan; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, rod-shaped bacterium, forming yellow colonies and designated CDR SL 15T, was isolated from the surface of Padina sp., a brown macroalga, which grows in the Western coastal regions of the state of Goa, India. The 16S rRNA gene sequence phylogeny placed the strain in the genus Luteimonas and it showed closest sequence similarity to Luteimonas terricola BZ92rT (97.6 %) and <97.0 % to other species of the genus Luteimonas. Chemotaxonomic features, such as having iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl/iso-C17 : 1ω9c) as the major fatty acids and Q-8 as the only ubiquinone further supported its placement within this genus. There were some critical differences in phenotypic properties between Luteimonas padinae sp. nov. CDR SL 15T and L. terricola DSM 22344T i.e. temperature range for growth and salinity range and optimum for growth (L. terricola is a psychrotolerant bacterium with a lower optimum temperature for growth), acid production and assimilation of substrates, enzyme activities and resistance to certain antibiotics. The DNA-DNA relatedness value of the novel strain with its closest phylogenetic relative was only 40 %, below the 70 % threshold value recommended for species delineation. All these characteristics are consistent with strain CDR SL 15T representing a novel species of the genus Luteimonas, for which the name Luteimonas padinae sp. nov. is proposed. The type strain is CDR SL 15T (=DSM 101536T=KCTC 52403T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; India; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seaweed; Sequence Analysis, DNA; Ubiquinone; Xanthomonadaceae

A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121T, was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3-95.7 % sequence similarities, respectively), within the family Oceanospirillaceae. Strain MED121T was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be oxidase and catalase positive, its cells are cocci to short rods, it does not ferment carbohydrates and does not reduce nitrate to nitrite or gas and it requires at least 2.5 % (w/v) marine salts and tolerates up to 7 % (w/v) salts. Its major cellular fatty acids in order of abundance are C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c, C16 : 0 and C10 : 0 3-OH. Its genome had an approximate length of 5.1 million bases and a DNA G+C content equal to 40.9 mol%. Analysis of the annotated genes reveals the capacity for the synthesis of ubiquinone 8 (Q8) and the polar lipids phosphatidylglycerol and phosphatidylethanolamine, in agreement with other members of the genus. All the data collected supported the creation of a novel species to accommodate this bacterium, for which the name Marinomonas blandensis sp. nov. is proposed. The type strain is MED121T (=CECT 7076T=LMG 29722T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Marinomonas; Mediterranean Sea; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

An aerobic, Gram-stain-negative, non-motile coccus, designated strain GVCNT2(T), was isolated from the tonsils of a healthy adult female. Cells were oxidase- and catalase-positive, positive for the production of esterase (C4), esterase lipase (C8) and leucine arylamidase, and weakly positive for naphthol-AS-BI-phosphohydrolase and alkaline phosphatase. Cells were also capable of hydrolysing DNA. Growth was observed at 20-37 °C and in the presence of up to 1.5% NaCl. Phylogenetic analysis of near full-length 16S rRNA gene sequences indicated that the strain exhibited closest sequence similarity to Moraxella boevrei ATCC 700022(T) (94.68%) and an uncultured, unspeciated bacterial clone (strain S12-08; 99%). The major fatty acids were C18:1ω9c, C18 : 0, C16:0 and C16:1ω6c/C16:1ω7c. The DNA G+C content of strain GVCNT2(T) was 40.7 mol%. The major respiratory quinone identified was Q-8. Strain GVCNT2(T) exhibited a comparable phenotypic profile to other members of the genus Moraxella but could be distinguished based on its ability to produce acid (weakly) from d-glucose, melibiose, l-arabinose and rhamnose and on its ability to hydrolyse DNA. On the basis of phenotypic and phylogenetic differences from other members of the family Moraxellaceae, strain GVCNT2(T) is considered to represent a novel species of a new genus, for which the name Faucicola mancuniensis gen. nov., sp. nov. is proposed. The type strain of Faucicola mancuniensis is GVCNT2(T) ( =DSM 28411(T) =NCIMB 14946(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Female; Humans; Molecular Sequence Data; Moraxellaceae; Oropharynx; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9(T), isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9(T) identified Massilia haematophila CCUG 38318(T), M. niastensis 5516S-1(T) (both 97.7% similarity), M. aerilata 5516S-11(T) (97.4%) and M. tieshanensis TS3(T) (97.4%) as the next closest relatives. In partial gyrB and lepA sequences, NS9(T) shared the highest similarities with M. haematophila CCUG 38318(T) (94.5%) and M. aerilata 5516-11(T) (94.3%), respectively. These sequence data demonstrate the affiliation of NS9(T) to the genus Massilia. The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2-hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9(T) to the genus Massilia. Major fatty acids were summed feature 3 (C16:1ω7c and/or iso-C15 : 0 2-OH), C16:0, C18: 1ω7c and C10:0 3-OH. Dissimilarities in partial lepA and gyrB gene sequences as well as results from DNA-DNA hybridizations demonstrate that strain NS9(T) is a representative of an as-yet undescribed species of the genus Massilia that is also distinguished from its close relatives based on physiological and biochemical traits. Hence, we describe a novel species, for which we propose the name Massilia norwichensis sp. nov., with the type strain NS9(T) ( = CCUG 65457(T) =LMG 28164(T)).

Topics: Air Microbiology; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; United Kingdom

A Gram-stain-negative, flagellated, aerobic and rod-shaped or ovoid bacterial strain, designated HJTF-7(T), was isolated from a tidal flat on the South Sea of South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain HJTF-7(T) grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees, based on 16S rRNA gene sequences, showed that strain HJTF-7(T) joined the cluster comprising the type strains of species of the genera Spongiibacter and Zhongshania. Strain HJTF-7(T) exhibited 16S rRNA gene sequence similarities of 90.4-92.5% to the type strains of species of the genera Spongiibacter and Zhongshania and of less than 91.5% to the type strains of other recognized species. Strain HJTF-7(T) contained Q-8 as the predominant ubiquinone. The major fatty acids were iso-C17:1ω9c, iso-C15:0, iso-C17:0, iso-C11:0 3-OH and C17:1ω8c and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The fatty acid and polar lipid profiles of strain HJTF-7(T) were distinct from those of members of the genera Spongiibacter and Zhongshania. The DNA G+C content of strain HJTF-7(T) was 55.9 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain HJTF-7(T) represents a novel genus and species within the class Gammaproteobacteria, for which the name Litorivivens lipolytica gen. nov., sp. nov. is proposed. The type strain of Litorivivens lipolytica is HJTF-7(T) ( =KCTC 42157(T) =CECT 8654(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Molecular Sequence Data; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-staining-negative, rod-shaped, motile and facultatively anaerobic bacterial strain, designated X2(T), was isolated from the sludge of an anaerobic, denitrifying, sulfide-removal bioreactor, and found to oxidize sulfide anaerobically with nitrate as electron acceptor. The strain grew at salinities of 0-3% (w/v) NaCl (optimum, 0-1%). Growth occurred at pH 6.0-10.0 (optimum, pH 8.0) and 10-37 °C (optimum, 30 °C). The genomic DNA G+C content was 59 mol%. Q-8 and Q-9 were detected as the respiratory quinones. The major fatty acids (>10 %) were C16:1ω7c and/or C16: 1ω6c, C18: 1ω7c and C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and one unidentified phospholipid. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain X2(T) formed a novel clade within the family Pseudomonadaceae, with the highest sequence similarity to Pseudomonas caeni KCTC 22292(T) (93.5%). On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, it is proposed that this strain represents novel genus and species within the family Pseudomonadaceae, for which the name Thiopseudomonas denitrificans gen. nov., sp. nov. is proposed. The type strain is X2(T) ( =CCTCC M 2013362(T) =DSM 28679(T) = KCTC 42076(T)).

Topics: Bacterial Typing Techniques; Base Composition; Bioreactors; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phospholipids; Phylogeny; Pseudomonadaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone

A slightly thermophilic, Gram-staining-negative and strictly aerobic bacteria, designated strain YIM 78141(T), was isolated from a sediment sample collected at Hehua hot spring, Tengchong, Yunnan province, south-west China. Cells of the strain were short-rod-shaped and colonies were yellowish and circular. The strain grew at pH 6.0-10.0 (optimum, pH 8.0-9.0) and 10-55 °C (optimum, 40-50 °C). Phylogenetic analyses based on 16S rRNA gene sequence comparison demonstrated that strain YIM 78141(T) belongs to the family Neisseriaceae, and strain YIM 78141(T) also showed low levels of 16S rRNA gene sequence similarity (below 93.4%) with all other genera in this family. The only quinone was ubiquinone 8 and the genomic DNA G+C content was 67.3 mol%. Major fatty acids (>5%) were C12:0, C16:0, C18:1ω7c and summed feature 3. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phospholipids of unknown structure containing aminoglycophospholipid and three unidentified polar lipids. On the basis of the morphological, physiological and biochemical characteristics as well as genotypic data, this strain should be classified as a representative of a novel genus and species of the family Neisseriaceae, for which the name Crenobacter luteus gen. nov., sp. nov. is proposed. The type strain is YIM 78141(T) ( =BCRC 80650(T) =KCTC 32558(T) =DSM 27258(T)).

Topics: Bacteria, Aerobic; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Geologic Sediments; Gram-Negative Aerobic Rods and Cocci; Hot Springs; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A floc-forming, Gram-stain-negative, petroleum hydrocarbon-degrading bacterial strain, designated Buc(T), was isolated from a petroleum hydrocarbon-contaminated site in Hungary. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Buc(T) formed a distinct phyletic lineage within the genus Zoogloea. Its closest relative was found to be Zoogloea caeni EMB43(T) (97.2% 16S rRNA gene sequence similarity) followed by Zoogloea oryzae A-7(T) (95.9%), Zoogloea ramigera ATCC 19544(T) (95.5%) and Zoogloea resiniphila DhA-35(T) (95.4%). The level of DNA-DNA relatedness between strain Buc(T) and Z. caeni EMB43(T) was 31.6%. Cells of strain Buc(T) are facultatively aerobic, rod-shaped, and motile by means of a polar flagellum. The strain grew at temperatures of 5-35 °C (optimum 25-28 °C), and at pH 6.0-9.0 (optimum 6.5-7.5). The predominant fatty acids were C16:0, C10 : 0 3-OH, C12:0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major respiratory quinone was ubiquinone-8 (Q-8) and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 63.2 mol%. On the basis of the chemotaxonomic, molecular and phenotypic data, isolate Buc(T) is considered to represent a novel species of the genus Zoogloea, for which the name Zoogloea oleivorans sp. nov. is proposed. The type strain is Buc(T) ( =DSM 28387(T) =NCAIM B 02570(T)).

Topics: Bacterial Typing Techniques; Base Composition; Biodegradation, Environmental; Biofilms; DNA, Bacterial; Fatty Acids; Hungary; Hydrocarbons; Molecular Sequence Data; Nucleic Acid Hybridization; Petroleum; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Zoogloea

A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, strain 2-9(T), was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain was transparent on 1/5 strength marine broth plate but became easily visible when the plate was supplemented with pyruvate. Phylogenetic analyses based on the 16S rRNA gene sequence showed that the strain fell within the class Gammaproteobacteria and was most closely related to the genus Arenicella (92.7-93.0 % 16S rRNA gene sequence similarities to type strains of species of this genus) of an unclassified order within this class. The DNA G+C content of strain 2-9(T) was 41.7 mol%. The major fatty acids were C18 : 1ω7c (37.6 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3; 19.1 %), C18 : 0 (10.8 %), C16 : 0 (10.2 %) and an unidentified fatty acid with an equivalent chain-length value of 11.799 (9.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. Ubiquinone-8 (Q-8) was detected as the sole isoprenoid quinone. From these taxonomic data, it is proposed that strain 2-9(T) represents a novel species of a new genus, Perspicuibacter marinus gen. nov., sp. nov. The type strain of the type species is 2-9(T) ( = NBRC 110144(T) = KCTC 42196(T)). A new family, Arenicellaceae fam. nov. (type genus Arenicella), and order, Arenicellales ord. nov., of the class Gammaproteobacteria are proposed to accommodate the novel taxon.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Japan; Molecular Sequence Data; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Two Gram-negative, rod-shaped strains, T2.1(T) and W5.1.1(T), isolated from larvae of the mosquito Anopheles arabiensis, were investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity studies, strains T2.1(T) and W5.1.1(T) were shown to belong to the genus Thorsellia, both showing 97.8 % similarity to the type strain of Thorsellia anophelis, with 98.1 % similarity to each other. Chemotaxonomic data supported the allocation of the strains to the genus Thorsellia: their major fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0 and they harboured a ubiquinone Q-8 quinone system and a polyamine pattern with the major compound 1,3-diaminopropane. Qualitative and quantitative differences in their polar lipid profiles distinguished strains T2.1(T) and W5.1.1(T) from each other and from T. anophelis. Average nucleotide identity (ANI), DNA-DNA hybridization, multilocus sequence analysis (MLSA) as well as physiological and biochemical tests allowed T2.1(T) and W5.1.1(T) to be distinguished both genotypically and phenotypically from each other and from the type strain of T. anophelis. Thus, we propose that these isolates represent two novel species of the genus Thorsellia, named Thorsellia kenyensis sp. nov. (type strain T2.1(T) = CCM 8545(T) = LMG 28483(T) = CIP 110829(T)) and Thorsellia kandunguensis sp. nov. (type strain W5.1.1(T) = LMG 28213(T) = CIP 110794(T)). Furthermore, phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the genus Thorsellia forms a separate branch, distinct from the families Enterobacteriaceae, Pasteurellaceae and Orbaceae. As a consequence, a new family Thorselliaceae fam. nov. is proposed. An emended description of Thorsellia anophelis is also provided.

Topics: Animals; Anopheles; Bacterial Typing Techniques; Base Composition; Diamines; DNA, Bacterial; Enterobacteriaceae; Fatty Acids; Genes, Bacterial; Kenya; Larva; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Polyamines; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A yellowish-pigmented bacterium, designated strain PLGR-1(T), was isolated from the root of Bergenia scopulosa collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain PLGR-1(T) were Gram-stain-negative, strictly aerobic, rod-shaped, non-spore-forming and motile with a single polar flagellum. Growth occurred at 7-33 °C (optimum, 25-28 °C), at pH 5.0-10.0 (optimum, pH 6.0-7.0) and with 0-0.5 % (w/v) NaCl (optimum, 0 %). The predominant respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polyamines were putrescine and 2-hydroxyputrescine and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 69.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain PLGR-1(T) belonged to the class Betaproteobacteria and formed a tight phyletic lineage with members of the genus Rhizobacter. Strain PLGR-1(T) was most closely related to Rhizobacter dauci DSM 11587(T) and Rhizobacter fulvus DSM 19916(T), with 16S rRNA gene sequence similarities of 98.5 and 98.0 %, respectively. The DNA-DNA relatedness values between strain PLGR-1(T) and the type strains of Rhizobacter dauci and Rhizobacter fulvus were 46.3 and 14.7 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain PLGR-1(T) is considered to represent a novel species of the genus Rhizobacter, for which the name Rhizobacter bergeniae sp. nov. is proposed. The type strain is PLGR-1(T) ( = CCTCC AB 2013018(T) = KCTC 32299(T) = LMG 27607(T)).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; China; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Pigmentation; Plant Roots; Putrescine; RNA, Ribosomal, 16S; Saxifragaceae; Sequence Analysis, DNA; Ubiquinone

A taxonomic study was carried out on strain YN3(T), which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0-10.0 and 4-32 °C in the presence of 0-9.0 % (w/v) NaCl. Strain YN3(T) was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3(T) should be assigned to the genus Gilvimarinus. 'Gilvimarinus agarilyticus' KCTC 23325 and Gilvimarinus chinensis QM42(T) had the closest phylogenetic relationship to strain YN3(T), and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA-DNA hybridization studies, we propose that strain YN3(T) represents a novel species of the genus Gilvimarinus, for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3(T) ( = KCTC 32438(T) = JCM 19198(T)). An emended description of the genus Gilvimarinus is also presented.

Topics: Agar; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Glycolipids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Seaweed; Sequence Analysis, DNA; Ubiquinone

A Gram-stain negative, facultatively anaerobic, non-motile, rod-shaped bacterium, designated strain THG-A13(T), was isolated from Aglaia odorata rhizosphere soil in Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-A13(T) had close similarity with Lysobacter niabensis GH34-4(T) (98.5 %), Lysobacter oryzae YC6269(T) (97.9 %) and Lysobacter yangpyeongensis GH19-3(T) (97.3 %). Chemotaxonomic data revealed that strain THG-A13(T) possesses ubiquinone-8 (Q8) as the predominant isoprenoid quinone and iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c as the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol) and diphosphatidylglycerol. The G+C content was 66.3 mol%. The DNA-DNA relatedness values between strain THG-A13(T) and its closest phylogenetic neighbours were below 18.0 %. These data corroborated the affiliation of strain THG-A13(T) to the genus Lysobacter. These data suggest that the isolate represents a novel species for which the name Lysobacter terrae sp. nov. is proposed, with THG-A13(T) as the type strain ( = KACC 17646(T) = JCM 19613(T)).

Topics: Aglaia; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Lysobacter; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-reaction-negative, aerobic, rod-shaped, non-spore-forming, non-motile bacterial strain, designated BUT-6(T), was isolated from activated sludge of a wastewater-treatment facility. The strain grew at 15-35 °C (optimum 30 °C), pH 4.0-10.0 (optimum pH 7.0) and 0-3.0 % (w/v) NaCl (optimum 1.0 %). Phylogenetic analysis based on 16S rRNA sequences showed that strain BUT-6(T) was most closely related to Tahibacter aquaticus PYM5-11(T) (98.6 % similarity). However, the DNA-DNA relatedness between strain BUT-6(T) and T. aquaticus PYM5-11(T) was 47.1 %. The major fatty acids (>10 % of total fatty acids) of strain BUT-6(T) were iso-C15 : 0, iso-C17 : 1ω9c and iso-C17 : 0. The major respiratory quinone was ubiquinone Q-8. The profile of polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and unidentified phospholipids. The DNA G+C content of strain BUT-6(T) was 71.7 mol%. On the basis of the data from the polyphasic taxonomic study presented, strain BUT-6(T) is considered to represent a novel species of the genus Tahibacter, for which the name Tahibacter caeni sp. nov. is proposed. The type strain is BUT-6(T) ( = CCTCC AB 2013266(T) = KACC 17139(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone; Xanthomonadaceae

An ivory/yellow, Gram-stain-negative, short-rod-shaped, aerobic bacterial strain, designated JC2948(T), was isolated from a soil sample taken from Gwanak Mountain, Republic of Korea. 16S rRNA gene sequence analysis indicated that strain JC2948(T) belongs to the genus Burkholderia. The test strain showed highest sequence similarities to Burkholderia tropica LMG 22274(T) (97.6 %), Burkholderia acidipaludis NBRC 101816(T) (97.5 %), Burkholderia tuberum LMG 21444(T) (97.5 %), Burkholderia sprentiae LMG 27175(T) (97.4 %), Burkholderia terricola LMG 20594(T) (97.3 %) and Burkholderia diazotrophica LMG 26031(T) (97.1 %). Based on average nucleotide identity (ANI) values, the new isolate represents a novel genomic species as it shows less than 90 % ANI values with other closely related species. Also, other phylosiological and biochemical comparisons allowed the phenotypic differentiation of strain JC2948(T) from other members of the genus Burkholderia. Therefore, we suggest that this strain should be classified as the type strain of a novel species of the genus Burkholderia. The name Burkholderia monticola sp. nov. (type strain, JC2948(T) = JCM 19904(T) = KACC 17924(T)) is proposed.

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; Cardiolipins; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Five beige bacterial strains (176/10(T), 178/10, 182/10, 185/7 and 193/8) were isolated from white storks in Poland and found to share identical 16S rRNA gene sequences; they were also investigated in a polyphasic taxonomic study. The cells of all isolates were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequences of these organisms with the sequences of the type strains of the most closely related species of the genus Psychrobacter showed highest sequence similarities to the type strains of Psychrobacter pulmonis and Psychrobacter faecalis (both 97.1 %). The 16S rRNA gene sequence similarities to all other species of the genus Psychrobacter were below 96.3 %. All five isolates showed an identical profile of physiological reactions and almost identical fatty acid profiles consisting of mainly C18 : 1ω9c, but also C12 : 0 3-OH as a characteristic hydroxylated fatty acid. A quinone system with mainly ubiquinone Q-8 was detected and the polar lipid profile of the type strain, 176/10(T), was mainly composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and diphosphatidylglycerol, plus some hitherto uncharacterized phospholipids and one aminolipid. The major polyamines were spermidine and putrescine. DNA-DNA hybridizations between 176/10(T) and the type strains of P. pulmonis and P. faecialis resulted in relatedness values below 70 %. These results indicate that the strains represent a novel species, for which the name Psychrobacter ciconiae sp. nov. (type strain 176/10(T) = CIP 110777(T) = LMG 28175(T) = CCM 8519(T)) is proposed.

Topics: Animals; Bacterial Typing Techniques; Birds; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Poland; Psychrobacter; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Ubiquinone

An aerobic and Gram-stain-negative bacterial strain, designated 9NM-14(T), was isolated from abandoned lead-zinc ore from Meizhou, Guangdong Province, south China. Strain 9NM-14(T) was motile by means of a single polar flagellum. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain 9NM-14(T) was affiliated with the genus Lysobacter and was most closely related to Lysobacter xinjiangensis RCML-52(T) and Lysobacter bugurensis ZLD-29(T) (97.4 % and 96.3 % 16S rRNA gene sequence similarity, respectively). The DNA-DNA relatedness value between strain 9NM-14(T) and L. xinjiangensis RCML-52(T) was 30.1±7.6 %. The major respiratory quinone was unbiquinone 8 (Q-8) and the major cellular fatty acids consisted of iso-C17 : 1ω9c (29.1 %), iso-C15 : 0 (28.9 %), iso-C17 : 0 (9.4 %), iso-C16 : 0 (8.6 %), iso-C11 : 0 3-OH (6.9 %) and iso-C11 : 0 (5.8 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminolipid and five unidentified phospholipids. The genomic DNA G+C content of strain 9NM-14(T) was 70.7±0.1 mol%. On the basis of the data from this polyphasic taxonomic study, strain 9NM-14(T) should be assigned to a novel species of the genus Lysobacter, for which the name Lysobacter mobilis sp. nov. is proposed. The type strain is 9NM-14(T) ( = GIMCC 1.659(T) = CCTCC AB 2014273(T) = DSM 27574(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Lead; Lysobacter; Mining; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Zinc

Strain BUT-8(T), a Gram-stain-negative, non-motile and rod-shaped aerobic bacterium, was isolated from the activated sludge of a herbicide-manufacturing wastewater treatment facility. Comparative 16S rRNA gene sequence analysis revealed that strain BUT-8(T) clustered with species of the genus Lysobacter and was closely related to Lysobacter ruishenii DSM 22393(T) (98.3 %) and Lysobacter daejeonensis KACC 11406(T) (98.7 %). The DNA G+C content of the genomic DNA was 70.6 mol%. The major respiratory quinone was ubiquinone-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an aminolipid. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, iso-C11 : 0, iso-C11 : 0 3OH and summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 010-methyl). The DNA-DNA relatedness between strain BUT-8(T) and its closest phylogenetic neighbours was below 70 %. Phylogenetic, chemotaxonomic and phenotypic results clearly demonstrated that strain BUT-8(T) belongs to the genus Lysobacter and represents a novel species for which the name Lysobacter caeni sp. nov. is proposed. The type strain is BUT-8(T) ( = CCTCC AB 2013087(T) = KACC 17141(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Lysobacter; Molecular Sequence Data; Nucleic Acid Hybridization; Pesticides; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone; Waste Disposal, Fluid

A Gram-stain-negative, facultatively anaerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain SYM1(T), was isolated from a culture of Symbiodinium sp., an algal symbiont of the sea anemone Aiptasia tagetes collected in Puerto Rico. Growth was observed at 4-40 °C (optimum 30 °C), at pH 5.0-11.0 (optimum pH 8.0) and with 0.5-8 % (optimum 2 %) (w/v) NaCl. Phylogenetic analyses of 16S rRNA gene sequences showed that strain SYM1(T) was a member of the genus Neptunomonas with the type strain of Neptunomonas naphthovorans as the closest phylogenetic relative with a pairwise sequence similarity of 98.15 %. However, DNA-DNA relatedness between strain SYM1(T) and N. naphthovorans CIP 106451(T) was 24 %. Moreover, strain SYM1(T) could be distinguished from its closest relative by several phenotypic characteristics such as NaCl, pH and temperature tolerance, nitrate reduction and utilization of carbon substrates. The major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content of strain SYM1(T) was 45 mol%. Ubiquinone-8 (Q-8) was the only respiratory quinone detected. Based on a polyphasic taxonomic characterization, strain SYM1(T) represents a novel species of the genus Neptunomonas, for which the name Neptunomonas phycophila sp. nov. is proposed. The type strain is SYM1(T) ( = LMG 28329(T) = CECT 8716(T)).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Dinoflagellida; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oceanospirillaceae; Phylogeny; Puerto Rico; RNA, Ribosomal, 16S; Sea Anemones; Sequence Analysis, DNA; Symbiosis; Ubiquinone

A Gram-stain negative, rod-shaped, non-spore-forming, obligate aerobic bacterial strain, JC2949(T), was isolated from grassland soil in Gwanak Mountain, Seoul, Republic of Korea. Phylogenetic analysis, based on 16S rRNA sequences, indicated that strain JC2949(T) belongs to the genus Burkholderia, showing highest sequence similarities with Burkholderia grimmiae R27(T) (98.8 %), Burkholderia cordobensis LMG 27620(T) (98.6 %), Burkholderia jiangsuensis MP-1T(T) (98.6 %), Burkholderia zhejiangensis OP-1(T) (98.5 %), Burkholderia humi LMG 22934(T) (97.5 %), Burkholderia terrestris LMG 22937(T) (97.3 %), Burkholderia telluris LMG 22936(T) (97.2 %) and Burkholderia glathei ATCC 29195(T) (97.0 %). The major fatty acids of strain JC2949(T) were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Its predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown amino phospholipid. The dominant isoprenoid quinone was ubiquinone Q-8. The pairwise average nucleotide identity values between strain JC2949(T) and the genomes of 30 other species of the genus Burkholderia ranged from 73.4-90.4 %, indicating that the isolate is a novel genomic species within this genus. Based on phenotypic and chemotaxonomic comparisons, it is clear that strain JC2949(T) represents a novel species of the genus Burkholderia. We propose the name for this novel species to be Burkholderia megalochromosomata sp. nov. The type strain is JC2949(T) ( = KACC 17925(T) = JCM 19905(T)).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Bacterial; Fatty Acids; Grassland; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A novel type of mineral-weathering bacterium was isolated from the weathered surface of rock (mica schist) collected from Susong (Anhui, China). Cells of strain L226(T) were Gram-stain-negative. The strain grew optimally at 30 °C, with 1 % (w/v) NaCl and at pH 7.0 in trypticase soy broth. On the basis of 16S rRNA gene phylogeny, strain L226(T) was shown to belong to the genus Burkholderia and the closest phylogenetic relatives were Burkholderia sprentiae WSM5005(T) (98.3 %), Burkholderia acidipaludis NBRC 101816(T) (98.2 %), Burkholderia tuberum STM678(T) (97.2 %) and Burkholderia diazotrophica JPY461(T) (97.1 %). The DNA G+C content was 63.5 mol% and the respiratory quinone was Q-8. The major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The polar lipid profile of strain L226(T) consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, unknown lipids and unidentified aminophospholipids. Based on the low level of DNA-DNA relatedness (ranging from 25.8 % to 34.4 %) to the tested type strains of species of the genus Burkholderia and unique phenotypic characteristics, it is suggested that strain L226(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia susongensis sp. nov., is proposed. The type strain is L226(T) ( = CCTCC AB2014142(T) = JCM 30231(T)).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; China; DNA, Bacterial; Fatty Acids; Minerals; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

An antifungal bacterial strain, designated YC6258(T), was isolated from the rhizosphere of a halophyte (Carex scabrifolia Steud.) growing in a tidal flat area of Namhae Island, Korea. Cells of the strain were Gram-stain-negative, facultatively anaerobic, moderately halophilic, rod-shaped and motile by a single polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YC6258(T) formed a phyletic lineage distinct from members of the most closely related genera, Saccharospirillum and Reinekea, with less than 91.2 % sequence similarities. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and Summed feature 3 (C16 : 1ω7c/ C16 : 1ω6c). The quinone system of strain YC6258(T) consisted mainly of ubiquinone Q-8. The polar lipid profile exhibited phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unknown lipids. The DNA G+C content was 48.9 mol%. Based on the phylogenetic and phenotypic characteristics, strain YC6258(T) should be classified as a representative of a novel species in a novel genus for which the name Gynuella sunshinyii gen. nov., sp. nov. is proposed. The type strain is YC6258(T) (KCCM 43015(T) = NBRC 109345(T)).

Topics: Bacterial Typing Techniques; Base Composition; Carex Plant; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Salt-Tolerant Plants; Sequence Analysis, DNA; Ubiquinone

A novel strategy to finely control a large metabolic flux by using a "metabolic transistor" approach was established. In this approach a small change in the level or availability of an essential component for the process is controlled by adding a competitive reaction that affects a precursor or an intermediate in its biosynthetic pathway. The change of the basal level of the essential component, considered as a base current in a transistor, has a large effect on the flux through the major pathway. In this way, the fine-tuning of a large flux can be accomplished. The "metabolic transistor" strategy was applied to control electron transfer chain function by manipulation of the quinone synthesis pathway in Escherichia coli. The achievement of a theoretical yield of lactate production under aerobic conditions via this strategy upon manipulation of the biosynthetic pathway of the key participant, ubiquinone-8 (Q8), in an E. coli strain provides an in vivo, genetically tunable means to control the activity of the electron transfer chain and manipulate the production of reduced products while limiting consumption of oxygen to a defined amount.

Topics: Electron Transport Chain Complex Proteins; Escherichia coli; Escherichia coli Proteins; Lactic Acid; Oxygen Consumption; Ubiquinone

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated THG-DD7(T), was isolated from tomato plant rhizosphere soil. Strain THG-DD7(T) grew optimally at 25-30 °C, at pH 7.0-7.5 and in the presence of 0.5% (w/v) NaCl. According to the results of 16S rRNA gene sequence comparisons, strain THG-DD7(T) was most closely related to Rhodanobacter umsongensis GR24-2(T) (98.2%), Rhodanobacter panaciterrae LnR5-47(T) (98.0%), Rhodanobacter soli DCY45(T) (97.9%), Rhodanobacter terrae GP18-1(T) (97.9%) and Dyella ginsengisoli Gsoil 3046(T) (97.7%). The DNA G+C content was 65.2 mol%. In DNA-DNA hybridization, the DNA relatedness levels between strain THG-DD7(T) and its closest phylogenetically neighbours were below 40.0%. The predominant isoprenoid quinone was ubiquinone Q-8. The major polar lipids were diphosphatidylglycerol, phosphtidylethanolamine, phosphatidyl-N-methylethanolamine and phosphatidylglycerol. The major fatty acids were iso-C(15 : 0), iso-C(16 : 0), iso-C(17 : 0), anteiso-C(15 : 0) and iso-C(17 : 1)ω9c and/or C(16 : 0) 10-methyl (summed feature 9). These data supported the affiliation of strain THG-DD7(T) to the genus Rhodanobacter . The results of physiological and biochemical tests enabled strain THG-DD7(T) to be differentiated genotypically and phenotypically from the species of the genus Rhodanobacter with validly published names. Therefore, the novel isolate represents a novel species, for which the name Rhodanobacter koreensis sp. nov. is proposed. The type strain is THG-DD7(T) ( = KACC 17650(T) = JCM 19614(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Solanum lycopersicum; Ubiquinone; Xanthomonadaceae

A Gram-stain-negative, halophilic bacterium, designated strain BH195(T), was isolated from the sediment of the solar saltern pond located in Gomso, Republic of Korea. Strain BH195(T) was a strictly aerobic, non-motile rod, which grew at pH 3.5-10.5 (optimum, pH 7.5), at 4-55 °C (optimum, 30 °C) and at salinities of 0.5-11% (w/v) NaCl [optimum, 2-3% (w/v) NaCl]. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain BH195(T) belongs to the genus Idiomarina , showing the highest sequence similarity to Idiomarina salinarum ISL-52(T) (97.4%), Idiomarina homiensis PO-M2(T) (96.8%), Idiomarina aestuarii KYW314(T) (96.7%), and Idiomarina tainanensis PIN1(T) (96.7%). The major cellular fatty acids of strain BH195(T) were iso-C(11 : 0) 3-OH, iso-C(15 : 0) and iso-C(11 : 0). The DNA G+C content was 51.3 mol% and the major respiratory quinone was ubiquinone 8. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. DNA-DNA relatedness between strain BH195(T) and I. salinarum KCTC 12971(T) was 33%. On the basis of this polyphasic analysis, strain BH195(T) represents a novel species of the genus Idiomarina for which the name Idiomarina halophila sp. nov. is proposed. The type strain is BH195(T) ( = KACC 17610(T) = NCAIM B 02544(T)).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

A novel marine bacterium, designated strain 4k5(T), was isolated from a sediment sample of the Pacific Ocean. The strain was Gram-stain-negative, strictly aerobic, non-motile, oxidase-positive and catalase-positive and required Na(+) for growth. Its major isoprenoid quinone was ubiquinone 8 (Q-8), and its cellular fatty acid profile consisted mainly of C18 : 1v9c (71.4%), C16 : 1v7c (9.1%) and C18 : 0. The DNA G+C content was 45.3 mol%. 16S rRNA gene sequence analysis suggested that strain 4k5(T) is a member of the genus Psychrobacter . Strain 4k5(T) exhibited the closely phylogenetic affinity to Psychrobacter pacificensis IFO 16270(T) (99.4% 16S rRNA gene sequence similarity), P. piscatorii T-3-2(T) (97.7%), P. nivimaris 88/2-7(T) (97.7%), P. celer SW-238(T) (97.7%), P. aestuarii SC35(T) (97.6%) and P. vallis CMS39(T) (97.6%). DNA-DNA hybridization between strain 4k5(T) and P. pacificensis NBRC 103191(T), P. piscatorii JCM 15603(T). P. nivimaris DSM 16093(T), P. celer JCM 12601(T), P. aestuarii JCM 16343(T) and P. vallis DSM 15337(T) was 42.5, 47.0, 38.1, 23.7, 9.0 and 27.4%, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on the 16S rRNA gene sequence and DNA-DNA relatedness data, the isolate merits classification within a novel species, for which the name Psychrobacter oceani sp. nov. is proposed. The type strain is 4k5(T) ( = JCM 30235(T) =NCIMB 14948(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Nucleic Acid Hybridization; Pacific Ocean; Phylogeny; Psychrobacter; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel exopolysaccharide-producing bacterium, designated strain 9a2(T), was isolated from Pacific Ocean sediment. The strain was Gram-stain-negative, motile, strictly aerobic, oxidase- and catalase-positive, and required NaCl for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile consisted mainly of C16 : 1ω7c, C18 : 1ω9c and C16 : 0. The DNA G+C content was 46.6 mol%. 16S rRNA gene sequence analysis suggested that strain 9a2(T) is a member of the genus Alteromonas . Strain 9a2(T) exhibited closest phylogenetic affinity to Alteromonas macleodii NBRC 102226(T) (99.3% 16S rRNA gene sequence similarity), A. marina SW-47(T) (99.3%), A. litorea TF-22(T) (99.0%), A. australica H17(T) (98.7%), A. simiduii BCRC 17572(T) (98.5%), A. stellipolaris LMG 21861(T) (98.3%) and A. hispanica F-32(T) (98.2%). The DNA-DNA reassociation values between strain 9a2(T) and A. macleodii JCM 20772(T), A. marina JCM 11804(T), A. litorea JCM 12188(T), A. australica CIP 109921(T), A. simiduii JCM 13896(T), A. stellipolaris LMG 21861(T) and A. hispanica LMG 22958(T) were below 70%. Strain 9a2(T) contained phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid. Owing to differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA relatedness data, the isolate merits classification as representing a novel species, for which the name Alteromonas gracilis sp. nov. is proposed. The type strain of this species is 9a2(T) ( =JCM 30236(T) =NCIMB 14947(T)).

Topics: Alteromonas; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Nucleic Acid Hybridization; Pacific Ocean; Phospholipids; Phylogeny; Polysaccharides, Bacterial; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Bexsero, a new vaccine against Neisseria meningitidis serogroup B (MenB), is composed of 3 main recombinant proteins and an outer membrane vesicle component. One of the main bactericidal antigens, neisseria heparin binding antigen (NHBA), is present as a fusion protein with the accessory protein genome-derived neisserial antigen (GNA) 1030 to further increase its immunogenicity. The gene encoding for GNA1030 is present and highly conserved in all Neisseria strains, and although orthologs are present in numerous species, its biologic function is unknown. Native mass spectrometry was used to demonstrate that GNA1030 forms a homodimer associated with 2 molecules of ubiquinone-8 (Ub8), a cofactor mainly involved in the electron transport chain and with antioxidant properties. Disc diffusion assays on the wild-type and knockout mutant of GNA1030, in the presence of various compounds, suggested that GNA1030 is not involved in oxidative stress or electron chain transport per se, although it contributes to constitutive refilling of the inner membrane with Ub8. These studies shed light on an accessory protein present in Bexsero and reveal functional insights into the family of related proteins. On the basis of our findings, we propose to name the protein neisseria ubiquinone binding protein (NUbp).

Topics: Amino Acid Sequence; Anti-Bacterial Agents; Antigens, Bacterial; Antimycin A; Bacterial Proteins; Blotting, Western; Cell Survival; Cloning, Molecular; Disulfides; Electron Transport Complex III; Hydrogen Peroxide; Mass Spectrometry; Meningococcal Vaccines; Methacrylates; Molecular Sequence Data; Mutation; Neisseria meningitidis; Oxidants; Periplasmic Proteins; Protein Binding; Protein Multimerization; Thiazoles; Ubiquinone

A Gram-stain-negative, Na(+)-requiring bacterial strain, designated B20-1(T), was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1(T) belonged to the genus Marinomonas , sharing highest sequence similarities with Marinomonas rhizomae IVIA-Po-145(T) (97.6%), Marinomonas dokdonensis DSW10-10(T) (97.0%) and Marinomonas foliarum IVIA-Po-155(T) (96.9%). The predominant cellular fatty acids of strain B20-1(T) were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1(T) was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1(T) ( =DSM 28136(T) =LMG 28077(T)) as the type strain.

Topics: Avicennia; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Geologic Sediments; Marinomonas; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative heterotrophic bacterium, designated GSD6(T), capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6(T) was observed at 4-37 °C (optimum 30 °C), at pH 5.5-9.0 (optimum pH 6.5-7.5) and in the presence of 1-9% (w/v) NaCl (optimum 2%). Strain GSD6(T) contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C17  : 0 10-methyl and C17 : 1ω8c as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6(T) formed a phylogenetic lineage with members of the genus Aliiglaciecola . Strain GSD6(T) was most closely related to Aliiglaciecola lipolytica E3(T) with a 16S rRNA gene sequence similarity of 97.4%, but their DNA-DNA hybridization value was 39.1 ± 7.1%. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6(T) represents a novel species of the genus Aliiglaciecola , for which the name Aliiglaciecola aliphaticivorans sp. nov. is proposed. The type strain is GSD6(T) ( =KACC 18129(T) =JCM 30133(T)). An emended description of the genus Aliiglaciecola is also proposed.

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Hydrocarbons; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A yellow-pigmented strain, designated strain 3.5X(T), was isolated from oil-contaminated saline soil in Gudao, Shandong Province, China, and was characterized taxonomically. The results showed that the isolate was a Gram-stain-negative, aerobic, motile, rod-shaped cell with a polar flagellum. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family Xanthomonadaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. The closest relative of strain 3.5X(T) was Fulvimonas soli DSM 14263(T) (94% similarity). The genomic DNA G+C content was 67 mol% by thermal denaturation and 66.3 mol% from genome sequences. The cells mainly consisted of branched fatty acids, with iso-C17 : 0, iso-C15 : 0, iso-C17 : 1ω9c and/or C16 : 010-methyl and iso-C11 : 0 as the major fatty acids. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol and phosphatidylethanolamine. In addition, ubiquinone Q-8 was the major component of the quinone system and the polyamine pattern contained the major compound spermidine plus minor amounts of putrescine and spermine. On the basis of phenotypic, genotypic and phylogenetic distinctiveness, it is proposed that the isolate represents a novel species in a novel genus, namely Oleiagrimonas soli gen. nov., sp. nov. The type strain is 3.5X(T) ( =NBRC 110685(T) =KCTC 42351(T) =CPCC 100614(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Oil and Gas Fields; Phospholipids; Phylogeny; Pigmentation; Polyamines; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Ubiquinone; Xanthomonadaceae

A Gram-stain-negative, rod-shaped (1.2-2.1 μm × 0.8-0.9 μm), flagellated and motile marine bacterium, designated MEBiC05461T, was isolated from a marine sponge inhabiting Micronesia. Strain MEBiC05461T was oxidase-negative and catalase-positive. Growth was observed at 8.0-35.6 °C (optimum 30.0 °C), at pH 5.0-9.0 (optimum pH 7.0) and with 1.5-6.0 % (w/v, optimum 2.0-2.5 %) NaCl. 16S rRNA gene sequence analysis revealed that strain MEBiC05461T showed high similarity to members of the genus Amphritea (96.4-96.6 %). The predominant cellular fatty acids were C16:0 (23.9 %), summed feature 3 (C16:1ω7c and/or C16:1ω6c; 39.7 %) and summed feature 8 (C18:1ω7c and/or C18:1ω6c; 22.0 %). The DNA G+C content was 48.5 mol%. The major respiratory quinone was Q-8.Phosphatidylethanolamine, phosphatidylglycerol, one unidentified glycolipid, one unidentified aminolipid, one unidentified glycophospholipid and two unidentified lipids were detected as the major polar lipids. On the basis of the data from this polyphasic taxonomic study, strain MEBiC05461T should be classified as a representative of a novel species in the genus Amphritea, and the name proposed is Amphritea spongicola sp. nov. The type strain is MEBiC05461T ( = KCCM 42943T = JCM 16668T). Emendations of the genus Amphritea and species Amphritea atlanticaGärtner et al. 2008 and Amphritea balenaeMiyazaki et al. 2008 are were also given.

Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Glycolipids; Micronesia; Molecular Sequence Data; Oceanospirillaceae; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Porifera; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A strain designated PYM3-14T was isolated from the drinking water network of Budapest (Hungary) and was studied by polyphasic taxonomic methods. The straight-rod-shaped cells stained Gram-negative, were aerobic and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence of strain PYM3-14T revealed a clear affiliation with members of the family Xanthomonadaceae within the class Gammaproteobacteria. The 16S rRNA gene sequence of strain PYM3-14T showed the closest sequence similarities to Arenimonas daechungensis CH15-1T (96.2 %), Arenimonas oryziterrae YC6267T (95.2 %) and Lysobacter brunescens UASM DT (94.4 %). The DNA G+C content of strain PYM3-14T, measured by two different methods (52.0 mol% and 55.9 mol%, respectively), was much lower than that of any member of the genus Arenimonas. The predominant fatty acids (>8 %) were iso-C16:0, iso-C15:0, iso-C14:0, iso-C17:1ω9c and C16:1ω7c alcohol. Strain PYM3-14T contained Q-8 as the major ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmonomethylethanolamine as the major polar lipids. According to phenotypic and genotypic data strain PYM3-14T represents a novel species of the genus Arenimonas, for which the name Arenimonas subflava sp. nov. is proposed. The type strain is PYM3-14T ( = NCAIM B 02508T = DSM 25526T). On the basis of new data obtained in this study, an emended description of the genus Arenimonas is also proposed.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Drinking Water; Fatty Acids; Hungary; Lysobacter; Molecular Sequence Data; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Supply; Xanthomonadaceae

A Gram-staining-negative, strictly aerobic bacterial strain, designated SM-6T, was isolated from a sea tidal flat of the Dangjin bay, South Korea. Strain SM-6T was able to degrade a broad range of aliphatic hydrocarbons. Cells were catalase- and oxidase-positive and non-motile rods. Growth of strain SM-6T was observed at 10-37 °C (optimum, 20-25 °C), at pH 5.5-9.0 (optimum, pH 6.5-7.5) and in the presence of 0-10 % (w/v) NaCl (optimum, 2-3 %). The only isoprenoid quinone detected was ubiquinone-8 (Q-8). C17:1ω8c, C11:0 3-OH, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c), C9:0 3-OH and C10:0 3-OH were observed as the major cellular fatty acids and phosphatidylethanolamine, phosphatidylglycerol and four unidentified lipids were detected as polar lipids. The G+C content of the genomic DNA was 47.5 mol%. Strain SM-6T was most closely related to Pseudomaricurvus alkylphenolicus KU41GT (95.5 %), Maricurvus nonylphenolicus KU41ET (94.4 %) and Pseudoteredinibacter isoporae SW-11T (94.3 %), based on 16S rRNA gene sequences, and phylogenetic analyses showed that strain SM-6T formed a phyletic lineage distinct from the closely related genera. On the basis of phenotypic, chemotaxonomic and molecular features, strain SM-6T represents a novel genus and species of the order Alteromonadales in the class Gammaproteobacteria, for which name Aestuariicella hydrocarbonica gen. nov., sp. nov. is proposed. The type strain is SM-6T ( = KACC 18121T = JCM 30134T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Hydrocarbons; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A taxonomic study employing a polyphasic approach was carried out on strain FT102(T), which was isolated from a deep-sea sediment sample collected in the south-west Indian Ocean at a depth of 2784 m. The strain was Gram-stain-negative, non-motile, rod-shaped and non-spore-forming. It grew optimally at 37-42 °C, pH 6.5-8.5 and in the presence of 1-4% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences confirmed the separation of the novel strain from recognized members of the genus Kangiella that are available in public databases. Strain FT102(T) exhibited 95.5-98.6% 16S rRNA gene sequence similarity to the type strains of the eight recognized species of the genus Kangiella. The chemotaxonomically characteristic fatty acid iso-C15:0 and ubiquinone Q-8 were also detected. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G + C content of strain FT102(T) was 45.0 mol%. The mean DNA-DNA relatedness values between strain FT102(T) and the type strains of Kangiella aquimarina and Kangiella koreensis were 47.3% and 13.7%, respectively. The combined results of phylogenetic, physiological and chemotaxonomic studies indicated that strain FT102(T) was affiliated with the genus Kangiella but differed from the recognized species of the genus Kangiella. Therefore, strain FT102T represents a novel species of the genus Kangiella, for which the name Kangiella profundi sp. nov. is proposed. The type strain is FT102(T) ( = CGMCC 1.12959(T) = KCTC 42297(T) = JCM 30232(T)).

Topics: Alcanivoraceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Indian Ocean; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, white-pigmented and rod-shaped bacterium, designated strain XH122T, was isolated from a surface seawater sample collected from the South Pacific Gyre (45° 58' E 163° 11' S) during Integrated Ocean Drilling Program Expedition 329.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH122T belonged to the genus Leucothrix and showed highest 16S rRNA gene sequence similarity to Leucothrix mucor DSM 2157T (94.3%). It showed lower sequence similarities ( < 90.7%) with all other representatives of the class Gammaproteobacteria. Optimal growth occurred in the presence of 2% (w/v) NaCl, at pH 8.0 and at 28 °C. The DNA G+C content of strain XH122T was 46.2 mol%. The major fatty acids were C16 : 0, C16 : 1ω9c and C18 : 1ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of data from this polyphasic study, strain XH122T is considered to represent a novel species of the genus Leucothrix, for which the name Leucothrix pacifica sp. nov. is proposed. The type strain is XH122T ( = DSM 25984T = JCM 18388T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Pacific Ocean; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Thiotrichaceae; Ubiquinone

A Gram-staining-negative, facultatively anaerobic, rod-shaped, nitrogen-fixing bacterial strain, designated TULL-AT, was isolated from a farmland soil sample in Yixing, China. The optimal conditions for growth were 30 °C, pH 7.0-8.0 and 0% (w/v) NaCl. Q8 was the dominant respiratory quinone and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and aminophospholipid. Phylogenetic analysis of 16S rRNA gene sequences showed that strain TULL-AT was most closely related to Mangrovibacter plantisponsor MSSRF40T (99.6%), followed by Salmonella enterica subsp. diarizonae DSM 14847T (96.8%) and Cronobacter condimenti 1330T (96.8 %). Sequence analysis of the genes rpoB, gyrB and hsp60 revealed that those of strain TULL-AT also exhibit high sequence similarity with those of the species M. plantisponsor MSSRF40T (95.5, 94.1 and 93.4%). The genomic DNA G+C content was 52 mol%. The major fatty acids of strain TULL-AT were C16 : 0, C16 : 1ω7c and/or C16 : 1ω6c, C18 : 1ω7c /C18 : 1ω6c, C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I and iso-C17 : 1 I and/or anteiso-C17 : 1 B. Strain TULL-AT showed low DNA-DNA relatedness with M. plantisponsor MSSRF40T (35.10 ± 1.41%). Based on the multiple genotypic and phenotypic data, strain TULL-AT is considered to represent a novel species of the genus Mangrovibacter, for which the name Mangrovibacter yixingensis sp. nov. is proposed. The type strain is TULL-AT ( = ACCC 19709T = KCTC 42181T).

Topics: Agriculture; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Enterobacteriaceae; Fatty Acids; Genes, Bacterial; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A taxonomic study was carried out on strain YQH10T, which was isolated from mangrove sediment collected from Zhangzhou, China during the screening of acetaldehyde-degrading bacteria. Cells of strain YQH10T were Gram-stain-negative rods and pale brown-pigmented. Growth was observed at salinities from 0 to 11% and at temperatures from 4 to 42 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YQH10T is affiliated to the genus Shewanella, showing the highest similarity with Shewanella haliotis DW01T (95.7%) and other species of the genus Shewanella (91.4-95.6 %). The principal fatty acids were iso-C15 : 0 and C17 : 1ω8c. The major respiratory quinone was Q-8. The polar lipids comprised phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA had a G+C content of 48.3 mol%. Strain YQH10T can completely degrade 0.02% (w/v) acetaldehyde on 2216E at 28 °C within 48 h. Based on these phenotypic and genotypic data, strain YQH10T represents a novel species of the genus Shewanella, for which the name Shewanella mangrovi sp. nov. is proposed. The type strain is YQH10T ( = MCCC 1A00830T = JCM 30121T).

Topics: Avicennia; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Shewanella; Ubiquinone

A Gram-stain-negative, strictly aerobic, non-pigmented, motile bacterium with a single polar flagellum, designated H29T, was isolated from coastal sediment of Jeju Island, South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain H29T was observed at 10-40 °C (optimum, 20-25 °C) and pH 6.0-9.0 (optimum, pH 7.0-8.0), and in the presence of 1-4% (w/v) NaCl (optimum, 2-3%). Strain H29T contained C16 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) as the major fatty acids and ubiquinone-8 (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 46.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H29T formed a phyletic lineage with Rheinheimera hassiensis E48T within the genus Rheinheimera of the family Chromatiaceae. Strain H29T was most closely related to Rheinheimera pacifica KMM 1406T, Rheinheimera muenzenbergensis E49T, Rheinheimera hassiensis E48T and Rheinheimera baltica OSBAC1T with 97.8%, 97.6%, 97.4% and 97.2% 16S rRNA gene sequence similarities, respectively. However, DNA-DNA hybridization values of strain H29T with type strains of these species were lower than 70%. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain H29T represents a novel species of the genus Rheinheimera, for which the name Rheinheimeraaestuarii sp. nov. is proposed. The type strain is H29T ( = KACC 18251T = JCM 30404T).

Topics: Bacterial Typing Techniques; Base Composition; Chromatiaceae; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel aerobic, Gram-staining-negative bacterium, designated strain LAM-WHM-ZC(T), was isolated from coastal sediment samples from the Bohai Sea, near Yantai, China. Cells of LAM-WHM-ZC(T) were non-motile, short-rod- or coccoid-shaped. The temperature and pH ranges for growth were 4-40 °C (optimum: 20-33 °C) and pH 5-9 (optimum: pH 7.5). The strain did not require NaCl for growth but tolerated up to 10% NaCl (w/v). The major fatty acids of strain LAM-WHM-ZC(T) were summed feature 3, C12 : 0, C16 : 0, summed feature 2 and summed feature 8. The predominant respiratory quinone was ubiquinone Q-8. The main polar lipids were diphosphatidyglycerol, phosphatigylethanolamine, phosphatidyglycerol, one phospholipid and four unidentified glycolipids. The DNA G+C content was 59.3 mol% as determined by the melting temperature (Tm) method. Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Oceanisphaera and was closely related to Oceanisphaera arctica KCTC 23013(T), Oceanisphaera litoralis DSM 15406(T), Oceanisphaera sediminis KACC 15117(T) and Oceanisphaera donghaensis KCTC 12522(T) with 97.7%, 97.1%, 96.6% and 96.6% sequence similarity, respectively. The DNA-DNA hybridization values between strain LAM-WHM-ZC(T) and the four reference strains were 47.4 ± 2.8%, 33.5 ± 2.2%, 28.4 ± 1.8% and 13.7 ± 0.8%, respectively. Based on its phenotypic and genotypic properties, strain LAM-WHM-ZC(T) is suggested to represent a novel species of the genus Oceanisphaera, for which the name Oceanisphaera psychrotolerans sp. nov. is proposed. The type strain is LAM-WHM-ZC(T) ( = ACCC 06516(T) = JCM 30466(T)).

Topics: Aeromonadaceae; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Geologic Sediments; Glycolipids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Temperature; Ubiquinone

A novel Gram-stain-negative, facultatively aerobic and rod-shaped strain, designated SL-205(T), was isolated from the biofilms of a denitrifying reactor using poly(3-hydoxybutyrate-co-3-hydroxyvalerate) as the sole carbon source in Beijing, PR China. A polyphasic taxonomic characterization was performed on the novel isolate. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain SL-205(T) is a member of the genus Diaphorobacter. High levels of 16S rRNA gene sequence similarity were found between strain SL-205(T) and Diaphorobacter nitroreducens NA10B(T) (99.4%) and Diaphorobacter oryzae RF3(T) (98.5%), respectively. However, the DNA-DNA relatedness values between strain SL-205(T) and D. nitroreducens NA10B(T) and D. oryzae RF3(T) were 57 ± 1% and 45 ± 1.5%, respectively. The G+C content of the genomic DNA of strain SL-205(T) was 66.8 mol%. The major fatty acids consisted of summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. Ubiquinone Q-8 was the only respiratory quinone; the polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one uncharacterized phospholipid. We conclude that strain SL-205(T) represents a novel species of the genus Diaphorobacter for which the name Diaphorobacter polyhydroxybutyrativorans is proposed; the type strain is SL-205(T) ( = ACCC 19739(T) = DSM 29460(T)).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Beijing; Biofilms; Bioreactors; Comamonadaceae; DNA, Bacterial; Fatty Acids; Manure; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Polyesters; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Swine; Ubiquinone

A Gram-staining-negative, non-motile, catalase- and oxidase-positive, facultatively aerobic bacterium, designated IMCC1962(T) was isolated from a surface seawater sample from the Yellow Sea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC1962(T )belonged to the genus Eionea, forming a robust clade with members of the genus, and was most closely related to Eionea nigra (97.3% similarity). DNA-DNA relatedness between strain IMCC1962(T) and Eionea nigra DSM 19752(T) was 21.8-26.3%, which indicated strain IMCC1962(T) represents a novel genomic species of the genus Eionea. The G+C content of the DNA of strain IMCC1962(T) was 48.7 mol%. The major isoprenoid quinone was ubiquinone Q-8 and major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c (43.4%), C18 : 1ω7c and/or C18 : 1ω6c (19.3%) and C16 : 0 (17.2%). The polar lipids found in strain IMCC1962(T) were phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, unknown phospholipid, and four unknown polar lipids. Strain IMCC1962(T) and Eionea nigra DSM 19752(T) differed from each other in diverse phenotypic characteristics including motility, colony colour and enzyme activities. On the basis of phenotypic and genotypic data, strain IMCC1962(T) ( = KACC 17481(T)= NBRC 109703(T)) represents a novel species of the genus Eionea, for which the name Eionea flava sp. nov. is proposed. An emended description of the genus Eionea is also provided.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

Strains Y-12(T) and Y-47(T) were isolated from mountain forest soil and strain WR43(T) was isolated from rhizosphere soil, at Daejeon, Korea. The three strains grew at 10-55 °C (optimal growth at 28-30 °C), at pH 3.0-8.0 (optimal growth at pH 6.0) and in the presence of 0-4.0% (w/v) NaCl, growing optimally in the absence of added NaCl. On the basis of 16S rRNA gene sequence analysis, the three strains were found to belong to the genus Burkholderia, showing the closest phylogenetic similarity to Burkholderia diazotrophica JPY461(T) (97.2-97.7%); the similarity between the three sequences ranged from 98.3 to 98.7%. Additionally, the three strains formed a distinct group in phylogenetic trees based on the housekeeping genes recA and gyrB. The predominant ubiquinone was Q-8, the major fatty acids were C16 : 0 and C17  : 0 cyclo and the DNA G+C content of the novel isolates was 61.6-64.4 mol%. DNA-DNA relatedness among the three strains and the type strains of the closest species of the genus Burkholderia was less than 50%. On the basis of 16S rRNA, recA and gyrB gene sequence similarities, chemotaxonomic and phenotypic data, the three strains represent three novel species within the genus Burkholderia, for which the names Burkholderia humisilvae sp. nov. (type strain Y-12(T)= KACC 17601(T) = NBRC 109933(T) = NCAIM B 02543(T)), Burkholderia solisilvae sp. nov. (type strain Y-47(T) = KACC 17602(T)= NBRC 109934(T) = NCAIM B 02539(T)) and Burkholderia rhizosphaerae sp. nov. (type strain WR43(T) = KACC 17603(T) = NBRC 109935(T) = NCAIM B 02541(T)) are proposed.

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Bacterial; Fatty Acids; Forests; Genes, Bacterial; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Psychrophilic bacterial strains were isolated from alpine glaciers in Switzerland and characterized taxonomically. On the basis of phylogenetic analysis of partial 16S rRNA and rpoB genes, three of those strains, strain 79 ( = CCOS 247), strain 4/58 ( = CCOS 250) and strain 4/56 ( = CCOS 258) clustered together with strain Cr9-12T and separately from the type strains Glaciimonas immobilis Cr9-30T and Glaciimonas singularis LMG 27070T. Strain Cr9-12T has been previously described as a strain of G. immobilis. The three newly isolated strains were compared phenotypically with strain Cr9-12T and with the type strains of the species G. immobilis and G. singularis. Cr9-12T and the three novel strains from an alpine glacier in Switzerland were Gram-stain-negative, non-motile, rod-shaped and psychrophilic and showed good growth throughout a temperature range of 1-20 °C and characteristically oxidized d-mannitol, l-fucose and bromosuccinic acid. The predominant cellular fatty acids of strain Cr9-12T and the three novel strains were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The respiratory quinone of these strains was ubiquinone 8 (UQ-8). The genomic DNA G+C content of Cr9-12T was 49.2 mol%. The combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies strongly support the reclassification of strain Cr9-12T as representing a novel species. This strain and the isolates 79 ( = CCOS 247), 4/58 ( = CCOS 250) and 4/56 ( = CCOS 258) are representatives of a novel species of the genus Glaciimonas, for which the name Glaciimonas alpina sp. nov. is proposed. The type strain of Glaciimonas alpina is Cr9-12T ( = CCOS 761T = DSM 22814T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Ice Cover; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Switzerland; Ubiquinone

A bacterial strain, designated Npb-02T, was isolated from a freshwater river in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain Npb-02T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, rod-shaped and non-motile. Growth occurred at 15–40 °C (optimum 25–30 °C), at pH 7.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl (optimum 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-02T belonged to the genus Vogesella and was most closely related to Vogesella perlucida DS-28T with sequence similarity of 98.3 %. Strain Npb-02T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major respiratory quinone was Q-8.The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and an uncharacterized phospholipid. The genomic DNA G+C content of strain Npb-02T was 64.1 mol%. The DNA–DNA hybridization values for strain Npb-02T with Vogesella perlucida DS-28T, Vogesella mureinivorans 389T and Vogesella lacus GR13T were less than 25 %. On the basis of phylogenetic inference and phenotypic data, strain Npb-02T represents a novel species of the genus Vogesella, for which the name Vogesella amnigena sp. nov. is proposed. The type strain is Npb-02T ( = BCRC 80887T = LMG 28419T = KCTC 42195T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Molecular Sequence Data; Neisseriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Polyesters; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone; Water Microbiology

The phenotypic and genotypic characteristics of four Bordetella hinzii-like strains from human respiratory specimens and representing nrdA gene sequence based genogroups 3, 14 and 15 were examined. In a 16S rRNA gene sequence based phylogenetic tree, the four strains consistently formed a single coherent lineage but their assignment to the genus Bordetella was equivocal. The respiratory quinone, polar lipid and fatty acid profiles generally conformed to those of species of the genus Bordetella and were characterized by the presence of ubiquinone 8, of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several aminolipids, and of high percentages of C16 : 0, cyclo-C17 : 0 and summed feature 2, as major chemotaxonomic marker molecules, respectively. The DNA G+C content was about 66 mol%, which corresponded with that of the high-percentage DNA G+C content genera of the family Alcaligenaceae including the genus Bordetella. DNA–DNA hybridization experiments revealed the presence of three distinct genomospecies and thus confirmed phenotypic differences as revealed by means of extensive biochemical characterization. We therefore propose to formally classify Bordetella genogroups 3, 14 and 15 as Bordetella bronchialis sp. nov. (type strain LMG 28640T = AU3182T = CCUG 56828T), Bordetella sputigena sp. nov. (type strain LMG 28641T = CCUG 56478T) and Bordetella flabilis sp. nov. (type strain LMG 28642T = AU10664T = CCUG 56827T). In addition, we propose to reclassify Achromobacter sediminum into the novel genus Verticia, as Verticia sediminum, gen. nov., comb. nov., on the basis of its unique phylogenetic position, its marine origin and its distinctive phenotypic, fatty acid and polar lipid profile.

Topics: Achromobacter; Bacterial Typing Techniques; Base Composition; Bordetella; DNA, Bacterial; Fatty Acids; Genotype; Humans; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Respiratory System; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Thirty-three suspected strains of the family Pasteurellaceae isolated from the oral cavity of polar and brown bears were characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA gene and rpoB sequences showed that the investigated isolates formed two closely related monophyletic groups, representing two novel species of a new genus. Based on 16S rRNA gene sequence comparison Bibersteinia trehalosi was the closest related species with a validly published name, with 95.4 % similarity to the polar bear group and 94.4 % similarity to the brown bear group. Otariodibacter oris was the closest related species based on rpoB sequence comparison with a similarity of 89.8 % with the polar bear group and 90 % with the brown bear group. The new genus could be separated from existing genera of the family Pasteurellaceae by three to ten phenotypic characters, and the two novel species could be separated from each other by two phenotypic characters. It is proposed that the strains should be classified as representatives of a new genus, Ursidibacter gen. nov., with two novel species: the type species Ursidibacter maritimus sp. nov., isolated from polar bears (type strain Pb43106T = CCUG 65144T = DSM 28137T, DNA G+C content 39.3 mol%), and Ursidibacter arcticus sp. nov., isolated from brown bears (type strain Bamse61T = CCUG 65145T = DSM 28138T).

Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Molecular Sequence Data; Mouth; Pasteurellaceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Ursidae

A novel bacterial strain, designated THG-RS2OT, was isolated from fallow-land soil previously cultivated with Brassica oleracea in Yongin, South Korea. Cells were Gram-stain-negative, aerobic, non-motile rods, catalase- and oxidase-positive. Strain THG-RS2OT grew optimally at 25–37 °C, at pH 7.0 and in the absence of NaCl. 16S rRNA gene sequence analysis demonstrated that strain THG-RS2OT shows highest sequence similarity with Massilia kyonggiensis KACC 17471T followed by Massilia aerilata KACC 12505T, Massilia niastensis KACC 12599T, Massilia tieshanensis KACC 14940T and Massilia haematophila KCTC 32001T. Levels of DNA–DNA relatedness between strain THG-RS2OT and the closest phylogenetic neighbours were below 55.0 % and the DNA G+C content of strain THG-RS2OT was 63.2 mol%. Major fatty acids were C16 : 0, cyclo-C17 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The major respiratory quinone was identified as ubiquonone-8 and predominant polar lipids were determined to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Characterization by 16S rRNA gene sequence analysis, DNA–DNA hybridization, ubiquinone, polar lipid, fatty acid composition, and physiological and biochemical parameters revealed that strain THG-RS2OT represents a novel species of the genus Massilia. Hence, the present study describes a novel species for which the name Massilia arvi sp. nov. is proposed. The type strain is THG-RS2OT ( = KCTC 42609T = CCTCC AB 2015115T).

Topics: Agriculture; Bacterial Typing Techniques; Base Composition; Brassica; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phosphatidylethanolamines; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100 % similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2 %) and Xenophilus arseniciresistens YW8T (95.0 %), and less than 95.0 % sequence similarities with members of other species. Their major fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and C16 : 1ω7c/C16 : 1ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0 mol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T ( = CFCC 12099T = KCTC 42091T).

Topics: Bacterial Typing Techniques; Base Composition; China; Comamonadaceae; DNA, Bacterial; Endophytes; Fatty Acids; Molecular Sequence Data; Phospholipids; Phylogeny; Plant Bark; Populus; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel Gram-stain-negative, oxidase- and catalase-positive, aerobic bacterium, designated strain SM1351T, was isolated from surface seawater of the Atlantic Ocean. This strain grew at 4-45 °C and with 5-90 g NaCl l- 1. It did not reduce nitrate to nitrite and could not hydrolyse starch or DNA. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was affiliated with the genus Haliea in the family Alteromonadaceae, with sequence similarities with the type strains of Haliea salexigens and Haliea mediterranea, the two recognized species of the genus Haliea, of 96.2 and 94.6 %, respectively. The major fatty acids of strain SM1351T were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C17 : 1ω8c, C18 : 1ω7c and C16 : 0 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major respiratory quinone was ubiquinone Q-8. The genomic DNA G+C content of strain SM1351T was 62 mol%. On the basis of the polyphasic characterization of strain SM1351T in this study, it is considered to represent a novel species in the genus Haliea, for which the name Haliea atlantica sp. nov. is proposed. The type strain is SM1351T ( = CCTCC AB 2014266T = JCM 30304T). Moreover, the transfer of Haliea mediterraneaLucena et al. 2010 to Parahaliea gen. nov. as Parahaliea mediterranea comb. nov. (type strain 7SM29T = CECT 7447T = DSM 21924T) and an emended description of the genus Haliea are also proposed.

Topics: Alteromonadaceae; Atlantic Ocean; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

A novel Gram-reaction-negative, rod-shaped, aerobic and motile strain, designated MEBiC06469T, was isolated from tidal flat sediment of the Taean province, South Korea. Strain MEBiC06469T produced ivory-coloured colonies on marine agar 2216 medium and could degrade carboxymethyl-cellulose. On the basis of 16S rRNA gene sequence similarity, the closest relative was Pseudomaricurvus alkylphenolicus KU41GT with 96.5 % similarity. The isolate was catalase-positive but oxidase-negative. Growth was observed at 16-38 °C (optimum, 32 °C), at pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0.0-8.0 % (w/v) NaCl (optimum, 1.5 %). The only isoprenoid quinone was Q-8.The dominant fatty acids were summed feature 3 (comprised of C15 : 0 2-OH and/or C16 : 1ω7c; 20.4 %) and C17 : 1ω8c (30.9 %), summed feature 8 (comprised of C18 : 1ω7c and/or C18 : 1ω6c; 9.5 %), C16 : 0 (9.0 %), C15 : 1ω8c (5.3 %), and C11 : 0 3-OH (5.2 %). Based on these phenotypic properties and phylogenetic data, strain MEBiC06469T should be classified as a novel species within the genus Pseudomaricurvus for which the name Pseudomaricurvus alcaniphilus sp. nov. is proposed. The type strain is MEBiC06469T ( = KCCM 42976T = JCM 18313T). Emended descriptions of the genus Pseudomaricurvus, Pseudomaricurvus alkylphenolicusIwaki et al. 2014, and Maricurvus nonylphenolicusIwaki et al. 2012 are also provided.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Two aerobic, rod-shaped, non-motile, non-sporulating and Gram-staining-negative bacterial strains, namely NH6-24T and Za3-11, were isolated from the surface seawater of the South China Sea and the estuary of the Yangtze River, respectively. The two isolates grew at 14–44 °C (optimum 37–40 °C) and pH 6.0–8.5 (optimum pH 7.0–7.5). The sea salt ranges for growth were 0.5–10 % (w/v) (optimum 1–2.5 %) for strain NH6-24T and 0–12 % (w/v) (optimum 0.5–4.5 %) for strain Za3-11.Both strains could grow in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates showed closest affinity to the genera Fontimonas (96.0 %) and Solimonas (94.1–95.1 %) and formed a single lineage in the cluster of the family Solimonadaceae. The predominant isoprenoid quinone was ubiquinone-8.The major fatty acids were C18 : 1ω7c, iso-C16 : 0 and C16 : 0.The dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 65 mol%. Based on the polyphasic taxonomic characterization, strains NH6-24T and Za3-11 are considered to represent a novel species of a novel genus, for which the name Sinimarinibacterium flocculans gen. nov., sp. nov. is proposed. The type strain of the type species is NH6-24T ( = CGMCC 1.10815T = JCM 17607T) and an additional strain is Za3-11 ( = CGMCC 1.10816 = JCM 17606).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, aerobic, motile and rod-shaped strain, THG-DN7.3T, was isolated from a waterfall. Strain THG-DN7.3T grew well at 18-28 °C and at pH 6.0-7.5 on Reasoner's 2A agar. Based on 16S rRNA gene sequence comparisons, strain THG-DN7.3T was most closely related to Undibacterium jejuense JS4-4T (97.3 % 16S rRNA gene sequence similarity) and Undibacterium seohonense SHS5-24T (96.5 %). The G+C content of the genomic DNA was 57.4 mol%. The mean DNA-DNA relatedness of strain THG-DN7.3T with U. jejuense KACC 12607T was 40 ± 1 % (reciprocal 50 ± 2.1 %). The major cellular fatty acids of strain THG-DN7.3T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (47.4 %), C16 : 0 (30.4 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) (6.8 %) and C12 : 0 (6.2 %). The predominant isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The results of the DNA-DNA hybridization and genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrated that strain THG-DN7.3T represents a novel species of the genus Undibacterium, for which the name Undibacterium aquatile sp. nov. is proposed. The type strain is THG-DN7.3T ( = KCTC 42243T = CCTCC AB 2015119T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

A beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar 'DES-119') in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA-DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA-DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).

Topics: Alabama; Bacterial Typing Techniques; Comamonadaceae; DNA, Bacterial; Fatty Acids; Gossypium; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Roots; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel strain (designated sjH1T), characterized as aerobic, Gram-stain-negative, oxidase-positive, catalase-negative, motile and rod-shaped, was isolated from mine wastewater. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain sjH1T belonged to the genus Rhodanobacter. Strain sjH1T was closely related to Rhodanobacter thiooxydans LCS2T (98.0% 16S rRNA gene sequence similarity), Rhodanobacter denitrificans 2APBS1T (97.7%), Rhodanobacter soli DCY45T (97.2%) and Rhodanobacter caeni MJ01T (97.0%). The DNA G+C content of strain sjH1T was 69.2 mol%. DNA-DNA relatedness ( < 60%) indicated that strain sjH1T represents a distinct species that is separate from R. thiooxydans, R. denitrificans, R. soli and R. caeni. The major ubiquinone was Q-8, and major fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. Based on data from this polyphasic study, it is proposed that sjH1T ( = KCTC 42660T = JCM 30774T) is the type strain of a novel species, Rhodanobacter aciditrophus sp. nov.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Mining; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Pigmentation; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Wastewater; Xanthomonadaceae

Four bacterial strains, SN-14T, SN-4, M6-46 and M6-58B, were isolated from water of ponds of two salterns located in Huelva (Spain). They were Gram-stain-negative, aerobic and slightly curved rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the four strains belong to the genus Idiomarina, being related most closely to Idiomarina fontislapidosi F23T (98.4-98.0% sequence similarity), Idiomarina seosinensis CL-SP19T (98.3-98.0%), Idiomarina piscisalsi TPS4-2T (97.9-97.4%), Idiomarina baltica OS145T (97.5-97.4%) and Idiomarina zobellii KMM 231T (97.6-97.0%). The level of similarity with the type species of the genus, Idiomarina abyssalis KMM 227T, was 97.2-96.7%. The novel strains exhibited optimal growth at 5-10% (w/v) total salts, pH 7 and 37 °C. The major fatty acids of strain SN-14T were iso-C15 : 0, iso-C17 : 0, C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and iso-C17 : 1ω9c/C16 : 0 10-methyl. The DNA G+C content range was 47.6-50.8 mol%. The level of DNA-DNA relatedness between strain SN-14T and I. fontislapidosi F23T was 13%, while those between strain SN-14T and the other three new isolates were between 77 and 99%. These data demonstrated that the four isolates constitute a novel species of the genus Idiomarina. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, the four strains represent a novel species of the genus Idiomarina, for which the name Idiomarina aquatica sp. nov. is proposed. The type strain is SN-14T ( = CCM 8471T = CECT 8360T = LMG 27613T).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Spain; Ubiquinone; Water Microbiology

A novel Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain RSG39T, was isolated from the gut of a Korean rockfish, Sebastes schlegelii. The 16S rRNA gene sequence analysis revealed that strain RSG39T belonged to the genus Simplicispira in the class Betaproteobacteria and its highest sequence similarity was shared with S. psychrophila (98.4 %). The isolate grew optimally at 20 °C, at pH 7 and with 0 % (w/v) NaCl. The main respiratory quinone of the isolate was ubiquinone Q-8. The major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The polar lipids of the isolate were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and six unidentified lipids. The DNA-DNA hybridization values showed < 7.4 % genomic relatedness with closely related strains. The genomic DNA G+C content was 65.2 mol %. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain RSG39T represents a novel species of the genus Simplicispira, for which the name Simplocospira piscis sp. nov. is proposed. The type strain is RSG39T ( = KACC 17539T = JCM 19291T).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Intestines; Molecular Sequence Data; Nucleic Acid Hybridization; Perciformes; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, facultatively anaerobic bacterium, strain QBLM2T, was isolated from rearing water of a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated through a polyphasic approach. Cells of strain QBLM2T were non-spore-forming rods, motile by means of a single polar flagellum. Positive for oxidase and catalase. Growth occurred at 15-40 °C (optimum 30 °C), at pH 6.5-10.5 (optimum pH 7.5-8.5) and in the presence of 0-5.0 % (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QBLM2T formed a distinct lineage within the genus Thalassotalea and exhibited sequence similarities of 94.5-96.3 % to members of the genus Thalassotalea. The predominant fatty acids (>10 %) were C17 : 1ω8c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 (Q-8) was the major ubiquinone. The DNA G+C content was 37.1 mol%. Based on the data above, strain QBLM2T is considered to represent a novel species of the genus Thalassotalea, for which the name Thalassotalea marina sp. nov. is proposed. The type strain is QBLM2T ( = CGMCC 1.12814T = KCTC 42731T). Phylogenetic analyses indicated that Thalassomonas eurytherma Za6a-12T fell within the genus Thalassotalea, so it is reclassified as Thalassotalea eurytherma comb. nov. and the description of the genus Thalassotalea is emended.

Topics: Aquaculture; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Seven strains, ICMP 19430T, ICMP 19429, ICMP 19431, WSM4637, WSM4638, WSM4639 and WSM4640, were isolated from nitrogen-fixing nodules on roots of the invasive South African legume Dipogon lignosus (subfamily Papilionoideae, tribe Phaseoleae) in New Zealand and Western Australia, and their taxonomic positions were investigated by using a polyphasic approach. All seven strains grew at 10-37 °C (optimum, 25-30 °C), at pH 4.0-9.0 (optimum, pH 6.0-7.0) and with 0-2 % (w/v) NaCl (optimum growth in the absence of NaCl). On the basis of 16S rRNA gene sequence analysis, the strains showed 99.0-99.5 % sequence similarity to the closest type strain, Burkholderia phytofirmans PsJNT, and 98.4-99.7 % sequence similarity to Burkholderia caledonica LMG 19076T. The predominant fatty acids were C18 : 1ω7c (21.0 % of the total fatty acids in strain ICMP 19430T), C16 : 0 (19.1 %), C17 : 0 cyclo (18.9 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 10.7 %) and C19 : 0 cyclov ω8c (7.5 %). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The major isoprenoid quinone was Q-8 and the DNA G+C content of strain ICMP 19430T was 63.2 mol%. The DNA–DNA relatedness of the novel strains with respect to the closest neighbouring members of the genus Burkholderia was 55 % or less. On the basis of 16S rRNA and recA gene sequence similarities and chemotaxonomic and phenotypic data,these strains represent a novel symbiotic species in the genus Burkholderia, for which the name Burkholderia dipogonis sp. nov. is proposed, with the type strain ICMP 19430T (=LMG28415T=HAMBI 3637T).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Bacterial; Fabaceae; Fatty Acids; Introduced Species; Molecular Sequence Data; New Zealand; Nitrogen Fixation; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Western Australia

A yellow-pigmented bacterial strain, designated Y2T, was isolated from farmland soil in Bengbu, Anhui province, China. Cells of strain Y2T were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Strain Y2T grew optimally at pH 7.0, 30 °C and in the presence of 2 % (w/v) NaCl. The DNA G+C content was 68.9 mol%. The major fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C11 : 0 3-OH and iso-C11 : 0. The major respiratory quinone was ubiquinone-8 (Q-8), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain Y2T was most closely related to Luteimonas mephitis B1953/27.1T (99.1 % 16S rRNA gene sequence similarity), followed by Luteimonas lutimaris G3T (98.6 %), Luteimonas abyssi XH031T (96.2 %) and Luteimonas aquatica RIB1-20T (96.0 %). Strain Y2T exhibited low DNA-DNA relatedness with Luteimonas mephitis B1953/27.1T (43.6 ± 0.5 %) and Luteimonas lutimaris G3T (43.9 ± 2.1 %). On the basis of phenotypic, genotypic and phylogenetic evidence, strain Y2T represents a novel species of the genus Luteimonas, for which the name Luteimonas soli sp. nov. is proposed. The type strain is Y2T ( = ACCC 19799T = KCTC 42441T).

Topics: Agriculture; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

Ten strains of Gram-stain-negative, non-spore-forming, non-motile coccobacilli were isolated from the plaster wall surface of 1300-year-old mural paintings inside the stone chamber of the Takamatsuzuka tumulus in Asuka village (Asuka-mura), Nara Prefecture, Japan. Based on 16S rRNA gene sequence analysis of the isolates, they belonged to the proteobacterial genus Bordetella (class Betaproteobacteria) and could be separated into three groups representing novel lineages within the genus Bordetella. Three isolates were selected, one from each group, and identified carefully using a polyphasic approach. The isolates were characterized by the presence of Q-8 as their major ubiquinone system and C16 : 0 (30.0-41.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 10.1-27.0 %) and C17 : 0 cyclo (10.8-23.8 %) as the predominant fatty acids. The major hydroxy fatty acids were C12 : 0 2-OH and C14 : 0 2-OH. The DNA G+C content was 59.6-60.0 mol%. DNA-DNA hybridization tests confirmed that the isolates represented three separate novel species, for which the names Bordetella muralis sp. nov. (type strain T6220-3-2bT = JCM 30931T = NCIMB 15006T), Bordetella tumulicola sp. nov. (type strain T6517-1-4bT = JCM 30935T = NCIMB 15007T) and Bordetella tumbae sp. nov. (type strain T6713-1-3bT = JCM 30934T = NCIMB 15008T) are proposed. These results support previous evidence that members of the genus Bordetella exist in the environment and may be ubiquitous in soil and/or water.

Topics: Archaeology; Bacterial Typing Techniques; Base Composition; Bordetella; DNA, Bacterial; Fatty Acids; Japan; Molecular Sequence Data; Nucleic Acid Hybridization; Paintings; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Biochemical and molecular genetic studies were performed on three novel Gram-stain-negative, catalase- and oxidase-positive, bacilli-shaped organisms isolated from the tonsils of two pigs and one wild boar. The micro-organism was identified as a species of the genus Pelistega based on its cellular morphological and biochemical tests. The closest phylogenetic relative of the novel bacilli was Pelistega indica HM-7T (98.2 % 16S rRNA gene sequence similarity to the type strain). groEL and gyrB sequence analysis showed interspecies divergence from the closest 16S rRNA gene phylogenetic relative, P. indica of 87.0.% and 69 %, respectively. The polyamine pattern contains predominantly putrescine and 2-hydroxyputrescine. The major quinone is ubiquinone Q-8 and in the polar lipid profile, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid are predominant. The novel bacterial isolate can be distinguished from P. indica by several biochemical characteristics, such as the production of l-pyrrolydonil arylamidase but not gamma-glutamyl-transferase, and the utilization of different carbon sources. Based on both phenotypic and phylogenetic findings, the novel bacterium is classified as representing a novel species of the genus Pelistega, for which the name Pelistega suis sp. nov. is proposed. The type strain is 3340-03T ( = CECT 8400T = CCUG 64465T).

Topics: Alcaligenaceae; Animals; Animals, Domestic; Animals, Wild; Bacterial Typing Techniques; DNA, Bacterial; Genes, Bacterial; Molecular Sequence Data; Nucleic Acid Hybridization; Palatine Tonsil; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Swine; Ubiquinone

A Gram-staining-negative and halotolerant bacterium, designated SN2T, capable of biodegrading polycyclic aromatic hydrocarbons, was isolated from a tidal flat contaminated with crude oil in Korea. Cells were strictly aerobic, catalase- and oxidase-positive, motile rods, with a single polar flagellum. Growth was observed at 4-37 °C (optimum, 25-30 °C) at pH 6.0-9.0 (optimum, pH 7.0-7.5) and in the presence of 0.5-9.0% (w/v) NaCl (optimum, 2.0%). Only ubiquinone 8 was detected as the isoprenoid quinone, and summed feature 3 (comprising C16:1ω7c and/or iso-C15:0 2-OH), C16:0, C18:1ω7c and C12:0 were observed as the major cellular fatty acids. The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, an aminolipid and three unidentified lipids. The DNA G+C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SN2T formed a phylogenetic lineage with Alteromonas stellipolaris and Alteromonas addita within the genus Alteromonas, which was consistent with multilocus phylogenetic and MALDI-TOF MS analyses. Strain SN2T was most closely related to the type strains of A. stellipolaris, A. addita and Alteromonas macleodii, with 16S rRNA gene sequence similarities of 99.5, 99.3 and 98.4% and DNA-DNA relatedness of 48.7 ± 6.6, 24.9 ± 7.5 and 27.9 ± 8.4%, respectively. In conclusion, strain SN2T represents a novel species of the genus Alteromonas, for which the name Alteromonas naphthalenivorans sp. nov. is proposed. The type strain is SN2T ( = KCTC 11700BPT = JCM 17741T =KACC 18427T).

Topics: Alteromonas; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Nucleic Acid Hybridization; Petroleum Pollution; Phospholipids; Phylogeny; Polycyclic Aromatic Hydrocarbons; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel exopolysaccharide-producing bacterium, designated strain SE3(T), was isolated from Pacific Ocean sediment. The strain was Gram-stain-negative, motile, strictly aerobic, oxidase-positive and catalase-positive, and required Na(+) for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile mainly consisted of C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The DNA G+C content was 46.9 mol%. 16S rRNA gene sequence analysis suggested that strain SE3(T) is a member of the genus Pseudoalteromonas. Strain SE3(T) exhibited close phylogenetic affinity to Pseudoalteromonas arabiensis JCM 17292(T) (99.0 % 16S rRNA gene sequence similarity), Pseudoalteromonas lipolytica LMEB 39(T) (98.39 %) and Pseudoalteromonas donghaensis HJ51(T) (97.65 %). The DNA-DNA reassociation values between strain SE3(T) and P. arabiensis JCM 17292(T), P. lipolytica JCM 15903(T) and P. donghaensis LMG 24469(T) were 31, 26 and 44 %, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA relatedness data, the new isolate merits classification as a representative of novel species, for which the name Pseudoalteromonas shioyasakiensis is proposed. The type strain is SE3(T) ( = JCM 18891(T) = NCIMB 14852(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Nucleic Acid Hybridization; Pacific Ocean; Phylogeny; Polysaccharides, Bacterial; Pseudoalteromonas; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A bacterial strain, designated strain LP01(T), was isolated from a laboratory-scale microcosm packed with a mixture of soil and sewage sludge compost designed to study the evolution of microbial biodiversity over time. The bacterial strain was selected for its potential ability to store polyhydroxyalkanoates (PHAs) as intracellular granules. The cells were aerobic, Gram-stain-negative, non-endospore-forming motile rods. Phylogenetically, the strain was classified within the genus Massilia, as its 16S rRNA gene sequence had similarity of 99.2 % with respect to those of Massilia albidiflava DSM 17472(T) and M. lutea DSM 17473(T). DNA-DNA hybridization showed low relatedness of strain LP01(T) to the type strains of other, phylogenetically related species of the genus Massilia. It contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acid(s). It was found to contain small amounts of the fatty acids C18 : 0 and C14 : 0 2-OH, a feature that served to distinguish it from its closest phylogenetic relatives within the genus Massilia. The DNA G+C content was 66.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data obtained in this study suggest that strain LP01(T) represents a novel species of the genus Massilia, for which the name Massilia umbonata sp. nov. is proposed. The type strain is LP01(T) ( = CECT 7753(T) = DSM 26121(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; Polyesters; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Soil; Soil Microbiology; Spain; Ubiquinone

A newly isolated facultatively methylotrophic bacterium (strain 3t(T)) was investigated. Cells of the isolate were Gram-stain-negative, asporogenous, non-motile rods that multiplied by binary fission. The strain utilized methanol, methylamine and a variety of multicarbon compounds as carbon and energy sources. Growth occurred at pH 6.5-8.5 (optimally at 7.0-7.5) and at 10-45 °C (optimally at 30-37 °C). The major fatty acids of methanol-grown cells were C16 : 1ω7c and C16 : 0. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol. The major ubiquinone was Q-8. Strain 3t(T) possessed pyrroloquinoline quinone (PQQ)-linked methanol dehydrogenase and assimilated C1 units at the level of formaldehyde and CO2 via the serine cycle. The DNA G+C content of the strain was 63.6 mol% (Tm). On the basis of 16S rRNA gene sequence similarity (98.1 %) and rather low DNA-DNA relatedness (30 %) with the type strain of the type species of the genus Methyloversatilis (Methyloversatilis universalis FAM5(T)), and physiological and biochemical characteristics, the isolate was classified as a representative of a new species of the genus and named Methyloversatilis thermotolerans 3t(T) ( = VKM B-2692(T) = CCUG 61694(T) = DSM 25156(T)).

Topics: Alcohol Oxidoreductases; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Hot Springs; Methanol; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Rhodocyclaceae; RNA, Ribosomal, 16S; Russia; Ubiquinone

Two bacterial strains, designated JS4-4(T) and SHS5-24(T), were isolated from forest soil of Jeju Island and fresh water of Seoho lake in Suwon city, respectively, South Korea. Both strains were Gram-stain-negative, aerobic, motile rods. Strains JS4-4(T) and SHS5-24(T) showed high sequence similarities (97.6-95.8 %) and (96.5-95.6 %), respectively, to the members of the genus Undibacterium. The sequence similarity between strains JS4-4(T) and SHS5-24(T) was 97.0 %. A phylogenetic tree showed that these strains fell within the radius of the genus Undibacterium. The main fatty acids of strains JS4-4(T) and SHS5-24(T) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (50.1 and 58.7 %, respectively) and C16 : 0 (28.3 and 24.5 %, respectively). Both strains had ubiquinone 8 as the only respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. Strain JS4-4(T) showed <70 % DNA-DNA hybridization with members of the genus Undibacterium. Thus, based on the evidence of a polyphasic study, it is proposed that strains JS4-4(T) and SHS5-24(T) represent two novel species, for which the names Undibacterium jejuense sp. nov. (type strain JS4-4(T) = KACC 12607(T) = NBRC 108922(T)) and Undibacterium seohonense sp. nov. (type strain SHS5-24(T) = KACC 16656(T) = NBRC 108929(T)) are proposed.

Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Lakes; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A novel aerobic marine bacterium, strain AN44(T), was isolated from the coral Fungia echinata sampled from the Andaman Sea, India. Cells were Gram-negative, motile and rod-shaped. Oxidase and catalase tests were positive. Heterotrophic growth was observed at pH 5.5-10 and at 16-42 °C, with optimum growth at pH 7-8 and 28 °C. Strain AN44(T) grew in the presence of 0.5-11% (w/v) NaCl; the optimal NaCl concentration for growth was 3-5%. The DNA G+C content was 47.8 mol%. Predominant cellular fatty acids of strain AN44(T) were C(18 : 1)ω7c, C(16 : 1)ω7c/C(16 : 1)ω6c, C(16 : 0), C(10 : 0) 3-OH, C(12 : 0), C(10 : 0), C(14 : 0) and C(18 : 0). The sole isoprenoid ubiquinone was Q-8. The polar lipids were an unidentified phospholipid, an unidentified aminophospholipid and two unidentified glycolipids. 16S rRNA gene sequence comparisons revealed that strain AN44(T) clustered within the radiation of the genus Marinomonas and showed similarity of 97.9% with Marinomonas ostreistagni UST010306-043(T), 97.8% with Marinomonas aquimarina 11SM4(T), 97.1% with Marinomonas brasilensis R-40503(T) and 97.0% with Marinomonas communis 8(T). However, DNA-DNA relatedness between strain AN44(T) and closely related type strains was well below 70%. On the basis of the data from the present polyphasic taxonomic study, strain AN44(T) is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas fungiae sp. nov. is proposed. The type strain is AN44(T) ( = JCM 18476(T) = LMG 27065(T)).

Topics: Animals; Anthozoa; Base Composition; DNA, Bacterial; Fatty Acids; Glycolipids; India; Marinomonas; Molecular Sequence Data; Nucleic Acid Hybridization; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Ubiquinone

A Gram-stain-negative, non-motile, aerobic rod, designated 8604S-37(T), was isolated from an outdoor air sample collected in Suwon region, Republic of Korea. The isolate was catalase-positive and oxidase-negative. 16S rRNA gene sequence analysis indicated that strain 8604S-37(T) was most closely related to Diaphorobacter nitroreducens NA10B(T) and Diaphorobacter oryzae RF3(T), with which it shared 97.0% 16S rRNA gene sequence similarity. Strain 8604S-37(T) grew at 10-37 °C (optimum 28 °C; no growth occurred at 4 or 40 °C) and pH 5-9 (optimum pH 7). The strain tolerated up to 3% NaCl (w/v) (optimum 0%). The only respiratory quinone was ubiquinone-8 (Q-8). The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown aminolipid. The major fatty acids were C16 : 0, summed feature 3 (comprising C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH), summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c) and C(17 : 0) cyclo, and the predominant hydroxy fatty acid was C(10 : 0) 3-OH. Strain 8604S-37(T) exhibited less than 50% DNA-DNA relatedness with Diaphorobacter nitroreducens KACC 13856(T) and Diaphorobacter oryzae KACC 16857(T). The DNA G+C content was 65 mol%. Strain 8604S-37(T) represents a novel species of the genus Diaphorobacter, for which the name Diaphorobacter aerolatus sp. nov. is proposed. The type strain is 8604S-37(T) ( = KACC 16536(T) = NBRC 108926(T)). An emended description of the genus Diaphorobacter is also proposed.

Topics: Air Microbiology; Bacterial Typing Techniques; Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-staining-negative, motile, weakly halophilic and facultatively aerobic bacterium, designated strain YA11(T), was isolated from tidal flat sediment at Yeongam Bay, South Korea. Strain YA11(T) grew at 10-30 °C (optimum, 20 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.5) and in the presence of 1-6% (w/v) NaCl (optimum, 2-3%). The major cellular fatty acids of the strain were summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c), summed feature 8 (C(18 : 1)ω7c and/or C(18 : 1)ω6c) and C(16 : 0). The DNA G+C content of the genomic DNA was 44.2 mol%. Strain YA11(T) contained Q-8 as the sole respiratory quinone. A phylogenetic tree based on 16S rRNA gene sequences showed that strain YA11(T) formed a distinct phyletic lineage within the genus Photobacterium and the 16S rRNA gene sequence similarities between strain YA11(T) and the type strains of species of the genus Photobacterium ranged between 94.0 and 96.4%. Based on the phenotypic, chemotaxonomic and molecular properties, strain YA11(T) represents a novel species of the genus Photobacterium, for which the name Photobacterium aestuarii sp. nov. is proposed, with strain YA11(T)( = KACC 16912(T) = JCM 18592(T)) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; Bays; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Photobacterium; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Three Gram-stain-negative, strictly aerobic, rod-shaped with single polar flagellum, yellow-pigmented bacteria, designated strains XH031(T), XH038-3 and XH80-1, were isolated from deep-sea sediment of the South Pacific Gyre (41° 51' S 153° 6' W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the genus Luteimonas and showed the highest 16S rRNA gene sequence similarity with Luteimonas aestuarii B9(T) (96.95%), Luteimonas huabeiensis HB2(T) (96.93%) and Xanthomonas cucurbitae LMG 690(T) (96.92 %). The DNA G+C contents of the three isolates were 70.2-73.9 mol%. The major fatty acids were iso-C(15 : 0), iso-C(16 : 0), iso-C(11 : 0) and C16 : 010-methyl and/or iso-C(17 : 1)ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown phospholipid. On the basis of data from polyphasic analysis, the three isolates represent a novel species of the genus Luteimonas, for which the name Luteimonas abyssi sp. nov. is proposed. The type strain is XH031(T) ( = DSM 25880(T) = CGMCC 1.12611(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Pacific Ocean; Phosphatidylethanolamines; Phosphatidylglycerols; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Xanthomonadaceae

A bacterium, designated XC21-2(T), was isolated from a saline-alkaline soil sample from China. Cells were Gram-stain-negative, rod-shaped and motile and grew optimally at 35-37 °C, pH 6.0-7.0 and in the presence of 0.5% (w/v) NaCl. Growth occurred in the range pH 5.5-9.0 and in the presence of up to 4 % (w/v) NaCl. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized amino-group-containing polar lipid. The major quinone was ubiquinone 8 (Q-8) and the G+C content of the genomic DNA was 66.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XC21-2(T) formed a tight phylogenetic lineage with Pseudoxanthomonas dokdonensis KCTC 12543(T) within the genus Pseudoxanthomonas and was most closely related to P. dokdonensis KCTC 12543(T) and P. mexicana ATCC 700993(T), with 97.9 and 97.5 % 16S rRNA gene sequence similarity, respectively. On the basis of the unique physiological profile of the isolate and its phylogenetic divergence from known species, strain XC21-2(T) represents a novel species within the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas wuyuanensis sp. nov. is proposed. The type strain is XC21-2(T) ( = CGMCC 1.10978(T) = KCTC 23877(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Hydrogen-Ion Concentration; Molecular Sequence Data; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; RNA, Ribosomal, 16S; Salinity; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A bacterial strain, ABC02-12(T), was isolated from spent mushroom compost, a waste product of button mushroom cultivation. Cells of the strain were Gram-stain-negative, catalase- and oxidase-positive, non-spore-forming, aerobic flagellated rods. Optimum growth occurred at 28 °C and pH 7.0. 16S rRNA gene sequence analysis showed that strain ABC02-12(T) shared the highest sequence similarities with Paenalcaligenes hominis CCUG 53761A(T) (96.0 %), Alcaligenes faecalis subsp. parafaecalis G(T) (95.7 %), Alcaligenes faecalis subsp. faecalis IAM 12369(T) (95.4 %) and Pusillimonas noertemannii BN9(T) (95.3 %). According to the phylogenetic tree, strain ABC02-12(T) formed a robust cluster with Paenalcaligenes hominis CCUG 53761A(T) and Paenalcaligenes hermetiae KBL009(T). The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The major fatty acids (>5 % of total fatty acids) were C16 : 0, C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3), C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8), C17 : 0 cyclo, and iso-C16 : 1 I, C14 : 0 3-OH and/or an unknown fatty acid (summed feature 2). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminolipid. Putrescine was the principal polyamine, with small amounts of 2-hydroxyputrescine and cadaverine. On the basis of the evidence presented in this study, strain ABC02-12(T) is a representative of a novel species within the genus Paenalcaligenes, for which the name Paenalcaligenes suwonensis sp. nov. is proposed. The type strain is ABC02-12(T) ( = KACC 16537(T) = NBRC 108927(T)).

Topics: Agaricales; Alcaligenaceae; Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phylogeny; Polyamines; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A bacterial strain designated CMJ-9(T) was isolated from a freshwater shrimp culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain CMJ-9(T) were strictly aerobic, Gram-negative, motile by a single polar flagellum, poly-β-hydroxybutyrate-containing and formed light-yellow colonies. Growth occurred at 10-37 °C (optimum, 20-30 °C), with 0-0.8 % NaCl (optimum, 0-0.1 %) and at pH 6.0-9.0 (optimum, pH 6.0-7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CMJ-9(T) belonged to the genus Undibacterium, and its closest neighbour was Undibacterium seohonense SHS5-24(T), with 96.7 % sequence similarity. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major cellular hydroxy fatty acid was C10 : 0 3-OH. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The polyamine profile was composed of the major compound putrescine and moderate amounts of 2-hydroxyputrescine. The major respiratory quinone was Q-8 and the DNA G+C content was 47.7 mol%. On the basis of the phylogenetic and phenotypic data, strain CMJ-9(T) should be classified within a novel species, for which the name Undibacterium macrobrachii sp. nov. is proposed. The type strain is CMJ-9(T) ( = BCRC 80406(T) = LMG 26891(T) = KCTC 23916(T)).

Topics: Animals; Aquaculture; Bacterial Typing Techniques; Base Composition; Decapoda; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Molecular Sequence Data; Oxalobacteraceae; Phylogeny; Polyamines; Polyesters; Ponds; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone

A novel aerobic bacterium, designated strain RR11(T), was isolated from peat soil and was characterized by using a polyphasic taxonomic approach and identified in order to determine its taxonomic position. Strain RR11(T) is a Gram-negative, non-sporulating, motile, short-rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus Burkholderia of the class Betaproteobacteria. The highest degrees of gene sequence similarity were found with Burkholderia tropica Ppe8(T) (98.0 %), B. bannensis E25(T) (97.3 %), B. ferrariae FeGI01(T) (97.1 %), B. unamae MTI-641(T) (97.1 %) and B. heleia SA41(T) (97.1 %). Strain RR11(T) had the following chemotaxonomic characteristics: the major ubiquinone was Q-8, the DNA G+C content was 60.8 mol%, the major fatty acids were C16 : 0, C19 : 0 cyclo ω8c and C17 : 0 cyclo and the polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown aminophospholipid. Based on its morphological, physiological and chemotaxonomic characteristics, together with 16S rRNA gene sequence comparison results, strain RR11(T) represents a novel species, for which the name Burkholderia eburnea sp. nov. is proposed. The type strain is strain RR11(T) ( = KEMC 7302-065(T) = JCM 18070(T)).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Russia; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Three strains of Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene sequence phylogeny, they were shown to belong to the genus Burkholderia, with the representative strain WSM3556(T) being most closely related to Burkholderia caledonica LMG 23644(T) (98.70 % 16S rRNA gene sequence similarity) and Burkholderia rhynchosiae WSM3937(T) (98.50 %). Additionally, these strains formed a distinct group in phylogenetic trees of the housekeeping genes gyrB and recA. Chemotaxonomic data, including fatty acid profiles and analysis of respiratory quinones, supported the assignment of our strains to the genus Burkholderia. Results of DNA-DNA hybridizations, MALDI-TOF MS analysis and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from their nearest neighbour species. Therefore, these strains represent a novel species, for which the name Burkholderia dilworthii sp. nov. is proposed, with the type strain WSM3556(T) ( = LMG 27173(T) = HAMBI 3353(T)).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Bacterial; Fabaceae; Fatty Acids; Genes, Bacterial; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Root Nodules, Plant; Sequence Analysis, DNA; South Africa; Ubiquinone

The genus Rhodospirillum is represented by four species, with three of them showing phylogenetic divergence compared to the type species, Rhodospirillum rubrum. Differences in the major diagnostic properties such as internal photosynthetic membranes, quinones, fatty acids, carotenoid composition and a few other phenotypic properties warrant the reclassification of members of this genus. Resultantly, a new genus, Pararhodospirillum gen. nov., is proposed based on the analysis of nine strains to accommodate Rhodospirillum photometricum, Rhodospirillum sulfurexigens and Rhodospirillum oryzae as Pararhodospirillum photometricum comb. nov., Pararhodospirillum sulfurexigens comb. nov. and Pararhodospirillum oryzae comb. nov., respectively. The type species of the genus is Pararhodospirillum photometricum comb. nov. An emended description of the genus Rhodospirillum is also proposed.

Topics: Carotenoids; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phylogeny; Rhodospirillum; RNA, Ribosomal, 16S; Ubiquinone

A Gram-staining-negative, rod-shaped bacterium, strain HMD2169(T), was isolated from a mesotrophic artificial lake in Korea. Strain HMD2169(T) grew in the presence of 0-3.0% (w/v) NaCl, at pH 5-10 and at 20-37 °C. The predominant quinone of strain HMD2169(T) was ubiquinone (UQ)-8. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 59.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD2169(T) was a representative of a lineage within the genus Chitinimonas. Strain HMD2169(T) was closely related to Chitinimonas taiwanensis (95.8 % sequence similarity) and Chitinimonas koreensis (94.6 %). On the basis of the evidence presented in this study, strain HMD2169(T) is a representative of a novel species of the genus Chitinimonas, for which the name Chitinimonas viridis sp. nov. is proposed with the type strain HMD2169(T) ( = KCTC 22839(T) = CECT 7703(T)).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; DNA, Bacterial; Fatty Acids; Lakes; Molecular Sequence Data; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-staining-negative bacterium, strain TS-T4(T), was isolated from Tuosu Lake, a saline lake (salinity 5.4 %, w/w) in Qaidam basin, Qinghai, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain TS-T4(T) were non-spore-forming rods, 0.4-0.8 µm wide and 1.7-2.3 µm long, and motile by means of a single polar flagellum. Strain TS-T4(T) was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Growth was observed in the presence of 0-7.0 % (w/v) NaCl (optimum, 3.0-4.0 %) and at 4-40 °C (optimum, 30-35 °C) and pH 7.0-10.5 (optimum, pH 8.5-9.0). Strain TS-T4(T) contained Q-8 as the sole respiratory quinone and phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids, as for other members of the genus Rheinheimera. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C17 : 1ω8c and C18 : 1ω7c. The DNA G+C content was 50.2 mol% (Tm). Phylogenetic trees based on sequences of the 16S rRNA gene and a conserved portion of the gyrase B gene (gyrB) showed that strain TS-T4(T) was associated with the genus Rheinheimera; the strain showed the highest 16S rRNA gene sequence similarity to Rheinheimera longhuensis LH2-2(T) (97.1 %) and then to Rheinheimera pacifica KMM 1406(T) (97.0 %). DNA-DNA relatedness of strain TS-T4(T) with R. longhuensis LH2-2(T) and R. pacifica NBRC 103167 was 53±2.5 and 48±2 %, respectively. Based on the data presented, it is concluded that TS-T4(T) represents a novel species of the genus Rheinheimera, for which the name Rheinheimera tuosuensis sp. nov. is proposed. The type strain is TS-T4(T) ( = CGMCC 1.12461(T) = JCM 19264(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; Chromatiaceae; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Lakes; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, oxidase and phosphatase-positive and catalase-negative, short rod-shaped bacterium was isolated from sediment of a drinking water reservoir in Germany. Based on 16S rRNA gene sequence and phenotypic properties, the bacterium belongs to the genus Rhodoferax within the family Comamonadaceae. The new taxon differed from related species mainly with respect to its fatty acid composition, low growth temperature, lack of pigments in young cultures and ability to utilize glycerol and d-mannose but not urea. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0, and C18 : 1ω7c. The only ubiquinone detected was ubiquinone Q-8. The DNA G+C content was 60.3-61 mol%. Because of the phenotypic and genotypic differences from the most closely related taxa, the new strain represents a novel species for which the name Rhodoferax saidenbachensis sp. nov. is proposed. The type strain is ED16(T) ( = CCUG 57711(T) = ATCC BAA-1852(T) = DSM 22694(T)). An emended description of the genus Rhodoferax is proposed. Based on the results of this study, strain T118(T) (Albidiferax ferrireducens) is properly placed in the genus Rhodoferax as Rhodoferax ferrireducens.

Topics: Bacterial Typing Techniques; Base Composition; Cold Temperature; Comamonadaceae; DNA, Bacterial; Drinking Water; Fatty Acids; Genes, Bacterial; Geologic Sediments; Germany; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Supply

A Gram-staining-negative, aerobic, rod-shaped bacterium, designated strain T202(T), was isolated from the gill of a cultured flounder (Paralichthys olivaceus). Based on 16S rRNA gene sequence similarity, strain T202(T) was a member of the family Colwelliaceae and shared 93.32-96.58 % similarity with type strains of all members of the most closely related genus Thalassomonas. Phylogenetically, the isolate shared a root with the type strains of four marine species, Thalassomonas agariperforans M-M1(T), Thalassomonas agarivorans TMA1(T), Thalassomonas loyana CBMAI 722(T) and Thalassomonas ganghwensis JC2041(T). Optimal growth occurred in the presence of 2-4 % (w/v) NaCl, at pH 7.0-8.0 and at 28 °C. Ubiquinone 8 (Q-8) was the predominant respiratory quinone. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω9c and C17 : 1ω8c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain T202(T) was 37 mol%. On the basis of polyphasic analysis, especially the phylogenetic relationships and the lower DNA G+C content, strain T202(T) is considered to represent a novel species in a new genus, for which the name Thalassotalea piscium gen. nov., sp. nov. is proposed. The type strain of Thalassotalea piscium is T202(T) ( = JCM 18590(T) = DSM 26287(T) = KCTC 32144(T)). Because Thalassomonas agariperforans M-M1(T), Thalassomonas agarivorans TMA1(T), Thalassomonas loyana CBMAI 722(T) and Thalassomonas ganghwensis JC2041(T) formed a phylogenetic group together with strain T202(T) that was clearly separated from other known strains of Thalassomonas, these four species are reclassified as members of the genus Thalassotalea as Thalassotalea agariperforans comb. nov. (type strain M-M1(T) = KCTC 23343(T) = CCUG 60020(T)), Thalassotalea agarivorans comb. nov. (type strain TMA1(T) = BCRC 17492(T) = JCM 13379(T) = DSM 19706(T)), Thalassotalea loyana comb. nov. (type strain CBMAI 722(T) = LMG 22536(T)) and Thalassotalea ganghwensis comb. nov. (type strain JC2041(T) = IMSNU 14005(T) = KCTC 12041(T) = DSM 15355(T)). The type species of the genus Thalassotalea is Thalassotalea ganghwensis gen. nov., comb. nov. An emended description of the genus Thalassomonas is also proposed.

Topics: Animals; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Flounder; Gammaproteobacteria; Gills; Molecular Sequence Data; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain KIS83-12(T), was isolated from soil of Gaui island in the Taean region of South Korea. The strain grew at 15-33 °C (optimum, 28 °C), at pH 5.0-8.0 (optimum, pH 7.0). Growth did not occur in the presence of NaCl. The strain was catalase-negative and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that KIS83-12(T) was most closely related to Solimonas soli DCY12(T) (96.9 %), Solimonas variicoloris MN28(T) (96.5 %), Solimonas flava CW-KD 4(T) (96.5 %) and Solimonas aquatica NAA16(T) (96.0 %), and formed a robust phyletic lineage with members of the genus Solimonas. The main isoprenoid quinone was Q-8. Major polar lipids included phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acids present in large and moderate amounts (>5.0 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, C16 : 1ω5c, summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH) and C12 : 0. The DNA G+C content was 67.9 mol%. On the basis of the taxonomic data obtained in this study, KIS83-12(T) represents a novel species of the genus Solimonas, for which the name Solimonas terrae sp. nov. is proposed, with KIS83-12(T) ( = KACC 16967(T) = DSM 27281(T)) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated, rod-shaped bacterial strain, designated SM1222(T), was isolated from the deep-sea sediment of the South China Sea. The strain grew at 4-35 °C and with 0.5-8 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1222(T) was affiliated with the genus Oceanisphaera in the class Gammaproteobacteria. It shared the highest sequence similarity with the type strain of Oceanisphaera ostreae (96.8 %) and 95.4-96.6 % sequence similarities with type strains of other species of the genus Oceanisphaera with validly published names. Strain SM1222(T) contained summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c, C16 : 0, C12 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I) as the major fatty acids and ubiquinone Q-8 as the predominant respiratory quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain SM1222(T) was 51.5 mol%. On the basis of the evidence presented in this study, strain SM1222(T) represents a novel species of the genus Oceanisphaera, for which the name Oceanisphaera profunda sp. nov. is proposed. The type strain of Oceanisphaera profunda is SM1222(T) ( = CCTCC AB 2013241(T) = KCTC 32510(T)). An emended description of the genus Oceanisphaera Romanenko et al. 2003 emend. Choi et al. 2011 is also proposed.

Topics: Aeromonadaceae; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-staining-negative, strictly aerobic, white-colony-forming bacterium, designated strain 5-10(T), was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile rods or coccoids, showing oxidase- and catalase-positive reactions. Growth was observed at 10-37 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and in the presence of 0-1.0 % (w/v) NaCl (optimum, 0-0.5 %). The major cellular fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C10 : 0 3-OH and summed feature 8 (comprising C18 : 1ω6c and/or C18 : 1ω7c). The G+C content of the genomic DNA was 69.9 mol% and the only respiratory quinone detected was ubiquinone 8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5-10(T) formed a tight phyletic lineage with members of the genus Ramlibacter. Strain 5-10(T) was most closely related to Ramlibacter tataouinensis TTB310(T) (97.3 %), but the DNA-DNA relatedness level between the two strains was 38.2±1.8 %. Based on phenotypic, chemotaxonomic and molecular features, strain 5-10(T) was shown to represent a novel species of the genus Ramlibacter, for which the name Ramlibacter solisilvae sp. nov. is proposed. The type strain is 5-10(T) ( = KACC 17567(T) = JCM 19319(T)). An emended description of the genus Ramlibacter is also proposed.

Topics: Bacterial Typing Techniques; Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Trees; Ubiquinone; Vietnam

A taxonomic study was carried out on strain GCS-AN-3(T), which was isolated from a phenol-degrading consortium enriched from coking wastewater activated sludge of Beijing Shougang Company Limited during the screening of phenol-degrading bacteria. Cells of strain GCS-AN-3(T) were Gram-stain-negative, short rods, and oxidase-/catalase-positive. Growth was observed at salinities from 0 to 2.5 % and at temperatures from 10 to 37 °C. 16S rRNA gene sequence analysis showed that strain GCS-AN-3(T) was most closely related to Ottowia pentelensis DSM 21699(T) (96.2 %). The principal fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 0, summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and cyclo C17 : 0. The major respiratory quinone was Q-8. The polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. The G+C content of the genomic DNA was 67.6 mol%. Thiosulfate could be utilized as co-substrate for aerobic growth and was oxidized to sulfate. On the basis of phenotypic, chemotaxonomic and molecular data, strain GCS-AN-3(T) is considered to represent a novel species of the genus Ottowia, for which the name Ottowia beijingensis sp. nov. is proposed (type strain GCS-AN-3(T) = LMG 27179(T) = CGMCC 1.12324(T) = MCCC 1A01410(T)). An emended description of the genus Ottowia is also proposed.

Topics: Bacterial Typing Techniques; Base Composition; China; Coke; Comamonadaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone; Wastewater

A novel methane-oxidizing bacterium, strain IT-9(T), was isolated from a shallow submarine hydrothermal system occurring in a coral reef in Japan. Strain IT-9(T) was a Gram-negative, aerobic, motile, coccoid or oval-shaped bacterium with the distinctive intracytoplasmic membrane arrangement of a type I methanotroph. Strain IT-9(T) was a moderately thermophilic, obligate methanotroph that grew on methane and methanol at 30-55 °C (optimum 45-50 °C). The strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. NaCl was required for growth within a concentration range of 1-5 % (optimum 3 %). The hao gene encoding hydroxylamine oxidoreductase (HAO) involved in nitrification was detected by a PCR experiment. The major phospholipid fatty acids were C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The DNA G+C content was 66.0 mol%. The 16S rRNA gene sequence of strain IT-9(T) was only moderately related to the sequences of members of the closest genera Methylohalobius (94.1 % similarity) and Methylothermus (91.7-91.9 % similarity); however, those sequences formed a deeply branching monophyletic group within the order Methylococcales. Phylogenies based on 16S rRNA gene sequences, deduced partial PmoA sequences and deduced partial Hao sequences and physiological and chemotaxonomic characteristics revealed that strain IT-9(T) represents a novel species of a new genus, for which the name Methylomarinovum caldicuralii gen. nov., sp. nov. is proposed. The type strain of Methylomarinovum caldicuralii is IT-9(T) ( = JCM 13666(T) = DSM 19749(T)). In addition, we propose a new family, Methylothermaceae fam. nov., in the order Methylococcales, to accommodate the genera Methylothermus, Methylohalobius and Methylomarinovum. The genera Methylothermus and Methylohalobius have been recognized as being distinct from other genera in the methane-oxidizing order Methylococcales in the class Gammaproteobacteria. These genera form a distinctive monophyletic lineage within the order on the basis of 16S rRNA gene sequence phylogeny. This seems consistent with their distinctive physiological traits; the genus Methylothermus includes the most thermophilic species, and the genus Methylohalobius includes the most halophilic species, within the order. Although these two genera include only three species at the time of writing, similar sequences of 16S rRNA genes and pmoA genes encoding pMMO have been

Topics: Bacterial Typing Techniques; Base Composition; Coral Reefs; DNA, Bacterial; Hydrothermal Vents; Japan; Likelihood Functions; Methane; Methylococcaceae; Molecular Sequence Data; Oxidoreductases; Oxygenases; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

Strain AIS(T), an aerobic halophilic, Gram-reaction-negative, heterotrophic bacterium isolated from the water of Shira Lake in Khakasia, southern Siberia, was characterized using a polyphasic approach. Our analysis of the 16S rRNA gene sequences showed that 'Aliidiomarina haloalkalitolerans', 'Aliidiomarina sanyensis', Idiomarina maris and AIS(T) formed a distinct lineage. The sequence similarities between AIS(T) and the type strains of species of the genera Idiomarina and Aliidiomarina were 91.6-95.1 % and 94.0-96.9 %, respectively. The major isoprenoid quinone of AIS(T) was ubiquinone 8 (Q-8). Predominant cellular fatty acids were iso-C17 : 0, iso-C15 : 0 and summed feature 9. The genomic DNA G+C content was 45.8 mol%. It is concluded that AIS(T) represents a novel species of the genus Aliidiomarina, and the name Aliidiomarina shirensis sp. nov. is herein proposed for it. The type strain is AIS(T) ( = JCM 17761(T) = BCRC 80327(T)). Based on its fatty acid profile and our phylogenetic analysis, we propose that Idiomarina maris be transferred to the genus Aliidiomarina.

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Lakes; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Siberia; Ubiquinone

A Gram-stain-negative, non-spore-forming, rod-shaped bacterium, designated strain 1GB(T), was isolated from anodic biofilms of a glucose-fed microbial fuel cell. Strain 1GB(T) was facultatively anaerobic and chemo-organotrophic, having both a respiratory and a fermentative type of metabolism, and utilized a wide variety of sugars as carbon and energy sources. Cells grown aerobically contained Q-8 as the major quinone, but excreted Q-9 and a small amount of Q-10 when cultured with an electrode serving as the sole electron acceptor. The G+C content of the genomic DNA of 1GB(T) was 54.5 mol%. Multilocus sequence typing (MLST) analysis showed that strain 1GB(T) represented a distinct lineage within the genus Raoultella (98.5-99.4 % 16S rRNA gene sequence similarity and 94.0-96.5 % sequence similarity based on the three concatenated housekeeping genes gyrA, rpoB and parC. Strain 1GB(T) exhibited DNA-DNA hybridization relatedness of 7-43 % with type strains of all established species of the genus Raoultella. On the basis of these phenotypic, phylogenetic and genotypic data, the name Raoultella electrica sp. nov. is proposed for strain 1GB(T). The type strain is 1GB(T) ( = NBRC 109676(T) = KCTC 32430(T)).

Topics: Bacterial Typing Techniques; Base Composition; Bioelectric Energy Sources; Biofilms; Enterobacteriaceae; Fatty Acids; Genes, Bacterial; Glucose; Molecular Sequence Data; Multilocus Sequence Typing; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative bacterium, strain 5410S-62T, was isolated from an air sample collected in Suwon, Republic of Korea. It was aerobic, motile, mesophilic and formed rod-shaped cells. Colonies on R2A agar were convex, circular and pale orange with entire margins. Growth occurred at pH 5-9 (optimally at pH 7) and at 10-40 °C (optimally at 28 °C). It did not grow in the presence of 1% NaCl. Comparative analyses of 16S rRNA gene sequences demonstrated that the novel strain was closely related to members of the genus Noviherbaspirillum. Strain 5410S-62T showed the highest sequence similarity (98.2%) to Glaciimonas singularis A2-57T. It also showed high 16S rRNA gene sequence similarity (98.1-95.6%) to members of the genus Noviherbaspirillum (98.1% to Noviherbaspirillum aurantiacum SUEMI08T, 97.8% to Noviherbaspirillum soli SUEMI10T and Noviherbaspirillum canariense SUEMI03T, 97.6% to Noviherbaspirillum psychrotolerans PB1T and 95.6% to Noviherbaspirillum malthae CC-AFH3T). The strain contained summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c) as major fatty acids, Q-8 as the only ubiquinone and large amounts of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. Strain 5410S-62T revealed less than 70% DNA-DNA relatedness with the type strains of closely related species of the genera Noviherbaspirillum and Herbaspirillum and Glaciimonas singularis. Based on the physiological, biochemical and chemotaxonomic data obtained in this study, it is proposed that strain 5410S-62T represents a novel species, Noviherbaspirillum suwonense sp. nov., with 5410S-62T (=KACC 16657T= NBRC 108944T) as the type strain.

Topics: Air Microbiology; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Bacteria are thought to cope with fluctuating environmental solute concentrations primarily by adjusting the osmolality of their cytoplasm. To obtain insights into the underlying metabolic adaptations, we analyzed the global metabolic response of Escherichia coli to sustained hyperosmotic stress using nontargeted mass spectrometry. We observed that 52% of 1,071 detected metabolites, including known osmoprotectants, changed abundance with increasing salt challenge. Unexpectedly, unsupervised data analysis showed a substantial increase of most intermediates in the ubiquinone-8 (Q8) biosynthesis pathway and a 110-fold accumulation of Q8 itself, as confirmed by quantitative lipidomics. We then demonstrated that Q8 is necessary for acute and sustained osmotic-stress tolerance using Q8 mutants and tolerance rescue through feeding nonrespiratory Q8 analogs. Finally, in vitro experiments with artificial liposomes showed that mechanical membrane stabilization is a principal mechanism of Q8-mediated osmoprotection. Thus, we find that besides regulating intracellular osmolality, E. coli enhances its cytoplasmic membrane stability to withstand osmotic stress.

Topics: Cell Membrane; Data Interpretation, Statistical; Electron Transport; Escherichia coli; Image Processing, Computer-Assisted; Lipid Metabolism; Liposomes; Mass Spectrometry; Metabolomics; Microscopy, Fluorescence; Osmotic Pressure; Reactive Oxygen Species; Stress, Physiological; Ubiquinone

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)).

Topics: Agriculture; Arsenites; Bacterial Typing Techniques; Base Composition; China; Comamonadaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants; Ubiquinone

A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5%), Candidimonas bauzanensis BZ59(T) (97.3%) and Pusillimonas noertemannii BN9(T) (97.2%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C(16 : 0), C(17 : 0) cyclo, C(19 : 0) cyclo ω8c and C(14 : 0) 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) ( = DSM 25520(T) = NCAIM B 02512(T)).

Topics: Alcaligenaceae; Bacterial Typing Techniques; Base Composition; Coke; DNA, Bacterial; Fatty Acids; Hungary; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Ubiquinone; Wastewater

A taxonomic study was carried out on strain CY1(T), which is a novel bacterium isolated from wastewater sludge of a melamine-producing factory in Sanming city, Fujian, China. Strain CY1(T) was shown to rapidly and completely degrade melamine to NH3 and CO2 under aerobic conditions. The isolate was Gram-stain-negative, short-rod-shaped and motile by one unipolar flagellum. Growth was observed at salinities from 0 to 7% NaCl (optimum, 0.1%), at temperatures from 15 to 50 °C (optimum, 40-45 °C) and at pH 7-9.5 (optimum pH 9.5). Quinone-8 was detected as the major respiratory quinone. 16S rRNA gene sequence comparisons showed that strain CY1(T) was affiliated to the family Comamonadaceae in the class Betaproteobacteria. It was most closely related to members of the genera Alicycliphilus (95.5%), Diaphorobacter (94.6-95.1%), Acidovorax (92.9-95.4%), Delftia (93.0-93.6%) and Comamonas (92.6-93.9%). The average nucleotide identity (ANI) values between strain CY1(T) and those representing related genera ranged from 84.0 to 86.1% using Mummer, and from 74.9 to 81.1% using BLAST. The dominant fatty acids were C(16 : 1)ω7c and/or C(16 : 1)ω6c, C(16 : 0), C(10 : 0) 3-OH and C(18 : 1)ω7c and/or C(18 : 1)ω6c, and the major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one unidentified aminophospholipid. The G+C content of the chromosomal DNA was 69.5 mol%. On the basis of the phenotypic and phylogenetic data, strain CY1(T) represents a novel species of a new genus, for which the name Melaminivora alkalimesophila gen. nov., sp. nov. is proposed. The type strain of Melaminivora alkalimesophila is CY1(T) ( = CCTCC AB 2012024(T) = DSM 26006(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; Comamonadaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phosphatidylethanolamines; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Triazines; Ubiquinone

During a study to investigate the diversity of rhizobia associated with native legumes in South Africa's Cape Floristic Region, a Gram-negative bacterium designated VG1C(T) was isolated from the root nodules of Aspalathus abietina Thunb. Based on phylogenetic analyses of the 16S rRNA and recA genes, VG1C(T) belongs to the genus Burkholderia, with the highest degree of sequence similarity to the type strain of Burkholderia sediminicola (98.5% and 98%, respectively). The DNA G+C content of strain VG1C(T) was 60.1 mol%, and DNA-DNA relatedness values to the type strain of closely related species were found to be substantially lower than 70%. As evidenced by results of genotypic, phenotypic and chemotaxonomic tests provided here, we conclude that isolate VG1C(T) represents a novel rhizosphere-associated species in the genus Burkholderia, for which the name Burkholderia aspalathi sp. nov. is proposed, with the type strain VG1C(T) ( = DSM 27239(T) = LMG 27731(T)).

Topics: Aspalathus; Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Rec A Recombinases; RNA, Ribosomal, 16S; Root Nodules, Plant; Sequence Analysis, DNA; South Africa; Ubiquinone

Two motile, rod-shaped and agarolytic bacterial strains, designated PSC101(T) and KDW4(T), were isolated from seawater and gut microflora of abalone, respectively, collected from the South Sea (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive. Strains PSC101(T) and KDW4(T) showed high 16S rRNA gene sequence similarity to each other (98.6%). Psychrosphaera saromensis SA4-48(T) was the nearest neighbour of strains PSC101(T) and KDW4(T) with 96.6% and 97.0% 16S rRNA gene sequence similarity, respectively. DNA-DNA relatedness among strains PSC101(T), KDW4(T) and Psychrosphaera saromensis KCTC 23240(T) was less than 70%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belonged to the genus Psychrosphaera and formed a distinct phyletic line from Psychrosphaera saromensis SA4-48(T). The common major cellular fatty acids of the two novel isolates were C(16 : 0), C(17 : 1)ω8c and summed feature 3 (C(16 : 1)ω6c/C(16 : 1)ω7c). Flexirubin-type pigments were absent. The main ubiquinone was UQ-8 and the DNA G+C content of strains PSC101(T) and KDW4(T) was 49.5 and 42.5 mol%, respectively. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified amino lipid. On the basis of the polyphasic characterization of the two strains, it is suggested that the two isolates represent two novel species of the genus Psychrosphaera, for which the names Psychrosphaera aestuarii sp. nov. (type strain, PSC101(T) = KCTC 32274(T) = JCM 19496(T)) and Psychrosphaera haliotis sp. nov. (type strain, KDW4(T) = KCTC 22500(T) = JCM 16340(T)) are proposed. An emended description of the genus Psychrosphaera is also proposed.

Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Gastropoda; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A bacterial strain, designated Npb-03(T), was isolated from a freshwater river in Taiwan and was characterized using a polyphasic taxonomic approach. The cells were Gram-reaction-negative, straight rod-shaped, non-motile, non-spore-forming and facultatively anaerobic. Growth occurred at 10-37 °C (optimum, 30-35 °C), at pH 6.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.0% NaCl (optimum, 0%). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8 and the DNA G+C content was 64.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and three uncharacterized phospholipids. The major polyamines were putrescine, 2-hydroxyputrescine, cadaverine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-03(T) forms a distinct lineage with respect to closely related genera within the family Neisseriaceae of the class Betaproteobacteria, most closely related to the genera Aquaspirillum, Laribacter, Leeia and Microvirgula, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93%. On the basis of the genotypic and phenotypic data, strain Npb-03(T) represents a novel genus and species of the family Neisseriaceae, for which the name Rivicola pingtungensis gen. nov., sp. nov. is proposed. The type strain is Npb-03(T) ( = BCRC 80376(T) = LMG 26668(T) = KCTC 23712(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Neisseriaceae; Phospholipids; Phylogeny; Polyamines; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone; Water Microbiology

Topics: Escherichia coli; Osmotic Pressure; Stress, Physiological; Ubiquinone

A novel, yellow-pigmented bacterium, designated strain MO64(T), was isolated from the rhizoplane of field-grown soybean, collected from an experimental plot at Coimbatore, India. Cells were Gram-reaction-negative, motile, non-spore-forming rods that produced yellow-pigmented colonies on R2A agar. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain MO64(T) belonged to the genus Rhodanobacter. Strain MO64(T) was related most closely to Rhodanobacter ginsengisoli GR17-7(T) (98.0% 16S rRNA gene sequence similarity), Rhodanobacter spathiphylli B39(T) (97.9%), Rhodanobacter panaciterrae LnR5-47(T) (97.7%), Rhodanobacter terrae GP18-1(T) (97.6%), Rhodanobacter soli DCY45(T) (97.3%) and Rhodanobacter caeni MJ01(T) (97.2%); levels of similarity to the type strains of all other recognized species of the genus Rhodanobacter were less than 97.0%. Chemotaxonomic data (Q-8 as the predominant ubiquinone, and iso-C(16 : 0), iso-C(15 : 0), C(17 : 0) cyclo, iso-C(17 : 1)ω9c, iso-C(17 : 0) and iso-C(11 : 0) as the major fatty acids) also supported the affiliation of strain MO64(T) with the genus Rhodanobacter. The G+C content of the genomic DNA was 64 mol%. The results of DNA-DNA hybridization and phenotypic analysis showed that strain MO64(T) can be distinguished from all known species of the genus Rhodanobacter and therefore represents a novel species of the genus, for which the name Rhodanobacter glycinis sp. nov. is proposed. The type strain is MO64(T) ( = ICMP 17626(T) = NBRC 105007(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Glycine max; India; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

Two Gram-staining-negative, aerobic, rod-shaped bacterial strains, designated Za6a-12(T) and Za6a-17, were isolated from seawater of the East China Sea. Cells of Za6a-12(T) and Za6a-17 were approximately 1.5-2.0 µm×0.5-0.7 µm and motile by a single polar flagellum. Strains grew optimally at pH 7.5-8.0, 28 °C, and in the presence of 2.5-3.0% (w/v) NaCl. Chemotaxonomic analysis showed that the predominant respiratory quinone of strains Za6a-12(T) and Za6a-17 was ubiquinone-8 (>97%), and the major fatty acids were C(14 : 0), C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(16 : 0) and C(17 : 1)ω8c. Their DNA G+C contents were 42.7 mol% and 42.8 mol%, respectively. 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Thalassomonas and showed the highest sequence similarity to Thalassomonas loyana CBMAI 722(T) (95.9%). Strains Za6a-12(T) and Za6a-17 could be differentiated from T. loyana CBMAI 722(T) according to their phenotypic and chemotaxonomic features, DNA G+C contents and fatty acid composition. On the basis of these features, we propose strains Za6a-12(T) and Za6a-17 to be representatives of a novel species of the genus Thalassomonas with the name Thalassomonas eurytherma sp. nov. suggested. Strain Za6a-12(T) ( = CGMCC 1.12115(T) = JCM 18482(T)) is the type strain of this novel species.

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel bacterial strain, designated CJ29(T), was isolated from ginseng soil of Anseong in South Korea. Cells of strain CJ29(T) were Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile. Strain CJ29(T) grew optimally at 28-30 °C and pH 7.0. Based on 16S rRNA gene sequence analysis, strain CJ29(T) was shown to belong to the genus Lysobacter within the class Gammaproteobacteria and was related most closely to Lysobacter soli DCY21(T) (98.5% similarity) and Lysobacter niastensis GH41-7(T) (98.2%). DNA-DNA relatedness between strain CJ29(T) and its closest relatives was below 55.6%. The predominant cellular fatty acids of strain CJ29(T) were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major isoprenoid quinone was ubiquinone 8 (Q-8). The G+C content of the genomic DNA was 65.6 mol%. Phenotypic, genotypic and phylogenetic characteristics strongly supported the differentiation of strain CJ29(T) from related species of the genus Lysobacter. On the basis of data from this polyphasic taxonomic study, strain CJ29(T) is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter panacisoli sp. nov. is proposed. The type strain is CJ29(T) ( = KACC 17502(T) = JCM 19212(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Lysobacter; Molecular Sequence Data; Panax; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-negative, moderately halophilic, strictly aerobic strain, designated YIM 95345(T), was isolated from a soil sample of a hypersaline mine in Yunnan province, PR China, and subjected to a polyphasic taxonomic study. Strain YIM 95345(T) grew at 15-45 °C (optimum 30-35 °C), 3.0-23.0% (w/v) NaCl (optimum 10.0-11.0%, w/v) and pH 6.0-9.0 (optimum pH 7.0-8.0). Phylogenetic analyses based on 16S rRNA gene sequences revealed that the organism belongs to the genus Aquisalimonas and exhibited sequence similarity of 96.6% to the sole type strain Aquisalimonas asiatica CG12(T). The predominant isoprenoid quinone was Q-8 and the major fatty acids were C16 : 0, C19 : 0 cyclo ω8c and C18 : 1ω7c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, three aminolipids and three unidentified phospholipids. The G+C content of the genomic DNA was 59.4 mol%. Based on the results of our comparative phylogenetic, chemotaxonomic and physiological analyses, the new isolate is assigned to a novel species of the genus Aquisalimonas, for which the name Aquisalimonas halophila sp. nov. is proposed, with the type strain YIM 95345(T) ( = DSM 25902(T) = CCTCC AB 2012043(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Mining; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, strain 8-8(T), was isolated from surface seawater at Muroto, Kochi, Japan. The strain exhibited agar-degrading activity. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Alteromonadaceae and clustered distantly with members of the genus Glaciecola (≤ 94.0% similarity). The DNA G+C content was 41.8 mol%. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c and the major hydroxy fatty acid was C12 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid; lysophosphatidylethanolamine and unidentified polar lipids were found as minor components. The major quinone was Q-8. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 8-8(T) represents a novel species of a new genus, for which the name Agaribacter marinus gen. nov., sp. nov. is proposed. The type strain of Agaribacter marinus is 8-8(T) ( = NBRC 110023(T) = LMG 28167(T)).

Topics: Agar; Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Japan; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A bacterial strain, designated KBP-21(T), was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain KBP-21(T) were Gram-stain-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile rods that formed yellow colonies. Growth occurred at 15-40 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, pH 8.0) and with 0-2% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-21(T) belonged to the genus Paludibacterium within the family Neisseriaceae of the class Betaproteobacteria and the closest related neighbour was Paludibacterium yongneupense 5YN8-15(T) with a 16S rRNA gene sequence similarity value of 96.4%. Strain KBP-21(T) contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 62.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid and several uncharacterized phospholipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-21(T) represents a novel species in the genus Paludibacterium, for which the name Paludibacterium paludis sp. nov. is proposed. The type strain is KBP-21(T) ( = BCRC 80514(T)  = LMG 27230(T)  = KCTC 32182(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Hydroxybutyrates; Molecular Sequence Data; Neisseriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; Polyesters; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Taiwan; Ubiquinone; Wetlands

An aerobic, Gram-stain-negative, agarolytic rod-shaped bacterium, designated KMM 9504(T), was isolated from a sediment sample collected from the seashore of the Sea of Japan. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9504(T) belonged to the genus Simiduia as it was most closely related to Simiduia areninigrae KCTC 23293(T) (97.3% sequence similarity). Strain KMM 9504(T) was characterized by the major ubiquinone Q-8, and by the predominance of C(16 : 1)ω7c, C(17 : 1)ω8c, followed by C(16 : 0), C(15 : 0), C(17 : 0) and C(12 : 1) in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid, unknown phospholipids, and unknown lipids. Based on the distinctive phenotypic characteristics, phylogenetic analysis and DNA-DNA hybridization results, it is concluded that strain KMM 9504(T) represents a novel species of the genus Simiduia, for which the name Simiduia litorea sp. nov. is proposed. The type strain of the species is strain KMM 9504(T) ( = NRIC 0917(T) = JCM 19759(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Japan; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, elongated rod-shaped, motile by gliding, green-pigmented, aerobic bacterial strain, designated LY03(T), was isolated from lake water in Xiamen, Fujian Province, China. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Chitinimonas, which belongs to the family Burkholderiaceae. Strain LY03(T) was most closely related to Chitinimonas taiwanensis LMG 22011(T) (96.02 % 16S rRNA gene sequence similarity), followed by Chitinimonas koreensis KACC 11467(T) (94.85 %), and the three strains formed a distinct lineage from other strains in the phylogenetic analyses. Optimum conditions for growth were 37 °C, pH 7-9 and without NaCl. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and C10 : 0 3-OH. The DNA G+C content of strain LY03(T) was 63.6 mol% and the major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown polar lipids and unidentified phospholipids. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain LY03(T) from all other members of the genus Chitinimonas. On the basis of its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain LY03(T) represents a novel species of the genus Chitinimonas, for which the name Chitinimonas prasina sp. nov. is proposed. The type strain is LY03(T) ( = MCCC 1F01209(T) = KCTC 32574(T)).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; China; DNA, Bacterial; Fatty Acids; Lakes; Molecular Sequence Data; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Coenzyme Q (CoQ) is a medically valuable compound and a high yielding strain for CoQ will have several benefits for the industrial production of CoQ. To increase the CoQ(8) content of E. coli, we blocked the pathway for the synthesis of menaquinone by deleting the menA gene. The blocking of menaquinone pathway increased the CoQ(8) content by 81 % in E. coli (ΔmenA). To study the CoQ producing potential of E. coli, we employed previous known increasing strategies for systematic metabolic engineering. These include the supplementation with substrate precursors and the co-expression of rate-limiting genes. The co-expression of dxs-ubiA and the supplementation with substrate precursors such as pyruvate (PYR) and parahydroxybenzoic acid (pHBA) increased the content of CoQ(8) in E. coli (ΔmenA) by 125 and 59 %, respectively. Moreover, a 180 % increase in the CoQ(8) content in E. coli (ΔmenA) was realized by the combination of the co-expression of dxs-ubiA and the supplementation with PYR and pHBA. All in all, CoQ(8) content in E. coli increased 4.06 times by blocking the menaquinone pathway, dxs-ubiA co-expression and the addition of sodium pyruvate and parahydroxybenzoic acid to the medium. Results suggested a synergistic effect among different metabolic engineering strategies.

Topics: Alkyl and Aryl Transferases; Escherichia coli; Escherichia coli Proteins; Gene Expression Regulation, Bacterial; Industrial Microbiology; Metabolic Engineering; Parabens; Plasmids; Ubiquinone; Vitamin K 2

An aerobic, methane-oxidizing bacterium (strain S8(T)) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain is closely related to members of the genus Methylocaldum (97.6-97.9 % similarity) within the class Gammaproteobacteria. Strain S8(T) was a Gram-staining-negative, non-motile, coccoid or short rod-shaped organism. The temperature range for growth of strain S8(T) was 20-47 °C (optimum growth at 36 °C). It required NaCl (>0.5 %), tolerated up to 5 % NaCl and utilized methane and methanol. The major cellular fatty acid and major respiratory quinone were C16 : 0 and 18-methylene ubiquinone 8, respectively. The DNA G+C content was 59.7 mol%. Strain S8(T) possessed mmoX, which encodes soluble methane monooxygenase, as well as pmoA, which encodes the particulate methane monooxygenase. On the basis of this morphological, physiological, biochemical and genetic information, the first marine species in the genus Methylocaldum is proposed, with the name Methylocaldum marinum sp. nov. The type strain is S8(T) ( = NBRC 109686(T) = DSM 27392(T)). An emended description of the genus Methylocaldum is also provided.

Topics: Bacterial Typing Techniques; Base Composition; Bays; DNA, Bacterial; Fatty Acids; Geologic Sediments; Japan; Methylococcaceae; Molecular Sequence Data; Oxygenases; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A methyl parathion (MP) degrading bacterial strain, designated MP-1(T), was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1(T) is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0-1 % (w/v) and temperatures of 15-40 °C. Strain MP-1(T) could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1(T) belongs to the genus Burkholderia, showing highest sequence similarity to Burkholderia grimmiae DSM 25160(T) (98.5 %), and similar strains including Burkholderia zhejiangensis OP-1(T) (98.2 %), Burkholderia choica LMG 22940(T) (97.5 %), Burkholderia glathei DSM 50014(T) (97.4 %), Burkholderia terrestris LMG 22937(T) (97.2 %) and Burkholderia telluris LMG 22936(T) (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1(T) exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1(T) was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1(T) were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA-DNA relatedness values between strain MP-1(T) and the three type strains (B. grimmiae DSM 25160(T), B. zhejiangensis OP-1(T) and B. glathei DSM 50014(T)) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia jiangsuensis sp. nov. is proposed, the type strain is MP-1(T) (LMG 27927(T) = MCCC 1K00250(T)).

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; China; DNA, Bacterial; Fatty Acids; Insecticides; Methyl Parathion; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants; Ubiquinone

Strain GZ436(T) was Gram-stain-negative, aerobic, non-motile, rod-shaped and isolated from the soil of a coal mine. 16S rRNA gene phylogenetic analysis showed that this strain clustered with Thermomonas brevis LMG 21746(T) (97.5%), Thermomonas haemolytica A50-7-3(T) (96.3%), Thermomonas koreensis KCTC 12540(T) (96.4%), Thermomonas hydrothermalis SGM-6(T) (95.5%) and Thermomonas fusca LMG 21737(T) (95.1%). The major isoprenoid quinone was Q-8. The DNA G+C content was 67 mol%. Strain GZ436(T) contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unknown aminophospholipid, an unknown phospholipid and an unknown lipid as the major polar lipids. The predominant cellular fatty acids (>5%) were iso-C(15:0), iso-C(11:0), iso-C(11:0 3)-OH, iso-C(17:1)ω9c, C(16 : 0) and summed feature 3. The DNA-DNA relatedness value between strain GZ436(T) and T. brevis LMG 21746(T) was 54 ± 0.4%. According to phenotypic and phylogenetic characteristics, strain GZ436(T) represents a novel species of the genus Thermomonas, for which the name Thermomonas carbonis sp. nov. is proposed. The type strain is GZ436(T) ( =CCTCC AB 2013364(T) = KCTC 42013(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; Coal; DNA, Bacterial; Fatty Acids; Mining; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A Gram-reaction-negative, aerobic, rod-shaped (1.2-1.6 µm×0.6-0.8 µm), flagellated and motile marine bacterium, designated MEBiC06243(T), was isolated from a sediment collected at Daebu Island in the Yellow Sea (37° 20' N 126° 41' E), Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC06243(T) showed high similarity with Neptunomonas naphthovorans NAG-2N-126(T) (96.3%). Growth was observed at 10-39 °C (optimum 29 °C), at pH 6.0-9.0 (optimum pH 7) and with 0-7% (optimum 2.5%) NaCl. The predominant cellular fatty acids were C(10:0) 3-OH (6.1%), C(12:0) (5.8%), C(16:0) (30.5%), C(18:1)ω7c (21.6%) and summed feature 3 (comprising C(15:0) 2-OH and/or C(16:1)ω7c; 30.7%). The DNA G+C content was 41.4 mol%. The major respiratory quinone was Q-8. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified lipids, one unidentified aminophospholipid and three unidentified aminolipids were detected as major polar lipids. On the basis of this polyphasic taxonomic data, strain MEBiC06243(T) should be classified as a novel species of the genus Neptunomonas proposed as Neptunomonas acidivorans sp. nov. The type strain is MEBiC06243(T) ( =KCCM 42975(T) =JCM 18291(T)). An emended description of the genus Neptunomonas is also given.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Oceanospirillaceae; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, aerobic, non-flagellated and rod-shaped or ovoid bacterial strain, designated GJSW-36(T), was isolated from seawater at Geoje island in the South Sea, South Korea. Strain GJSW-36(T) grew optimally at pH 7.0-8.0, at 25 °C and in the presence of 2% (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain GJSW-36(T) fell within the clade comprising the type strains of species of the genus Thalassotalea and Thalassomonas fusca. Strain GJSW-36(T) exhibited 16S rRNA gene sequence similarity values of 94.2-96.0% to the type strains of species of the genus Thalassotalea and Thalassomonas fusca and of 93.8-94.5% to the type strains of the other species of the genus Thalassomonas. Strain GJSW-36(T) contained ubiquinone-8 (Q-8) as the predominant ubiquinone and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c), C(1:1)ω8c and C(16:0) as the major fatty acids. The major polar lipids of strain GJSW-36(T) were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain GJSW-36(T) was 45.1 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain GJSW-36(T) is separated from species of the genus Thalassotalea and Thalassomonas fusca. On the basis of the data presented, strain GJSW-36(T) is considered to represent a novel species of the genus Thalassotalea, for which the name Thalassotalea ponticola sp. nov. is proposed. The type strain is GJSW-36(T) ( =KCTC 42155(T) =CECT 8656(T)). From this study, it is also proposed that Thalassomonas fusca should be reclassified as a member of the genus Thalassotalea and the description of the genus Thalassotalea is emended.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel psychrophilic, marine, bacterial strain designated BJ-1(T) was isolated from the Iheya North hydrothermal field in the Okinawa Trough off Japan. Cells were Gram-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 16 °C, with the optimum between 9 and 12 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the closest relatives of strain BJ-1(T) were Shewanella denitrificans OS-217(T) (93.5% similarity), Shewanella profunda DSM 15900(T) (92.9%), Shewanella gaetbuli TF-27(T) (92.9%), Paraferrimonas sedimenticola Mok-106(T) (92.1%) and Ferrimonas kyonanensis Asr22-7(T) (91.7%). The major respiratory quinone was Q-8. The predominant fatty acids were C(16:1)ω7c and C(16:0). The G+C content of the novel strain was 40.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain BJ-1(T) represents a novel species in a new genus, for which the name Psychrobium conchae gen. nov., sp. nov. is proposed. The type strain of Psychrobium conchae is BJ-1(T) ( =JCM 30103(T) =DSM 28701(T)).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Bivalvia; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Hydrothermal Vents; Japan; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped bacterial strain, designated DMCK3-4(T), was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain DMCK3-4(T) grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain DMCK3-4(T) clustered with the strains of three members of the genus Simiduia, with which it exhibited 97.0-99.0% sequence similarity. Sequence similarities to the type strains of the other species with validly published names were less than 92.2%. Strain DMCK3-4(T) contained Q-8 as the predominant ubiquinone and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c), C(17:1)ω8c, C(16:0), C(17:0) and C(18:1)ω7c as the major fatty acids. The major polar lipids of strain DMCK3-4(T) were phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain DMCK3-4(T) was 51.8 mol% and its mean DNA-DNA relatedness values with Simiduia agarivorans KCTC 23176(T), Simiduia areninigrae KCTC 23293(T) and Simiduia litorea NRIC 0917(T) were 23-34%, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain DMCK3-4(T) is distinct from other species of the genus Simiduia. On the basis of the data presented, strain DMCK3-4(T) is considered to represent a novel species of the genus Simiduia, for which the name Simiduia curdlanivorans sp. nov. is proposed. The type strain is DMCK3-4(T) ( = KCTC 42075(T) =CECT 8570(T)). An emended description of the genus Simiduia is also proposed.

Topics: Bacterial Typing Techniques; Base Composition; beta-Glucans; DNA, Bacterial; Fatty Acids; Fresh Water; Gammaproteobacteria; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, non-flagellated, aerobic and ovoid or rod-shaped bacterium, designated J-MS1(T), was isolated from seashore sand in the South Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain J-MS1(T) was found to grow optimally at 30 °C and pH 7.0-8.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain J-MS1(T) belonged to the genus Rheinheimera, clustering coherently with the type strain of Rheinheimera chironomi and sharing 98.34% sequence similarity. Strain J-MS1(T) exhibited 16S rRNA gene sequence similarity of 94.26-96.98% to the type strains of the other species of the genus Rheinheimera. In the phylogenetic trees based on gyrB sequences, strain J-MS1(T) clustered with the type strain of R. chironomi, with which it shared the highest sequence similarity (86.97%). Strain J-MS1(T) contained Q-8 as the predominant ubiquinone and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c), C(16:0) and C(18:1)ω7c as the major fatty acids. The major polar lipids detected in strain J-MS1(T) and in the type strain of R. chironomi were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain J-MS1(T) was 49.8 mol% and its mean DNA-DNA relatedness value with R. chironomi LMG 23818(T) was 12%. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain J-MS1(T) is separated from recognized species of the genus Rheinheimera. On the basis of the data presented, strain J-MS1(T) is considered to represent a novel species of the genus Rheinheimera, for which the name Rheinheimera arenilitoris sp. nov. is proposed. The type strain is J-MS1(T) ( =KCTC 42112(T) =CECT 8623(T)).

Topics: Bacterial Typing Techniques; Base Composition; Chromatiaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Silicon Dioxide; Ubiquinone

A Gram-staining-negative, facultatively aerobic bacterium, designated SM-2(T), was isolated from a sea-tidal flat of Yellow Sea, South Korea. Cells were catalase- and oxidase-positive motile rods with a single polar flagellum. Growth of strain SM-2(T) was observed at 10-37 °C (optimum, 25-30 °C), at pH 5.5-8.5 (optimum, pH 7.0-7.5) and in the presence of 0-11% (w/v) NaCl (optimum, 2%). Strain SM-2(T) contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and C(17:1)ω8c, summed feature 3 (comprising C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(17:0) and C(18:1)ω7c as the major fatty acids. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified lipid were identified as the major cellular polar lipids. The G+C content of the genomic DNA was 52.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SM-2(T) formed a tight phyletic lineage with Zhongshania antarctica ZS5-23(T), Zhongshania guokunii ZS6-22(T) and Spongiibacter borealis CL-AS9(T), but that S. borealis CL-AS9(T) was distinct from other species of the genus Spongiibacter. Based on 16S rRNA gene sequence similarities, strain SM-2(T) was most closely related to S. borealis CL-AS9(T), Z. antarctica ZS5-23(T) and Z. guokunii ZS6-22(T), with similarities of 99.5%, 98.9% and 98.7%, respectively, but the DNA-DNA hybridization values among these species were clearly lower than 70%. On the basis of chemotaxonomic data and molecular properties, we propose strain SM-2(T) represents a novel species of the genus Zhongshania with the name Zhongshania aliphaticivorans sp. nov. (type strain SM-2(T) =KACC 18120(T) =JCM 30138(T)). We also propose the transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov. (type strain CL-AS9(T) =KCCM 90094(T) =JCM 17304(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Geologic Sediments; Hydrocarbons; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel, moderately thermophilic, bacterial strain (skMP5(T)) was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. Growth was observed at temperatures ranging from 25 to 52 °C, with optimum growth observed at 48-50 °C. The pH range for growth was pH 5.0-8.2, with optimum growth at pH 6.0-7.0. The G+C content of genomic DNA was 72 mol%. The major components in the fatty acid profile were iso-C17 : 0 and iso-C17 : 1ω9c. The predominant isoprenoid quinone of the strain was ubiquinone Q-8. The strain was facultatively anaerobic, and reduced nitrate to nitrite under anoxic conditions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was a member of the family Xanthomonadaceae within the class Gammaproteobacteria, showing highest sequence similarity with Tahibacter aquaticus RaM5-2 (93.6 %) and Metallibacterium scheffleri DKE6(T) (93.3 %). On the basis of phylogenetic and phenotypic properties, strain skMP5(T) represents a novel species of a new genus, Mizugakiibacter sediminis gen. nov., sp. nov. The type strain of the type species is skMP5(T) ( = DSM 27098(T) = NBRC 109608(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fresh Water; Geologic Sediments; Japan; Lakes; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Xanthomonadaceae

A bacterial strain, designated GAU11(T), was isolated from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic, non-motile rods. The 16S rRNA gene sequence of strain GAU11(T) showed high similarity to those of Comamonas zonglianii BF-3(T) (98.8 %), Pseudacidovorax intermedius CC21(T) (96.4 %), Acidovorax caeni R-24608(T) (96.2 %), Alicycliphilus denitrificans K601(T) (96.2 %), Pseudorhodoferax soli TBEA3(T) (95.9 %) and Comamonas terrigena LMG 1253(T) (95.9 %). Strain GAU11(T) contained ubiquinone 8 as the sole ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Its major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain GAU11(T) was 68.2 mol%. The DNA-DNA relatedness between strain GAU11(T) and C. zonglianii DSM 22523(T) was 52 or 68 % (reciprocal value). Phenotypic characterization indicated that strain GAU11(T) represents a member of the genus Comamonas, but at the same time distinguished it from C. zonglianii DSM 22523(T). From polyphasic characterization, this strain should be classified as representing a novel species of the genus Comamonas, for which the name Comamonas humi sp. nov. (type strain GAU11(T) = JCM 19903(T) = DSM 28451(T)) is proposed.

Topics: Bacterial Typing Techniques; Base Composition; Comamonas; DNA, Bacterial; Fatty Acids; Japan; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A translucent, white, Gram-reaction-negative, facultatively anaerobic, non-flagellated, slightly curved or curved bacterial strain, designated YT8(T), was isolated from the fresh water of the Maotai section of Chishui River, China. Cells were catalase-positive and oxidase-positive. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain YT8(T) is a member of the genus Arenimonas with similarity to other members of this genus ranging from 93.7 to 95.0 %. The major isoprenoid quinone was ubiquinone 8 (Q-8), major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, two unidentified phospholipids and two unidentified polar lipids, while major fatty acids were iso-C15 : 0, iso-C14 : 0 and anteiso-C15 : 0. The DNA G+C content of strain YT8(T) was 66.6 mol%. On the basis of phenotypic, phylogenetic and genotypic features studied, strain YT8(T) is suggested to represent a novel species of the genus Arenimonas, for which the name Arenimonas maotaiensis sp. nov. is proposed. The type strain is YT8(T) ( = CGMCC 1.12726(T) = JCM 19710(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Fresh Water; Molecular Sequence Data; Phospholipids; Phylogeny; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Xanthomonadaceae

A nitrogen-fixing marine bacterium, designated strain Gal22(T), was isolated from mangrove roots of Rhizophora mangle. Cells were Gram-stain-negative rods, motile with a single polar flagellum. Growth was observed at 4-42 °C, pH 5.5 to 10 and with 0-18 % (w/v) NaCl. Strain Gal22(T) was positive for catalase and oxidase. Q-8 was the predominant lipoquinone. The DNA G+C content was 57.0 mol%. Based on phylogenetic analysis of 16S rRNA gene, strain Gal22(T) belongs to the genus Marinobacterium. The closely related strains were shown to be Marinobacterium lutimaris DSM 22012(T) and Marinobacterium litorale IMCC1877(T) with 99 % and 96 % 16S rRNA gene sequence similarity, respectively. DNA-DNA relatedness analysis indicated that strain Gal22(T) was different from M. lutimaris DSM 22012(T). On the basis of genotypic, morphological and biochemical characteristics, a novel species, Marinobacterium mangrovicola sp. nov. (type strain, Gal22(T) = DSM 27697(T) = CIP 110653(T)), is proposed.

Topics: Alteromonadaceae; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nitrogen Fixation; Nucleic Acid Hybridization; Phylogeny; Plant Roots; Rhizophoraceae; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated RA1(T), was isolated from faeces collected from Beluga whale (Delphinapterus leucas) in Yeosu aquarium, South Korea. Strain RA1(T) grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain RA1(T) joins the cluster comprising the type strains of three species of the genus Amphritea, with which it exhibited 95.8-96.0 % sequence similarity. Sequence similarities to the type strains of other recognized species were less than 94.3 %. Strain RA1(T) contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain RA1(T) were phosphatidylethanolamine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain RA1(T) was 47.4 mol%. The differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain RA1(T) is separated from other species of the genus Amphritea. On the basis of the data presented, strain RA1(T) is considered to represent a novel species of the genus Amphritea, for which the name Amphritea ceti sp. nov. is proposed. The type strain is RA1(T) ( = KCTC 42154(T) = NBRC 110551(T)).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Beluga Whale; DNA, Bacterial; Fatty Acids; Feces; Molecular Sequence Data; Oceanospirillaceae; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-staining-negative, motile by flagella, non-pigmented, poly-β-hydroxybutyrate-producing, strictly aerobic and sphere-shaped bacterium, IMCC3490(T), was isolated from a coastal seawater sample from the Antarctic Peninsula. Optimal growth of strain IMCC3490(T) was observed at 20 °C, pH 8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain IMCC3490(T) belonged to the genus Granulosicoccus in the family Granulosicoccaceae. The strain was closely related to Granulosicoccus antarcticus IMCC3135(T) (98.8 % 16S rRNA gene sequence similarity) and Granulosicoccus coccoides Z 271(T) (98.5 %). The DNA-DNA relatedness values between IMCC3490(T) and type strains of the two species of the genus were far lower than 70 %, which indicated strain IMCC3490(T) is a novel genomic species of the genus Granulosicoccus. The major fatty acids of strain IMCC3490(T) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The isoprenoid quinone detected was ubiquinone-8 (Q-8) and predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 61.0 mol%. On the basis of phylogenetic analyses, DNA-DNA relatedness values and phenotypic data, it is suggested that strain IMCC3490(T) represents a novel species of the genus Granulosicoccus, for which the name Granulosicoccus marinus sp. nov. is proposed. The type strain is IMCC3490(T) ( = KACC 17483(T) = NBRC 109704(T)). An emended description of the genus Granulosicoccus is also provided.

Topics: Antarctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A Gram-stain-negative bacterium, designated SP-35(T), was isolated from compost and was subjected to a taxonomic study. This isolate was short-rod-shaped and non-spore-forming. Phylogenetic analysis based on 16S rRNA sequence comparison indicated the isolate was related to the genus Comamonas. 16S rRNA gene sequence analysis showed that its closest neighbours were the type strains Comamonas odontotermitis Dant 3-8(T) (96.8 % similarity), Comamonas testosteroni DSM 50244(T) (96.5 %), Comamonas guangdongensis CY01(T) (95.9 %) and Comamonas composti YY287(T) (95.6 %). Using phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics we could clearly distinguish strain SP-35(T) from type strains of the genus Comamonas. The genomic DNA G+C content of strain SP-35(T) was 63.1 mol%. The predominant cellular fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidlyglycerol. Differences in phenotypic and phylogenetic characteristics support the classification of strain SP-35(T) as a representative of a novel species in the genus Comamonas, for which the name Comamonas serinivorans sp. nov. is proposed. The type strain is SP-35(T) ( = DSM 26136(T) = JCM 18194(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; Comamonas; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Triticum; Ubiquinone

A reddish-brown bacterium, designated strain JA318(T), was purified from a photoheterotrophic enrichment culture obtained from the rhizosphere soil of paddy. Cells of strain JA318(T) are spiral shaped, Gram-stain-negative and motile by means of amphitrichous flagella. Strain JA318(T) has no NaCl requirement for growth but can tolerate up to 1.5 % (w/v) NaCl. Internal photosynthetic membranes are present as lamellar stacks. Photoorganoheterotrophy is the only growth mode observed. Strain JA318(T) contains bacteriochlorophyll a, lycopene and rhodopin as major carotenoids. Thiamine, niacin and para-aminobenzoic acid (PABA) are required as growth factors. Major fatty acids are C18 : 1ω7c and C16 : 0. Ubiquinone-8 and rhodoquinone-8 are the observed quinones. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid are the major polar lipids in strain JA318(T). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain JA318(T) clustered with species of the genus Rhodospirillum which belongs to the class Alphaproteobacteria. The highest sequence similarity of strain JA318(T) was found with Rhodospirillum sulfurexigens JA143(T) (99.9 %). The DNA-DNA reassociation values of strain JA318(T) with Rsp. sulfurexigens JA143(T) and Rhodospirillum photometricum DSM 122(T) were 52 ± 2 % and 45 ± 1 %, respectively. The genomic DNA G+C content of strain JA318(T) was 60.2 mol%. Based on the morphological, physiological, chemotaxonomical and molecular evidence, strain JA318(T) is significantly different from the type strains of species of the genus Rhodospirillum, of the family Rhodospirillaceae, and it is proposed that the strain be classified as a representative of a novel species for which the name Rhodospirillum oryzae sp. nov. is proposed. The type strain is JA318(T) (= KCTC 5960(T) = NBRC 107573(T)).

Topics: Bacterial Typing Techniques; Bacteriochlorophyll A; Base Composition; Carotenoids; DNA, Bacterial; Fatty Acids; India; Lycopene; Molecular Sequence Data; Nucleic Acid Hybridization; Oryza; Phylogeny; Rhizosphere; Rhodospirillum; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, aerobic, motile with one polar flagellum γ-proteobacterium, designated strain SBZ3-12(T), was isolated from surfaces of weathered potassic trachyte. Phylogenetic analysis of this strain based on 16S rRNA gene sequences showed that it was most closely related to Dyella japonica XD53(T) (97.9% 16S rRNA gene sequence similarity), Dyella terrae JS14-6(T) (97.7%), Dyella soli JS12-10(T) (97.5%) and Dyella koreensis BB4(T) (97.0%). The DNA G+C content of strain SBZ3-12(T) was 64.0 mol%. In addition, iso-C(17:1)ω9c, iso-C(15:0) and iso-C(16:0) were the major cellular fatty acids and ubiquinone Q-8 was the predominant respiratory quinone. The low DNA-DNA relatedness values between strain SBZ3-12(T) and recognized species of the genus Dyella and the many phenotypic properties supported the classification of strain SBZ3-12(T) as a representative of a novel species of the genus Dyella, for which the name Dyella jiangningensis sp. nov. is proposed. The type strain is SBZ3-12(T) ( =CCTCC AB 2012160(T) =KACC 16539(T) =DSM 26119(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Potassium; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A Gram-stain-negative bacterium, designated strain CBA4601(T), was isolated from a seawater sample obtained off the coast of Jeju Island, Korea. The organism grew in the presence of 0-4% (w/v) NaCl and at 20-35 °C and pH 7.0-9.0, with optimal growth in 2% NaCl, and at 25 °C and pH 8.0. Phylogenetic trees based on 16S rRNA gene sequences showed that strain CBA4601(T) was related to the genus Ferrimonas within the class Gammaproteobacteria. 16S rRNA gene sequence similarity between strain CBA4601(T) and Ferrimonas marina A4D-4(T), the most closely related species, was 96.9%. The G+C content of the genomic DNA from strain CBA4601(T) was 54.2 mol%, and the isoprenoid quinones menaquinone 7 (MK-7), ubiquinone 7 (Q-7) and ubiquinone 8 (Q-8) were detected. The major fatty acids were C(17:1)ω8c, C(18:1)ω9c and C(16:0), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified ninhydrin-positive phospholipid. On the basis of this taxonomic study using a polyphasic approach, strain CBA4601(T) represents a novel species of the genus Ferrimonas, for which the name Ferrimonas pelagia sp. nov. is proposed. The type strain is CBA4601(T) ( =KACC 16695(T) =KCTC 32029(T) =JCM 18401(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Vitamin K 2; Water Microbiology

A novel psychrotolerant, Gram-negative, shiny white, curved-rod-shaped, facultatively anaerobic bacterium PB1(T) was isolated from a soil sample collected from a glacier forefield of the Larsemann Hills, East Antarctica. Isolate PB1(T) has catalase and low urease activity and hydrolyses gelatin and starch. Strain PB1(T) is able to grow between -5 °C and 30 °C with optimum growth at 14-20 °C. Glycerol, dl-arabinose, d-xylose, d-galactose, d-fructose, d-lyxose, d-fucose and potassium gluconate are used as sole carbon sources. The major quinone is ubiquinone Q-8. The major fatty acids (>10%) for PB1(T) are C(16:0) (19.1%), C(16:1)ω7cis (44.6%) and C(18:1)ω7cis (16.2%). The major polyamines are putrescine [54.9 µmol (g dry weight)(-1)] and 2-hydroxy putrescine [18.5 µmol (g dry weight)(-1)]. DNA G+C content is 62.5 mol%. Strain PB1(T) is phylogenetically related to species of the genus Herbaspirillum, with highest 16S rRNA gene sequence similarities to Herbaspirillum canariense (97.3%), Herbaspirillum aurantiacum (97.2%), Herbaspirillum soli (97.2%) and Herbaspirillum frisingense (97.0%). The DNA-DNA relatedness values were below 30% between PB1(T) and the type strains of Herbaspirillum canariense, Herbaspirillum aurantiacum and Herbaspirillum soli. The different geographical origin of strain PB1(T) from its closest phylogenetic relatives resulted in different phenotypic and genotypic specifications, whereby strain PB(T) represents a novel species of the genus Herbaspirillum, for which the name Herbaspirillum psychrotolerans is proposed. The type strain is PB1(T) (DSM 26001(T) =LMG 27282(T)).

Topics: Antarctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Herbaspirillum; Ice Cover; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Polyamines; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel Gram-reaction-negative, yellow-pigmented, aerobic, non-motile and rod-shaped bacterium designated strain CC-YHH031(T) was isolated from an agricultural soil collected at Chiayi County, Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CC-YHH031(T) formed a discrete monophyletic lineage in the family Xanthomonadaceae, sharing high pairwise sequence similarity of 93.5-95.2 and 94.8% with species of the genus Dokdonella (94.9% similarity to the type strain of the type species) and Aquimonas voraii GPTSA 20(T), respectively. The genomic DNA G+C content of strain CC-YHH031(T) was 68.6 ± 0.7 mol% and the predominant respiratory quinone was ubiquinone Q-8. Spermidine was the principal polyamine, with minor amounts of putrescine. Major fatty acids (>5% of total fatty acids) were iso-C(16:00, iso-C(15:0), C(16:1)ω7c and/or C(16:1)ω6c (summed feature 3), iso-C(17:1)ω9c, iso-C(14:0), iso-C(11:0) and iso-C(11:0) 3-OH. The polar lipid profile of strain CC-YHH031(T) included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids (APL1-2) and four unidentified phospholipids (PL1-4). Strain CC-YHH031(T) was distinguished particularly from the type species of the genus Dokdonella (Dokdonella koreensis) by the presence of major amounts of iso-C(14:0) and summed feature 3 and minor amounts of iso-C(17:0) and by the complete absence of anteiso-C(17:0), the presence of PL1-3 and APL1-2, the absence of APL3 and the presence of putrescine in the former. On the basis of distinguishing genotypic and phenotypic evidence, strain CC-YHH031(T) is proposed to represent a novel genus and species within the family Xanthomonadaceae, for which the name Chiayiivirga flava gen. nov., sp. nov. is proposed. The type strain of Chiayiivirga flava is CC-YHH031(T) ( =BCRC 80274(T) =DSM 24163(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Taiwan; Ubiquinone; Xanthomonadaceae

A Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium (strain 107-E2(T)) was isolated from freshwater samples containing microbial mats collected at a lake in Skarvsnes, Antarctica (temporary lake name, Lake Tanago Ike). Strain 107-E2(T) grew between 5 and 25 °C, with an optimum of 23 °C. Moreover, colony formation was observed on agar media even at -5 °C. The pH range for growth was between 6.0 and 9.0, with an optimum of pH 7.0-8.0. The range of NaCl concentration for growth was between 0.0 and 0.5% (w/v), with an optimum of 0.0%. No growth was observed in media containing organic compounds at high concentrations, which indicated that strain 107-E2(T) was an oligotroph. In the late stationary phase, strain 107-E2(T) produced a dark brown water-soluble pigment. Esterase, amylase and protease production was observed. Antimicrobial-lytic activities for Gram-negative bacteria and yeast were observed. Ubiquinone-8 was the major respiratory quinone. The major fatty acids were iso-C15:0, iso-C(17:1)ω9c and iso-C(15:1) at 5. The G+C content of genomic DNA was 66.1 mol%. Analysis of the 16S rRNA gene sequences revealed that strain 107-E2(T) belonged to the genus Lysobacter, and low DNA-DNA relatedness values with closely related species distinguished strain 107-E2(T) from recognized species of the genus Lysobacter. The phylogenetic situation and physiological characteristics indicated that strain 107-E2(T) should be classified as a representative of a novel species of the genus Lysobacter, for which the name Lysobacter oligotrophicus sp. nov. is proposed. The type strain is 107-E2(T) ( =JCM 18257(T) =ATCC BAA-2438(T)).

Topics: Antarctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fresh Water; Lakes; Lysobacter; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A yellow-coloured bacterial strain, designated HB2(T), isolated from stratum water was investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a member of the genus Luteimonas, its three closest neighbours being Luteimonas aquatica BCRC 17731(T) (97.5% similarity), Luteimonas marina JCM 12488(T) (97.3%) and Luteimonas aestuarii DSM 19680(T) (96.9%). Strain HB2(T) could clearly be distinguished from these type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strain HB2(T) represents a novel species of the genus Luteimonas, for which the name Luteimonas huabeiensis sp. nov. is proposed. The type strain is HB2(T) ( =DSM 26429(T) =CICC 11005s(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oil and Gas Fields; Phylogeny; RNA, Ribosomal, 16S; Ubiquinone; Water Microbiology; Xanthomonadaceae

Takeout proteins are found across a diverse range of insect species and are thought to be involved in important aspects of insect physiology and behavior. These proteins act as ligand carriers, but the nature of their endogenous ligands remains unknown. The crystal structure of Epiphyas postvittana Takeout 1 (EpTo1), the only structure for any Takeout protein to date, revealed an α/β-wrap fold with a purely hydrophobic internal cavity of tubular shape. When recombinantly expressed in Escherichia coli, we previously showed that a surrogate ubiquinone-8 ligand binds within the internal cavity of EpTo1 with excellent shape complementarity. We have now expressed EpTo1 in an insect cell expression system devoid of ubiquinone-8, and solved its crystal structure at 2.2Å resolution. Using combined information from crystallography and mass spectrometry, we identify a mixture of fatty acid moieties, mostly myristic and palmitic acid, bound inside the EpTo1 cavity, mimicking the structure of the longer ubiquinone-8 compound. No significant alteration of the internal cavity was observed regardless of the bound ligands, ubiquinone-8 or fatty acids, suggesting that the internal cavity of EpTo1 forms a rigid scaffold that imposes strict structural constraints for selectivity and specificity of ligand(s) in vivo.

Topics: Animals; Binding Sites; Carrier Proteins; Crystallography, X-Ray; Fatty Acids; Hydrophobic and Hydrophilic Interactions; Insect Proteins; Lepidoptera; Ligands; Protein Conformation; Protein Folding; Ubiquinone

Four strains (08HL01032(T), 09HG994, 10HP82-6 and 10HL1960) were isolated from water of air-conditioning systems of various cooling towers in Guangzhou city, China. Cells were Gram-stain-negative coccobacilli without flagella, catalase-positive and oxidase-negative, showing no reduction of nitrate, no hydrolysis of urea and no production of H2S. Growth was characteristically enhanced in the presence of l-cysteine, which was consistent with the properties of members of the genus Francisella. The quinone system was composed of ubiquinone Q-8 with minor amounts of Q-9. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids (PL2, PL3), an unidentified aminophospholipid and an unidentified glycolipid (GL2). The polyamine pattern consisted of the major compounds spermidine, cadaverine and spermine. The major cellular fatty acids were C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 1 3-OH. A draft whole-genome sequence of the proposed type strain 08HL01032(T) was generated. Comparative sequence analysis of the complete 16S and 23S rRNA genes confirmed affiliation to the genus Francisella, with 95 % sequence identity to the closest relatives in the database, the type strains of Francisella philomiragia and Francisella noatunensis subsp. orientalis. Full-length deduced amino acid sequences of various housekeeping genes, recA, gyrB, groEL, dnaK, rpoA, rpoB, rpoD, rpoH, fopA and sdhA, exhibited similarities of 67-92 % to strains of other species of the genus Francisella. Strains 08HL01032(T), 09HG994, 10HP82-6 and 10HL1960 exhibited highly similar pan-genome PCR profiles. Both the phenotypic and molecular data support the conclusion that the four strains belong to the genus Francisella but exhibit considerable divergence from all recognized Francisella species. Therefore, we propose the name Francisella guangzhouensis sp. nov., with the type strain 08HL01032(T) ( = CCUG 60119(T) = NCTC 13503(T)).

Topics: Air Conditioning; Bacterial Typing Techniques; China; Cysteine; DNA, Bacterial; Fatty Acids; Francisella; Genes, Bacterial; Molecular Sequence Data; Phospholipids; Phylogeny; Polyamines; RNA, Ribosomal, 16S; RNA, Ribosomal, 23S; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

The gut of the Western honeybee, Apis mellifera, is colonized by a characteristic set of bacteria. Two distinct gammaproteobacteria are consistent members of this unique microbial community, and one has recently been described in a new genus and species with the name Gilliamella apicola. Here, we present the isolation and characterization of PEB0191(T), a strain belonging to the second gammaproteobacterial species present in the honeybee gut microbiota, formerly referred to as 'Gammaproteobacterium-2'. Cells of strain PEB0191(T) were mesophilic and had a mean length of around 2 µm, and optimal growth was achieved under anaerobic conditions. Growth was not obtained under aerobic conditions and was reduced in a microaerophilic environment. Based on 16S rRNA gene sequence analysis, strain PEB0191(T) belongs to the family Orbaceae, and its closest relatives, with around 95 % sequence similarity, are species of the genera Orbus and Gilliamella. Phylogenetic analyses suggest that PEB0191(T) is more closely related to the genus Orbus than to the genus Gilliamella. In accordance with its evolutionary relationship, further similarities between strain PEB0191(T) and other members of the family Orbaceae were revealed based on the respiratory quinone type (ubiquinone 8), the fatty acid profile and the DNA G+C content. Interestingly, like strains of the genus Gilliamella, PEB0191(T) exhibited a high level of resistance to oxytetracycline. The similar levels of sequence divergence from the genera Gilliamella and Orbus and its uncertain phylogenetic position within the family Orbaceae indicate that strain PEB0191(T) represents a novel species of a new genus, with the proposed name Frischella perrara gen. nov., sp. nov. The type strain of Frischella perrara is PEB0191(T) ( = NCIMB 14821(T) = ATCC BAA-2450(T)).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Bees; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Gastrointestinal Tract; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

An alginate lyase-producing bacterium, designated AlyHP32(T), was isolated from the gut of sea urchin (Hemicentrotus pulcherrimus) obtained from the South Sea, Republic of Korea. Cells of strain AlyHP32(T) were Gram-reaction-negative and motile with a single polar flagellum. The strain grew with 1-6 % (w/v) NaCl (optimum 2-4 %) and at 4-30 °C (optimum 15-25 °C). Phylogenetic analysis based on sequences of the 16S rRNA gene and five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) revealed that strain AlyHP32(T) belonged to the genus Vibrio and formed a compact clade with the Vibrio splendidus group. However, DNA-DNA hybridization and fingerprints using the repetitive primers BOX and REP indicated that strain AlyHP32(T) was distinct from closely related species of the genus Vibrio. The major fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The DNA G+C content was 44.1 mol%. The predominant quinone was ubiquinone Q-8. Based on genotypic, phenotypic and DNA-DNA hybridization analysis, strain AlyHP32(T) represents a novel species of the genus Vibrio; the name Vibrio hemicentroti sp. nov. (type strain AlyHP32(T) = KCTC 32085(T) = DSM 26178(T)) is proposed for this novel taxon.

Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Hemicentrotus; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Polysaccharide-Lyases; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Vibrio

Two strains of Gram-stain-negative, rod-shaped bacteria were isolated from root nodules of the South African legume Rhynchosia ferulifolia and authenticated on this host. Based on phylogenetic analysis of the 16S rRNA gene, strains WSM3930 and WSM3937(T) belonged to the genus Burkholderia, with the highest degree of sequence similarity to Burkholderia terricola (98.84 %). Additionally, the housekeeping genes gyrB and recA were analysed since 16S rRNA gene sequences are highly similar between closely related species of the genus Burkholderia. The results obtained for both housekeeping genes, gyrB and recA, showed the highest degree of sequence similarity of the novel strains towards Burkholderia caledonica LMG 19076(T) (94.2 % and 94.5 %, respectively). Chemotaxonomic data, including fatty acid profiles and respiratory quinone data supported the assignment of strains WSM3930 and WSM3937(T) to the genus Burkholderia. DNA-DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains WSM3930 and WSM3937(T) from the most closely related species of the genus Burkholderia with validly published names. We conclude, therefore, that these strains represent a novel species for which the name Burkholderia rhynchosiae sp. nov. is proposed, with strain WSM3937(T) ( = LMG 27174(T) = HAMBI 3354(T)) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Bacterial; Fabaceae; Fatty Acids; Genes, Bacterial; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Root Nodules, Plant; Sequence Analysis, DNA; South Africa; Ubiquinone

Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Burkholderia, with the representative strain WSM5005(T) being most closely related to Burkholderia tuberum (98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus Burkholderia. Results of DNA-DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus Burkholderia with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005(T) = LMG 27175(T) = HAMBI 3357(T)) is proposed.

Topics: Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Bacterial; Fabaceae; Fatty Acids; Genotype; Likelihood Functions; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Root Nodules, Plant; Sequence Analysis, DNA; South Africa; Ubiquinone

Twelve strains of iron-oxidizing acidithiobacilli isolated from acidic sites throughout the world, including some previously shown by multi-locus sequence analyses and DNA-DNA hybridization to comprise a distinct species, were characterized in terms of their physiologies. The bacteria were shown to be obligately chemolithotrophic, acidophilic and mesophilic, and grew in both oxic and anoxic environments, using ferrous iron, reduced sulfur or hydrogen as electron donors and oxygen or ferric iron as electron acceptors. Some of the strains grew at lower pH than those reported for the two recognized iron-oxidizing Acidithiobacillus species, Acidithiobacillus ferrooxidans and Acidithiobacillus ferrivorans. Tolerance of transition metals and aluminium, and also specific rates of iron oxidation and reduction, were more similar to those of A. ferrooxidans (to which the strains are more closely related) than to A. ferrivorans. The name Acidithiobacillus ferridurans sp. nov. is proposed to accommodate the 12 strains, with the type strain being JCM 18981(T) ( = ATCC 33020(T)).

Topics: Acidithiobacillus; Bacterial Typing Techniques; Base Composition; Chemoautotrophic Growth; Fatty Acids; Genes, Bacterial; Hydrogen; Iron; Molecular Sequence Data; Multilocus Sequence Typing; Nucleic Acid Hybridization; Oxidation-Reduction; Sulfur; Ubiquinone

An aerobic, Gram-negative, rod-shaped bacterium with polar flagella, strain CC-AFH3(T), was isolated from an oil-contaminated site located in Kaohsiung county, Taiwan. Strain CC-AFH3(T) grew at 20-40 °C, pH 5.0-10.0 and <2 % (w/v) NaCl. 16S rRNA gene sequence analysis indicated that strain CC-AFH3(T) showed the greatest degree of similarity to Herbaspirillum soli SUEMI10(T) (96.5 %), H. aurantiacum SUEMI08(T) (96.3 %), H. canariense SUEMI03(T) (96.0 %), H. psychrotolerans PB1(T) (95.4 %) and members of other Herbaspirillum species (94.1-95.2 %), and lower similarity to members of other genera (<94 %). Phylogenetic analyses also positioned the novel strain in the genus Herbaspirillum as an independent lineage. The major fatty acids in strain CC-AFH3(T) were C10 : 0 3-OH, C12 : 0, C14 : 0 2-OH, C16 : 0, iso-C15 : 0 3-OH, C17 : 0 cyclo, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids of strain CC-AFH3(T) were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The predominant quinone was ubiquinone 8 (Q-8) and the DNA G+C content was 63.4 mol%. On the basis of 16S rRNA gene sequence analysis in combination with physiological and chemotaxonomic data, strain CC-AFH3(T) represents a novel species in a new genus, for which we propose the name Noviherbaspirillum malthae gen. nov., sp. nov.; the type strain of Noviherbaspirillum malthae is CC-AFH3(T) ( = BCRC 80516(T) = JCM 18414(T)). We also propose the reclassification of Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and 'Herbaspirillum psychrotolerans' as Noviherbaspirillum soli comb. nov. (type strain SUEMI10(T) = LMG 26149(T) = CECT 7840(T)), Noviherbaspirillum aurantiacum comb. nov. (type strain SUEMI08(T) = LMG 26150(T) = CECT 7839(T)), Noviherbaspirillum canariense comb. nov. (type strain SUEMI03(T) = LMG 26151(T) = CECT 7838(T)) and Noviherbaspirillum psychrotolerans comb. nov. (type strain PB1(T) = DSM 26001(T) = LMG 27282(T)), respectively. An emended description of Herbaspirillum seropedicae is also presented.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Herbaspirillum; Molecular Sequence Data; Petroleum Pollution; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants; Taiwan; Ubiquinone

A thermotolerant, alkalitolerant, Gram-stain-negative and strictly aerobic bacterium, designated strain YIM 77974(T), was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were light brown and circular. The strain grew in the presence of 0-3 % (w/v) NaCl (optimum, 0-1 %) and at pH 7.0-10.0 (optimum, pH 8.0) and 30-55 °C (optimum, 45 °C). The only quinone was Q-8 and the genomic DNA G+C content was 68.3 mol%. Major fatty acids (>10 %) were iso-C16 : 0, iso-C17 : 0, iso-C15 : 0 and iso-C11 : 0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, three unidentified phospholipids and two unidentified polar lipids. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, it is proposed that this strain should be classified as a representative of a novel genus and species, Rehaibacterium terrae gen. nov., sp. nov., in the family Xanthomonadaceae. The type strain is strain YIM 77974(T) ( = DSM 25897(T) = CCTCC AB 2012062(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Hot Temperature; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

A strictly aerobic, Gram-stain-negative, rod-shaped, non-motile and yellow-pigmented bacterial strain, designated KMM 6208(T), was isolated from a sea urchin. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that this novel isolate was affiliated to the class Gammaproteobacteria and formed a robust cluster with Arenicella xantha KMM 3895(T) with 98.2 % 16S rRNA gene sequence similarity. Strain KMM 6208(T) grew in the presence of 0.5-5 % NaCl and at a temperature range of 4-38 °C. The isolate was oxidase-positive and hydrolysed aesculin, casein, chitin, gelatin, starch and Tweens 40 and 80. The prevalent fatty acids of strain KMM 6208(T) were C16 : 1ω7c, iso-C16 : 0, iso-C18 : 0, C18 : 1ω7c and C16 : 0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified aminophospholipid, and the major isoprenoid quinone was Q-8. The DNA G+C content of strain KMM 6208(T) was 46.3 mol%. The DNA-DNA relatedness value of strain KMM 6208(T) with Arenicella xantha KMM 3895(T) was 5 %. Molecular data in a combination with phenotypic findings strongly suggest inclusion of this novel strain in the genus Arenicella as a representative of a novel species for which the name Arenicella chitinivorans sp. nov. is proposed. The type strain is KMM 6208(T) ( = KCTC 12711(T) = LMG 26983(T)).

Topics: Animals; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Japan; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Strongylocentrotus; Ubiquinone

A novel Gram-stain-negative, facultatively anaerobic, non-motile and short rod-shaped bacterium, strain KBL009(T), was isolated from the larval gut of Hermetia illucens. Strain KBL009(T) grew optimally at 37 °C, at pH 6.0 and with 1-2 % (w/v) NaCl. The 16S rRNA gene sequence of strain KBL009(T) showed 97.6 % similarity to that of Paenalcaligenes hominis CCUG 53761A(T) indicating its classification with the genus Paenalcaligenes. The major fatty acids were cyclo-C17 : 0, C16 : 0 and summed feature 2 (comprising C14 : 0 3-OH/iso-C16 : 1). The respiratory quinones were ubiquinone-8 (Q-8), predominating, and a minor amount of Q-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unknown aminolipid and five unknown polar lipids. The polyamine pattern contained predominantly putrescine and relatively high amounts of spermidine. The betaproteobacterial-specific 2-hydroxyputrescine could only be detected in trace amounts. The G+C content of genomic DNA was 56.1 mol%. Results from DNA-DNA hybridization with P. hominis KCTC 23583(T) unambiguously demonstrated that strain KBL009(T) represents a novel species in the genus Paenalcaligenes. Based on phenotypic, genotypic and phylogenetic characterization, the novel species Paenalcaligenes hermetiae sp. nov. is proposed. The type strain is KBL009(T) ( = KACC 16840(T) = JCM 18423(T)). An emended description of the genus Paenalcaligenes is also provided.

Topics: Alcaligenaceae; Animals; Bacterial Typing Techniques; Base Composition; Diptera; DNA, Bacterial; Fatty Acids; Gastrointestinal Tract; Larva; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Polyamines; Putrescine; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Two Gram-negative, facultatively anaerobic, rod-shaped bacteria, strains EF212(T) and PS125(T), were isolated from the octocorals Eunicea fusca and Plexaura sp., respectively. EF212(T) was isolated from a specimen of E. fusca collected off the coast of Florida, USA, and PS125(T) was isolated from a specimen of Plexaura sp. collected off the coast of Bimini, Bahamas. Analysis of the nearly full-length 16S rRNA gene sequences showed that these novel strains were most closely related to Endozoicomonas montiporae CL-33(T), E. elysicola MKT110(T) and E. numazuensis HC50(T) (EF212(T), 95.6-97.2 % identity; PS125(T), 95.1-96.4 % identity). DNA-DNA hybridization values among EF212(T), PS125(T), E. montiporae LMG 24815(T) and E. elysicola KCTC 12372(T) were far below the 70 % cut-off, with all values for duplicate measurements being less than 35 %. Both EF212(T) and PS125(T) required NaCl for growth and showed optimal growth at 2-3 % NaCl, 22-30 °C and pH 8.0. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), C16 : 0 and C14 : 0. The DNA G+C content of EF212(T) was 48.6 mol% and that of PS125(T) was 47.5 mol%. In addition to the genotypic differences observed between the two novel strains and related type strains, phenotypic and chemotaxonomic experiments also revealed differences between strains. Thus, strains EF212(T) and PS125(T) represent novel species of the genus Endozoicomonas, for which the names Endozoicomonas euniceicola sp. nov. and Endozoicomonas gorgoniicola sp. nov., respectively, are proposed. The type strains are EF212(T) ( = NCCB 100458(T) = DSM 26535(T)) for Endozoicomonas euniceicola sp. nov. and PS125(T) ( = NCCB 100438(T) = CECT 8353(T)) for Endozoicomonas gorgoniicola sp. nov. An emended description of the genus Endozoicomonas is also provided to encompass differences observed in the results of genotypic, chemotaxonomic and phenotypic tests compared from the original and amended genus descriptions.

Topics: Animals; Anthozoa; Bacterial Typing Techniques; Bahamas; Base Composition; DNA, Bacterial; Fatty Acids; Florida; Gammaproteobacteria; Genotype; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A facultatively anaerobic nitrogen-fixing bacterium, strain C7(T), was isolated from a permafrost cryopeg on the Yamal Peninsula, Russia. Comparative analysis of 16S rRNA gene sequences revealed that this bacterium was closely related to Celerinatantimonas diazotrophica S-G2-2(T) with a similarity of 95.5 %. Strain C7(T) differed from Celerinatantimonas diazotrophica in its ability to hydrolyse gelatin and inability to use d-mannose, melibiose, l-rhamnose, myo-inositol, lactose, lactulose, d-mannitol, trehalose, dl-lactate, glycogen or l-proline as sole carbon sources. In addition, strain C7(T) grew over a temperature range of 0-34 °C with optimum growth at 18-22 °C. The whole-cell fatty acid profile included C16 : 0, C16 : 1ω7, C18 : 1ω7, C17 cyclo and summed feature 2 [comprising C12 : 0 aldehyde and/or unknown fatty acid 10.913 (MIDI designation) and/or iso-C16 : 1/C14 : 0 3-OH]. The DNA G+C content was 44.7 mol%. Strain C7(T) is thus considered to represent a novel species, for which the name Celerinatantimonas yamalensis sp. nov. is proposed. The type strain is C7(T) ( = VKM B-2511(T) = DSM 21888(T)).

Topics: Bacterial Typing Techniques; Base Composition; Cold Temperature; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Glycolipids; Molecular Sequence Data; Nitrogen Fixation; Oxidoreductases; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Russia; Salts; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A novel strain, yH16, was isolated on nutrient agar from soil samples collected at KyungHee University, Suwon City, Republic of Korea. Cells of strain yH16(T) were short rods, Gram-negative-staining, motile and non-spore-forming, with a polar flagellum. Biochemical and molecular characterization revealed that this strain was most similar to Pseudogulbenkiania subflava BP-5(T). Further 16S rRNA gene sequencing studies revealed that the new strain clustered with Pseudogulbenkiania subflava BP-5(T) (95.9 % similarity), Paludibacterium yongneupense 5YN8-15(T) (95.2 % similarity), Gulbenkiania mobilis E4FC31-5(T) (94.6 % similarity) and Chromobacterium aquaticum CC-SE-YA-1(T) (93.9 % similarity). The isolate was able to grow at 25-40 °C, 0.3-2 % NaCl and pH 5.5-7. The DNA G+C content was 65.9 ± 1.0 mol%. The predominant fatty acids were summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH) and C(16:0). Ubiquinone 8 was the major respiratory quinone. It was evident from the data obtained that the strain should be classified as a novel species of the genus Pseudogulbenkiania. The name proposed for this taxon is Pseudogulbenkiania gefcensis sp. nov., and the type strain is yH16(T) (=KCCM 90100(T) = JCM 17850(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Neisseriaceae; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-staining-negative, rod-shaped, non-spore-forming bacterium isolated as a contaminant from a biopharmaceutical process (strain CCUG 53591(T)) was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence similarity data, this strain was clearly allocated to the genus Herminiimonas. Herminiimonas saxobsidens was shown to be the most closely related species on the basis of 16S rRNA gene sequence similarity (99.9 %), followed by Herminiimonas glaciei (99.6 %) and Herminiimonas arsenicoxydans (98.8 %). Strain ND5, previously reported as H. glaciei, but showing 100 % 16S rRNA gene sequence similarity to strain CCUG 53591(T), was included in the comparative study. Similarities to all other species of the genus Herminiimonas were below 98.0 %. Chemotaxonomic data (major ubiquinone, Q-8; major polar lipids, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; and major fatty acids, C(17 : 0) cyclo, C(19 : 0) cyclo ω8c and C(16 : 0,) with C(10 : 0) 3-OH as hydroxylated fatty acid) supported the affiliation of the isolate to the genus Herminiimonas. DNA-DNA hybridization results (mean values) for strain CCUG 53591(T) with H. saxobsidens CCUG 59860(T) (34 %), H. glaciei DSM 21140(T) (57 %), H. arsenicoxydans DSM 17148(T) (17 %) and Herminiimonas fonticola S-94(T) (11 %) clearly supported the separate taxonomic position of this strain. Strain ND5 showed DNA-DNA similarities of 78, 56 and 52 % to strain CCUG 53591(T), H. glaciei DSM 21140(T) and H. saxobsidens CCUG 59860(T), respectively. Phenotypic differentiation of the isolate from the most closely related species was possible by various features. Hence, strain CCUG 53591(T) represents a novel species, for which the name Herminiimonas contaminans sp. nov. is proposed, with the type strain CCUG 53591(T) ( = CCM 7991(T)). Strain ND5 is a second strain of this species.

Topics: Bacterial Typing Techniques; DNA, Bacterial; Drug Contamination; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; Polyamines; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-staining-negative, rod-shaped and non-spore-forming bacterium, designated strain 333-1-0411(T), was isolated from a soil sample collected from Namucuo, Tibet Autonomous Region, China and characterized in a taxonomic study using a polyphasic approach. The major fatty acid components of strain 333-1-0411(T) were summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0); its major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. Q-8 was the dominant ubiquinone, and the G+C content of the genomic DNA was 66.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain 333-1-0411(T) fell within the evolutionary radiation encompassed by the genus Massilia. The 16S rRNA gene sequence similarities between strain 333-1-0411(T) and recognized species of the genus Massilia ranged from 95.4 % to 97.2 %, and the most closely related strains were Massilia flava Y9(T) (97.2 %) and Massilia albidiflava 45(T) (97.0 %). However, the DNA-DNA relatedness values between strain 333-1-0411(T) and M. flava Y9(T) and M. albidiflava 45(T) were 20.2 % and 27.2 %, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic properties, strain 333-1-0411(T) is considered to represent a novel species of the genus Massilia, for which the name Massilia namucuonensis sp. nov. is proposed. The type strain is 333-1-0411(T) (= CGMCC 1.11014(T) = DSM 25159(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Tibet; Ubiquinone

A Gram-staining-negative, rod-shaped, non-spore-forming bacterium, designated strain E103(T), was isolated from the skin of the medical leech Hirudo verbana. 16S rRNA gene sequence analysis showed that the isolate was closely related to species of the genus Castellaniella. Castellaniella ginsengisoli DCY36(T) was shown to be the most closely related (98.4 % 16S rRNA gene sequence similarity), followed by Castellaniella denitrificans NKNTAU(T) and Castellaniella daejeonensis MJ06(T) (both 97.8 %), then Castellaniella caeni Ho-11(T) (97.5 %). Chemotaxonomic data (major ubiquinone, Q-8; major polar lipids, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine; predominant polyamine, putrescine with a moderate amount of 2-hydroxyputrescine; and major fatty acids, C(17 : 0) cyclo, C(16 : 0) and summed feature 4 comprising C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH) supported the affiliation of the isolate to the genus Castellaniella. DNA-DNA hybridization values with the type strains of all species of the genus Castellaniella were 23 % (reciprocal, 18 %) with C. ginsengisoli KCTC 22398(T), 20 % (26 %) with C. daejeonensis KCTC 22454(T), 11 % (58 %) with C. denitrificans DSM 11046(T) and 13 % (12 %) with C. caeni KCTC 12197(T)(.) Phenotypic differentiation of strain E103(T) from its closest neighbours was possible. Strain E103(T) therefore represents a novel species of the genus Castellaniella, for which the name Castellaniella hirudinis sp. nov. is proposed, with the type strain E103(T) ( = CCUG 62394(T) = LMG 26910(T)).

Topics: Alcaligenaceae; Animals; Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Leeches; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A facultatively anaerobic bacterium, strain CY01(T), isolated from subterranean forest sediment collected from Guangdong Province, China, was investigated using a polyphasic taxonomic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CY01(T) showed highest sequence similarities to Comamonas thiooxydans S23(T) (98.0 %), Comamonas testosteroni JCM 5832(T) (97.9 %), Comamonas koreensis KCTC 12005(T) (97.7 %) and Comamonas odontotermitis LMG 23579(T) (97.0 %). The major respiratory quinone was ubiquinone-8. The major cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). Based on the phylogenetic analysis, DNA-DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain CY01(T) was clearly distinguishable from all recognized species of the genus Comamonas and should be classified as a representative of a novel species of the genus, for which the name Comamonas guangdongensis sp. nov. is proposed. The type strain is CY01(T) ( = CCTCC AB 2011133(T) = KACC 16241(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; Comamonas; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Trees; Ubiquinone

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterial strain, BB-Mw22(T), was isolated from a tidal flat sediment of the South Sea in South Korea. It grew optimally at 30-37 °C, at pH 7.0-7.5 and in the presence of 2-3 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain BB-Mw22(T) belonged to the genus Kangiella and the cluster comprising Kangiella species and strain BB-Mw22(T) was clearly separated from other taxa. Strain BB-Mw22(T) exhibited 95.3-98.7 % 16S rRNA gene sequence similarity to the type strains of recognized Kangiella species. Strain BB-Mw22(T) contained Q-8 as the predominant ubiquionone and iso-C15 : 0 and iso-C11 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The DNA G+C content of strain BB-Mw22(T) was 48.9 mol%, and its mean DNA-DNA hybridization values with Kangiella geojedonensis YCS-5(T), Kangiella japonica JCM 16211(T) and Kangiella taiwanensis JCM 17727(T) were 14-28 %. Phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain BB-Mw22(T) is distinguishable from all recognized Kangiella species. On the basis of the data presented, strain BB-Mw22(T) is considered to represent a novel species of the genus Kangiella, for which the name Kangiella sediminilitoris sp. nov. is proposed. The type strain is BB-Mw22(T) ( = KCTC 23892(T)  = CCUG 62217(T)).

Topics: Alcanivoraceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Two strains, designated Sac-22(T) and Sac-41(T), were isolated from rhizosphere soil and rhizoplane of field-grown sugar cane clone Co86032. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Betaproteobacteria, their closest relatives being Pseudoduganella violaceinigra and Duganella zoogloeoides with 16S rRNA gene sequence pairwise similarities of 96.4-97.2 % to the two novel strains. Strains Sac-22(T) and Sac-41(T) shared a 16S rRNA gene sequence similarity value of 97.6 %. Cells of the two strains were Gram-reaction-negative, aerobic, motile and rod-shaped. Ubiquinone (Q-8) was the respiratory quinone and the predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The main cellular fatty acids were C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH, C17 : 0 cyclo, C10 : 0 3-OH and C12 : 0. The DNA G+C content of the genomic DNA was 56.4 mol% for strain Sac-22(T) and 54.9 mol% for strain Sac-41(T). Based on the results of 16S rRNA gene sequence analysis and physiological and biochemical characterization, that differentiated strains Sac-22(T) and Sac-41(T) from all recognized species of the genus Duganella, it was concluded that strains represent two novel species in the genus Duganella for which the names Duganella sacchari sp. nov. (type strain Sac-22(T) = KCTC 22381(T) = NCIMB 14475(T)) and Duganella radicis sp. nov. (type strain Sac-41(T) = KCTC 22382(T) = NCIMB 14476(T)) are proposed.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phosphatidylethanolamines; Phosphatidylglycerols; Phylogeny; Rhizosphere; RNA, Ribosomal, 16S; Saccharum; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

An aerobic, Gram-stain-negative, yellow-pigmented, non-motile, rod-shaped bacterium designated strain KMM 9005(T) was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9005(T) belonged to the genus Luteimonas and was most closely related to Luteimonas cucumeris KCTC 23627(T) (96.5 % sequence similarity) and Luteimonas aquatica LMG 24212(T) (96.1 % sequence similarity). Strain KMM 9005(T) was characterized by the presence of thin fimbriae, the major ubiquinone Q-8, by the predominance of iso-C17 : 1 followed by iso-C16 : 0, iso-C15 : 0 and iso-C17 : 0 in its fatty acid profile, weak hydrolytic capacity and the inability to assimilate most organic substrates. Based on these distinctive phenotypic characteristics and phylogenetic analysis, strain KMM 9005(T) represents a novel species of the genus Luteimonas, for which the name Luteimonas vadosa sp. nov. is proposed. The type strain is KMM 9005(T) ( = NRIC 0881(T) = JCM 18392(T)).

Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Geologic Sediments; Japan; Molecular Sequence Data; Oceans and Seas; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Water Microbiology; Xanthomonadaceae

Two novel Gram-stain-negative, chemoheterotrophic and strictly aerobic bacteria, strains GY2(T) and SPO729(T), were isolated from a tidal flat at Gwangyang Bay in Korea and a marine sponge sample from the Pacific Ocean, respectively. The two strains were halotolerant, catalase- and oxidase-positive, and non-motile rods. Optimum temperature and pH for growth of both strains were observed to be 35 °C and pH 7.0-7.5, but optimum salinity for strain SPO729(T) [2-3 % (w/v)] was slightly higher than that for strain GY2(T) (1-2 %). The major cellular fatty acids of both strains were C16 : 0, iso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c, C18 : 1ω7c, iso-C11 : 0 and iso-C11 : 0 3-OH. The genomic DNA G+C contents of strains GY2(T) and SPO729(T) were 55.1 and 57.9 mol%, respectively, and ubiquinone 8 (Q-8) was detected as the sole respiratory quinone from the two strains. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains GY2(T) and SPO729(T) formed tight phyletic lineages with members of the genus Microbulbifer. Strain GY2(T) was closely related to Microbulbifer okinawensis ABABA23(T) (98.2 %), strain SPO729(T) (98.0 %) and Microbulbifer donghaiensis CN85(T) (97.0 %); strain SPO729(T) was closely related to M. okinawensis ABABA23(T) (98.3 %) and M. donghaiensis CN85(T) (98.2 %). The DNA-DNA relatedness values of strain GY2(T) with M. okinawensis ABABA23(T), strain SPO729(T) and M. donghaiensis CN85(T) were 40.0±2.1 %, 13.1±3.9 % and 16.2±5.8 %, respectively, whereas those of strain SPO729(T) with M. okinawensis ABABA23(T) and M. donghaiensis CN85(T) were 48.0±4.0 % and 34.6±9.3 %, respectively. On the basis of phenotypic and molecular features, it is concluded that the two strains GY2(T) and SPO729(T) represent two novel species of the genus Microbulbifer, for which the names Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus are proposed; the type strains are GY2(T) ( = KACC 16189(T) = JCM 17800(T)) and SPO729(T) ( = KCCM 42667(T) = JCM 14507(T)), respectively.

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; Bays; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

A Gram-stain-negative, non-motile, facultatively anaerobic, acid-tolerant rod, designated strain DKE6(T), was isolated from an acidic biofilm (pH 2.5) harvested in the pyrite mine Drei Kronen und Ehrt in Germany. The isolate grew optimally at pH 5.5, between 25 and 30 °C and only with casein as the carbon and energy source; although a variety of sugars were tested as growth substrates, none supported growth of the isolate. During casein consumption, strain DKE6(T) produced ammonium, which led to an alkalinization of the medium. This is a possible strategy to raise the pH in the direct vicinity of the cell and hence modulate the pH towards the growth optimum. The predominant fatty acids (>5 %) were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. The DNA G+C content was 66.6 %. Strain DKE6(T) was not able to oxidize iron or thiosulfate. Iron reduction was detected. The isolate showed 93.3 % 16S rRNA gene sequence similarity to the most closely related cultivable strain, Dokdonella koreensis DS-123(T), but <93.2 % sequence similarity with other type strains of closely related type species of the Gammaproteobacteria. On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Gammaproteobacteria, for which we propose the name Metallibacterium scheffleri gen. nov., sp. nov. The type strain of the type species is DKE6(T) ( = DSM 24874(T) = JCM 17596(T)).

Topics: Bacterial Typing Techniques; Base Composition; Biofilms; Cytochromes; DNA, Bacterial; Fatty Acids; Germany; Iron; Mining; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sulfides; Ubiquinone; Xanthomonadaceae

Azotobacter vinelandii, a soil nitrogen fixing bacterium, produces alginate a polysaccharide with industrial and medical relevant applications. In this work, we characterized a miniTn5 mutant, named GG101, that showed a 14-fold increase in the specific production of alginate when grown diazotrophically on solid minimal medium comparing to the parental E strain (also named AEIV). Quantitative real-time reverse transcription PCR analysis indicated that this increased alginate production was due to higher expression levels of several biosynthetic alg genes such as algD. Sequencing of the locus interrupted in GG101 indicated that the miniTn5 was inserted in the positive strand, and 10 bp upstream the start codon of the gene ubiA, encoding the enzyme for the second step in the biosynthesis of ubiquinone (Q8). Both the transcription of ubiA and the content of Q8 are decreased in the mutant GG101 when compared to the wild-type strain E. Genetic complementation of mutant GG101 with a wild-type copy of the ubiCA genes restored the content of Q8 and reduced the production of alginate to levels similar to those of the parental E strain. Furthermore, respirometric analysis showed a reproducible decrease of about 8 % in the respiratory capacity of mutant GG101, at exponential phase of growth in liquid minimal medium. Collectively, our data show that a decreased content in Q8 results in higher levels of alginate in A. vinelandii.

Topics: Alginates; Azotobacter vinelandii; Biosynthetic Pathways; Culture Media; DNA Transposable Elements; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genetic Complementation Test; Glucuronic Acid; Hexuronic Acids; Mutagenesis, Insertional; Nitrogen Fixation; Real-Time Polymerase Chain Reaction; Ubiquinone

A novel Gram-stain-negative, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain C7(T), was isolated from the gut of the butterfly Sasakia charonda. Strain C7(T) grew optimally at 20-25 °C, at pH 7-8 and with 1 % (w/v) NaCl. The strain was negative for oxidase activity but positive for catalase activity. The 16S rRNA gene sequences of strain C7(T) and Orbus hercynius CN3(T) shared 96.8 % similarity. The major fatty acids identified were C14 : 0, C16 : 0, C18 : 1ω7c and summed feature 2 (comprising C14 : 0 3-OH/iso-C16 : 1). The major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain C7(T) were phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid and two unidentified aminophospholipids. The G+C content of the genomic DNA extracted from strain C7(T) was 32.1 mol%. Taken together, the phenotypic, genotypic and phylogenetic analyses indicate that strain C7(T) represents a novel species of the genus Orbus, for which the name Orbus sasakiae sp. nov. is proposed. The type strain is C7(T) ( = KACC 16544(T) = JCM 18050(T)). An emended description of the genus Orbus is provided.

Topics: Animals; Bacterial Typing Techniques; Base Composition; Butterflies; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Gastrointestinal Tract; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel exopolysaccharide-producing bacterium, designated strain k53(T), was isolated from sediment from the Arabia Sea, Indian Ocean. The strain was Gram-negative, motile, strictly aerobic, oxidase-positive and catalase-positive, and required Na(+) for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile mainly consisted of C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The DNA G+C content was 43 mol%. 16S rRNA gene sequence analysis suggested that strain k53(T) is a member of the genus Pseudoalteromonas. Strain k53(T) exhibited close phylogenetic affinity to Pseudoalteromonas lipolytica LMEB 39(T) (98.0% 16S rRNA gene sequence similarity) and Pseudoalteromonas donghaensis HJ51(T) (97.3 %).The DNA-DNA reassociation values between strain k53(T) and P. lipolytica JCM 15903(T) and P. donghaensis LMG 24469(T) were 17 % and 12 %, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analysis based on the 16S rRNA gene sequence and DNA-DNA relatedness data, the isolate merits classification as a representative of a novel species, for which the name Pseudoalteromonas arabiensis is proposed. The type strain of this species is k53(T) ( = JCM 17292(T) = NCIMB 14688(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Geologic Sediments; Indian Ocean; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Polysaccharides, Bacterial; Pseudoalteromonas; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Gut-associated bacteria were isolated in axenic culture from the honey bee Apis mellifera and the bumble bees Bombus bimaculatus and B. vagans and are here placed in the novel genera and species Snodgrassella alvi gen. nov., sp. nov. and Gilliamella apicola gen. nov., sp. nov. Two strains from A. mellifera were characterized and are proposed as the type strains of Snodgrassella alvi (type strain wkB2(T) =NCIMB 14803(T) =ATCC BAA-2449(T) =NRRL B-59751(T)) and Gilliamella apicola (type strain wkB1(T) =NCIMB 14804(T) =ATCC BAA-2448(T)), representing, respectively, phylotypes referred to as 'Betaproteobacteria' and 'Gammaproteobacteria-1'/'Gamma-1' in earlier publications. These strains grew optimally under microaerophilic conditions, and did not grow readily under a normal atmosphere. The predominant fatty acids in both strains were palmitic acid (C16:0) and cis-vaccenic acid (C18:1ω7c and/or C18:1ω6c), and both strains had ubiquinone-8 as their major respiratory quinone. The DNA G+C contents were 41.3 and 33.6 mol% for wkB2(T) and wkB1(T), respectively. The Snodgrassella alvi strains from honey bees and bumble bees formed a novel clade within the family Neisseriaceae of the Betaproteobacteria, showing about 94% 16S rRNA gene sequence identity to their closest relatives, species of Stenoxybacter, Alysiella and Kingella. The Gilliamella apicola strains showed the highest 16S rRNA gene sequence identity to Orbus hercynius CN3(T) (93.9%) and several sequences from uncultured insect-associated bacteria. Phylogenetic reconstruction using conserved, single-copy amino acid sequences showed Gilliamella apicola as sister to the order 'Enterobacteriales' of the Gammaproteobacteria. Given its large sequence divergence from and basal position to the well-established order 'Enterobacteriales', we propose to place the clade encompassing Gilliamella apicola and O. hercynius in a new family and order, Orbaceae fam. nov. and Orbales ord. nov.

Topics: Animals; Bacterial Typing Techniques; Base Composition; Bees; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Gastrointestinal Tract; Molecular Sequence Data; Neisseriaceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Symbiosis; Ubiquinone

A novel strain, named S4(T), was obtained from industrial wastewater in Xiaoshan, Zhejiang Province, China. Cells were Gram-negative, neutrophilic and non-spore-forming and moved by means of a polar flagellum. Normal cells were 0.8-0.9 × 1.3-1.9 µm and the cells elongated to 10-25 µm when cultivated at high temperatures. Strain S4(T) grew at 15-50 °C (optimum at 48 °C), pH 5.5-8.5 (optimum 7.0-7.5) and 0-2% (optimum 0.5%) (w/v) NaCl. Ubiquinone-8 was the predominant respiratory quinone. C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and C17:0 cyclo were the major cellular fatty acids. The major 3-OH fatty acid was C10:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminoglycolipid. The genomic DNA G+C content was 68.8 mol%. Based on 16S rRNA gene sequences alignment, the most closely related strains were members of the genera Comamonas (94.6-95.6% similarities), Giesbergeria (94.9-95.6%), Acidovorax (94.8-95.4%), Brachymonas (94.1-95.2%) and Macromonas (95.1%). Phylogenetic analysis showed the closest relatives of strain S4(T) were members of the genus Macromonas. Based on phenotypic and phylogenetic characteristics, we suggest that strain S4(T) represents a novel species of a new genus of the family Comamonadaceae, for which the name Extensimonas vulgaris gen. nov., sp. nov. is proposed. The type strain of Extensimonas vulgaris is S4(T) (=CGMCC 1.10977(T)=JCM 17803(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; Comamonadaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Wastewater; Water Microbiology

A novel biosurfactant-producing strain, designated YW1(T), was isolated from agricultural soil. Its taxonomic position was investigated using a polyphasic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YW1(T) was a member of the genus Comamonas, and showed highest sequence similarities to Comamonas aquatica LMG 2370(T) (98.5%), Comamonas kerstersii LMG 3475(T) (97.7%) and Comamonas terrigena LMG 1253(T) (97.7%). Furthermore, DNA-DNA hybridization experiments against these three strains gave results that were clearly lower than 70% DNA-DNA similarity, and consequently confirmed that this new strain does not belong to a previously described species of the genus Comamonas. The major respiratory quinone was ubiquinone-8. The major fatty acids (>5%) were C16:0 (30.1%), summed feature 3 (C16:1ω6c and/or C16:1ω7c; 25.4%), summed feature 8 (C18:1ω6c and/or C18:1ω7c; 15.3%), C17:0 cyclo (7.4%) and C14:0 (5.8%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown phospholipids and unknown lipids. Based on the phylogenetic analysis, DNA-DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain YW1(T) was clearly distinguishable from all species of the genus Comamonas with validly published names and should be classified as a representative of a novel species of the genus Comamonas, for which the name Comamonas jiangduensis sp. nov. is proposed. The type strain is YW1(T) (=CCTCC AB 2012033(T)=KACC 16697(T)).

Topics: Agriculture; Bacterial Typing Techniques; Base Composition; China; Comamonas; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oryza; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Surface-Active Agents; Ubiquinone

A moderately halophilic, slightly acidophilic, aerobic bacterium, designated strain YTM-1(T), was isolated from the body surface of Malacocottus gibber. Cells were Gram-stain-negative, short rods or cocci, approximately 0.9-1.1 µm long and 1.0-1.8 µm wide. Strain YTM-1(T) was able to grow with 1-30% NaCl (optimum, 7.5-10%, w/v), at 4-30 °C (optimum, 20-25 °C) and at pH 3.8-9.5 (optimum, pH 5.0-5.5). Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain YTM-1(T) belonged to the genus Salinisphaera with low similarity values to the type strains of recognized species of this genus (<94.8-94.4%). The polar lipids of strain YTM-1(T) consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, three unknown phospholipids and one unknown lipid. The predominant isoprenoid quinone was Q-8. The major fatty acids were C19:0ω8c cyclo, C18:1ω7c, C16:1ω5c and C16:0. The DNA G+C content of strain YTM-1(T) was 67.3 mol%. These phylogenetic, physiological and chemotaxonomic data indicated that strain YTM-1(T) represents a novel species of the genus Salinisphaera, for which the name Salinisphaera japonica sp. nov. is proposed. The type strain is YTM-1(T) (=JCM 18087(T)=CECT 8012(T)). An emended description of the genus Salinisphaera is also proposed.

Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fishes; Gammaproteobacteria; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Two bacterial strains, designated JAM1(T) and JAM7(T), were isolated from a methanol-fed denitrification system treating seawater at the Montreal Biodome, Canada. They were affiliated within the genus Methylophaga of the Gammaproteobacteria by analysis of the 16S rRNA gene sequences. Strain JAM1(T) had the capacity to grow under denitrifying conditions by reducing nitrate into nitrite which is unique among the species of the genus Methylophaga. Major fatty acids were C16:1ω7c or ω6c, C16:0 and C18:1ω7c or ω6c. The major ubiquinone was Q8. Both strains required vitamin B12 and Na(+) ions for growth. The genomes of strains JAM1(T) and JAM7(T) have been completely sequenced and showed a DNA G+C content of 44.7 mol% and 47.8 mol%, respectively. Growth occurred at pH 6-11 and at 0.5-8% NaCl. Both genomes contained predicted ORFs encoding the key enzymes of the ribulose monophosphate pathway. Also, operons encoding two nitrate reductases (Nar), two nitric oxide reductases (Nor), one nitrous oxide reductase (Nos) and one truncated nitrite reductase (NirK) were clustered in a 67 kb chromosomal region in strain JAM1(T). No such operons were found in strain JAM7(T). These results supported the affiliation of the two strains as novel species within the genus Methylophaga. The names Methylophaga nitratireducenticrescens sp. nov. for type strain JAM1(T) (=DSM 25689(T)=ATCC BAA-2433(T)) and Methylophaga frappieri sp. nov. for type strain JAM7(T) (=DSM 25690(T)=ATCC BAA-2434(T)) are proposed.

Topics: Bacterial Typing Techniques; Base Composition; Biofilms; Canada; Denitrification; DNA, Bacterial; Fatty Acids; Methanol; Nitrates; Phylogeny; Piscirickettsiaceae; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone; Water Purification

The bacterial strain C3(T) was isolated from permafrost soil in Beijicun, Mohe County, Heilongjiang province, China. Cells of strain C3(T) were Gram-stain-negative rods, 0.3-0.4 µm in diameter and 1.0-2.6 µm in length. Strain C3(T) was strictly aerobic. Growth occurred at 15-37 °C but not at 4 or 42 °C, at pH 5.0-9.0 (optimum pH 6.0-7.0) and in the presence of 0-8 g NaCl l(-1) (optimum 0-1 g l(-1)). The analysis of 16S rRNA gene sequences indicated that strain C3(T) was phylogenetically related to members of the genus Undibacterium, with similarities ranging from 94.7 to 96.5%. Strain C3(T) contained ubiquinone 8 as the major respiratory quinone. The major cellular fatty acids were summed feature 3 (C16:1ω7c/C16:1ω6c), C17:0 cyclo, straight-chain C16:0, C12:0 and C10:0, unsaturated C18:1ω7c and hydroxylated fatty acids C10:0 3-OH and C12:0 2-OH. The polar lipids were mainly phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamines were putrescine and 2-hydroxyputrescine. The DNA G+C content was 57.4 mol% (determined from Tm). Based on these results, it is concluded that strain C3(T) represents a novel species of the genus Undibacterium, for which the name Undibacterium terreum sp. nov. is proposed, with C3(T) (=CGMCC 1.10998(T)=NBRC 108789(T)) representing the type strain.

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Oxalobacteraceae; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A bacterial strain, A2-57(T), recovered from a water sample collected in a uranium mine was taxonomically studied in detail. This strain was a Gram-reaction-negative, rod-shaped bacterium that grew optimally at 25 °C and at pH 6.0-7.0 and had a DNA G+C content of 55.0 mol%. Ubiquinone 8 (UQ-8) was the predominant respiratory quinone and the major fatty acids were C16:0, C17:0 cyclo, summed feature 3 (C16:1ω6c and/or ω7c and/or C15:0 iso 2-OH) and C18:1ω7c. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain A2-57(T) belonged to the family Oxalobacteraceae and formed a distinct branch with Glaciimonas immobilis Cr9-30(T). Strain A2-57(T) shared approximately 97.3% 16S rRNA sequence similarity with G. immobilis Cr9-30(T) and also showed high sequence similarity with members of the genera Herbaspirillum (96.3-97.0%) and Collimonas (96.2-97.0%). Although phylogenetically closely related to the type strain of G. immobilis, the low level of DNA-DNA hybridization between the two strains (21.6%) and several physiological and biochemical properties indicated that the novel strain could be clearly distinguished from G. immobilis LMG 25547(T). Therefore, it is concluded that strain A2-57(T) represents a novel species of the genus Glaciimonas, for which the name Glaciimonas singularis sp. nov. is proposed. The type strain is A2-57(T) (=CIP 110539(T)=LMG 27070(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Mining; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; Portugal; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Uranium; Wastewater; Water Microbiology

Two Gram-negative, aerobic, rod-shaped bacteria, designated strains SW104(T) and X07, were isolated from a seawater sample collected from the Indian Ocean. The strains grew at a temperature range of 12-50 °C (optimum, 35-37 °C), and at pH 6.0-9.0 (optimum pH 7.0-7.5). The predominant cellular fatty acids of strain SW104(T) were iso-C15 : 0 (41.2 %), iso-C17 : 1ω9c (15.2 %) and iso-C17 : 0 (11.1 %). The major respiratory quinone was ubiquinone 8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C contents of strains SW104(T) and X07 were 49.8 and 49.5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the new isolates were related to members of the genus Idiomarina, showing the highest similarity with Idiomarina taiwanensis PIT1(T) and Idiomarina maritima 908087(T) (96.1 and 95.9 %, respectively). On the basis of phenotypic, genotypic and phylogenetic characteristics, it is proposed that strains SW104(T) and X07 should be described as representatives of a novel species of the genus Idiomarina, for which the name Idiomarina indica sp. nov. is proposed. The type strain is SW104(T) ( = CGMCC 1.10824(T) = JCM 18138(T)).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Indian Ocean; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A rod-shaped, Gram-negative, non-motile, aerobic and non-endospore forming bacterium, designated strain DD-13(T), was isolated from the mangrove ecosystem of Goa, India. Strain DD-13(T) degraded polysaccharides such as agar, alginate, chitin, cellulose, laminarin, pectin, pullulan, starch, carrageenan, xylan and β-glucan. The optimum pH and temperature for growth was 7 and 36 °C, respectively. The strain grew optimally in the presence of 3 % NaCl (w/v). The DNA G+C content was 61.4 mol%. The predominant fatty acid of strain DD-13(T) was iso-C15 : 0. Ubiquinone-8 was detected as the major respiratory lipoquinone. Phylogenetic studies based on 16S rRNA gene sequence analysis demonstrated that strain DD-13(T) formed a coherent cluster with species of the genus Microbulbifer. Strain DD-13(T) exhibited 16S rRNA gene sequence similarity levels of 98.9-97.1 % with Microbulbifer hydrolyticus IRE-31(T), Microbulbifer salipaludis JCM 11542(T), Microbulbifer agarilyticus JAMB A3(T), Microbulbifer celer KCTC 12973(T) and Microbulbifer elongatus DSM 6810(T). However, the level of DNA-DNA relatedness between strain DD-13(T) and the five type strains of these species of the genus Microbulbifer were in the range of 26-33 %. Additionally, strain DD-13(T) demonstrates several phenotypic differences from these type strains of species of the genus Microbulbifer. Thus strain DD-13(T) represents a novel species of the genus Microbulbifer, for which the name Microbulbifer mangrovi sp. nov. is proposed with the type strain DD-13(T) ( = KCTC 23483(T) = JCM 17729(T)).

Topics: Alteromonadaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; India; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33(T), was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33(T) grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33(T) contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33(T) was most closely related to Gibbsiella quercinecans FRB 97(T) and Gibbsiella dentisursi NUM 1720(T), with 98.7 % similarities. DNA-DNA hybridization experiments indicated less than 40.7 ± 2 % relatedness to the closest phylogenetic species, G. quercinecans FRB 97(T). The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33(T) represents a novel species within the genus Gibbsiella, for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33(T) ( = KACC 16707(T) = JCM 18389(T)). An emended description of the genus Gibbsiella is also proposed.

Topics: Animals; Bacterial Typing Techniques; Base Composition; Butterflies; DNA, Bacterial; Enterobacteriaceae; Fatty Acids; Intestines; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115(T), was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115(T) was shown to belong to the Gammaproteobacteria, adjacent to members of the genera Marinicella, Arenicella and Kangiella, sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria. The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115(T) included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115(T) should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115(T) ( = CIP 110343(T) = DSM 25350(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Mediterranean Sea; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Two novel violet-pigmented, Gram-negative, rod-shaped, non-motile bacteria, designated strains M4-16(T) and M4-9, were isolated from sediment from an Arctic glacier. The predominant fatty acids of both strains were C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), C16 : 0, C14 : 0 and C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8) and both strains contained ubiquinone-8 as the respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified phospholipids and one unidentified aminolipid. 16S rRNA gene sequence analysis indicated that strains M4-16(T) and M4-9 were members of the genus Iodobacter and closely related to Iodobacter fluviatilis ATCC 33051(T) with pairwise sequence similarity of 98.9 %. The DNA-DNA relatedness between strains M4-9 and M4-16(T) was 92.5 %, while strains M4-9 and M4-16(T) had DNA-DNA relatedness values of 21.5 and 18.2 %, respectively, with Iodobacter fluviatilis JCM 9044(T). The RAPD-PCR banding patterns of strains M4-9 and M4-16(T) were similar but differed from that of Iodobacter fluviatilis JCM 9044(T). Based on data from the current polyphasic study, strains M4-16(T) and M4-9 represent a novel species of the genus Iodobacter, for which the name Iodobacter arcticus sp. nov. is proposed. The type strain of Iodobacter arcticus is M4-16(T) ( = CIP 1103011(T) = MTCC 11351(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Ice Cover; Molecular Sequence Data; Neisseriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

During a study intended to screen for agar-degrading bacteria, strain M2-5T was isolated from black sand off the shore of Jeju Island, Republic of Korea. Strain M2-5T exhibited agarase activity; the β-agarase gene of the isolate had 62 % amino acid sequence identity to the β-agarase gene of Microbulbifer thermotolerans JAMB A94T. The isolate was closely related to members of the genus Simiduia but was clearly discernible from reported Simiduia species, based on a polyphasic analysis. Cells of strain M2-5T were Gram-negative, catalase- and oxidase-positive, motile rods. The DNA G+C content was 53.3 mol%. The predominant isoprenoid quinone was Q-8. The major cellular fatty acids were C17:1ω8c (25.9 %), summed feature 3 (iso-C(15 : 0) 2-OH and/or C16:1ω7c; 17.2 %) and C17:0 (15.0 %). Phylogenetic analysis using 16S rRNA gene sequences showed that strain M2-5T had 96.6 % gene sequence similarity to Simiduia agarivorans SA1T, the most closely related type strain of the genus Simiduia. These results suggest that strain M2-5T represents a novel species in the genus Simiduia, for which the name Simiduia areninigrae sp. nov. is proposed; the type strain is M2-5T (=KCTC 23293T=NCAIM B 02424T).

Topics: Agar; Alteromonadaceae; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Glycoside Hydrolases; Molecular Sequence Data; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Silicon Dioxide; Ubiquinone

Childhood cerebellar ataxias, and particularly congenital ataxias, are heterogeneous disorders and several remain undefined. We performed a muscle biopsy in patients with congenital ataxia and children with later onset undefined ataxia having neuroimaging evidence of cerebellar atrophy. Significant reduced levels of Coenzyme Q10 (COQ10) were found in the skeletal muscle of 9 out of 34 patients that were consecutively screened. A mutation in the ADCK3/Coq8 gene (R347X) was identified in a female patient with ataxia, seizures and markedly reduced COQ10 levels. In a 2.5-years-old male patient with non syndromic congenital ataxia and autophagic vacuoles in the muscle biopsy we identified a homozygous nonsense mutation R111X mutation in SIL1 gene, leading to early diagnosis of Marinesco-Sjogren syndrome. We think that muscle biopsy is a valuable procedure to improve diagnostic assesement in children with congenital ataxia or other undefined forms of later onset childhood ataxia associated to cerebellar atrophy at MRI.

Topics: Biopsy; Cerebellar Ataxia; Child, Preschool; Chromatography, High Pressure Liquid; DNA Mutational Analysis; Female; Guanine Nucleotide Exchange Factors; Humans; Male; Muscle, Skeletal; Mutation; Ubiquinone

A bacterial isolate, designated strain TS3(T), was isolated from soil collected from a metal mine in Tieshan District, Daye City, Hubei Province, in central China. Cells of this strain were Gram-negative, motile and rod-shaped. The strain had ubiquinone Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids and summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(16:0) and C(18:1)ω7c as the major fatty acids. The G+C content was 65.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TS3(T) was most closely related to Massilia niastensis 5516S-1(T) (98.5%), Massilia consociata CCUG 58010(T) (97.6%), Massilia aerilata 5516S-11(T) (97.4%) and Massilia varians CCUG 35299(T) (97.2%). DNA-DNA hybridization revealed low relatedness between strain TS3(T) and M. niastensis KACC 12599(T) (36.5%), M. consociata CCUG 58010(T) (27.1%), M. aerilata KACC 12505(T) (22.7%) and M. varians CCUG 35299(T) (46.5%). On the basis of phenotypic and phylogenetic characteristics, strain TS3(T) belongs to the genus Massilia, but is clearly differentiated from other members of the genus. The strain represents a novel species, for which the name Massilia tieshanensis sp. nov. is proposed. The type strain is TS3(T) ( = CCTCC AB 2010202(T)  = KACC 14940(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Mining; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Bacterial strains 2APBS1(T) and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification. Cells of strain 2APBS1(T) and 116-2 were Gram-negative, non-spore-forming rods, 3-5 µm long and 0.25-0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1(T) and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus Rhodanobacter. Although strains 2APBS1(T) and 116-2 shared high 16S rRNA gene sequence similarity with Rhodanobacter thiooxydans LCS2(T) (>99 %), levels of DNA-DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1(T) and 116-2 are considered to represent a single novel species of the genus Rhodanobacter, for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1(T) ( = DSM 23569(T) = JCM 17641(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Groundwater; Molecular Sequence Data; Nitrates; Phylogeny; Radioactive Waste; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Uranium; Water Pollution, Chemical; Water Pollution, Radioactive; Xanthomonadaceae

A novel Gram-staining-negative, facultatively anaerobic, motile and rod-shaped bacterium, designated strain LHW37(T), was isolated from a dead ark clam collected on the south coast of Korea. The novel strain grew optimally at 37 °C, at pH 7.0-8.0 and with 2% (w/v) NaCl. The predominant cellular fatty acids were C(18:1)ω7c and summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH). The major isoprenoid quinone was ubiquinone-8 (Q-8) and the predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain was most closely related to Neptunomonas japonica JAMM 0745(T) (97.1% sequence similarity). The genomic DNA G+C content of strain LHW37(T) was 48.2 mol%. The DNA-DNA relatedness values recorded in hybridization experiments between the novel strain and its closest known relative were ≤ 18%. Based on the phenotypic, genotypic and phylogenetic data, strain LHW37(T) represents a novel species belonging to the genus Neptunomonas for which the name Neptunomonas concharum sp. nov. is proposed. The type strain is LHW37(T) (=KACC 15543(T) =JCM 17730(T)). An emended description of the genus Neptunomonas is also provided.

Topics: Animals; Bacterial Typing Techniques; Base Composition; Bivalvia; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Oceanospirillaceae; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

The taxonomic positions of two Gram-staining-negative, psychrophilic bacteria, which were isolated from alpine glacier cryoconite and designated strains Cr4-12(T) and Cr4-35(T), were investigated using a polyphasic approach. Both novel strains contained ubiquinone Q-8 as the sole quinone, summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c) and C(16:0) as the dominant cellular fatty acids, putrescine and 2-hydroxyputrescine as the major polyamines, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C contents of strains Cr4-12(T) and Cr4-35(T) were 61.3 mol% and 60.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the genus Polaromonas. Although the 16S rRNA gene sequences of strains Cr4-12(T) and Cr4-35(T) were very similar (98.7% sequence similarity), hybridizations indicated a DNA-DNA relatedness value of only 26.9% between the two novel strains. In pairwise comparisons with the type strains of recognized Polaromonas species, strains Cr4-12(T) and Cr4-35(T) showed 16S rRNA gene sequence similarities of 96.4-98.5% and 96.5-98.4%, respectively. Based on the phenotypic and phylogenetic evidence and DNA-DNA relatedness data, strains Cr4-12(T) and Cr4-35(T) represent two novel species within the genus Polaromonas, for which the names Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., respectively, are proposed. The type strain of Polaromonas glacialis sp. nov. is Cr4-12(T) (=DSM 24062(T) =LMG 26049(T) =KACC 15089(T)) and that of Polaromonas cryoconiti sp. nov. is Cr4-35(T) (=DSM 24248(T) =LMG 26050(T) =KACC 15090(T)).

Topics: Austria; Bacterial Typing Techniques; Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Ice Cover; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Two Gram-reaction-negative, motile bacteria, designated strains MJ01(T) and MJ14, were isolated from sludge collected from the Daejeon sewage disposal plant in South Korea. The taxonomic positions of both strains were determined using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strains MJ01(T) and MJ14 appeared indistinguishable and to be most closely related to members of the genus Rhodanobacter in the family Xanthomonadaceae of the Gammaproteobacteria (96.4-98.8% sequence similarity). Strain MJ01(T) exhibited a relatively high level of DNA-DNA relatedness with strain MJ14 (89.3 %) but relatively low DNA-DNA relatedness values with established species in the genus Rhodanobacter (<60 %). The genomic DNA G+C contents of strains MJ01(T) and MJ14 were 65.3 and 64.8 mol%, respectively. The major respiratory quinone of both novel strains was the ubiquinone Q-8. The major fatty acids of both strains were iso-C(15 : 0), iso-C(16 : 0), iso-C(17:0) and iso-C(17 : 1)ω9c, and the polar lipid profiles of the two strains contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and minor amounts of unidentified aminophospholipids and phospholipids. Based on the phenotypic, genotypic and phylogenetic evidence, strains MJ01(T) and MJ14 represent a single novel species in the genus Rhodanobacter, for which the name Rhodanobacter caeni sp. nov. is proposed. The type strain is MJ01(T) ( = KCTC 22449(T) = JCM 16242(T)), with MJ14 ( = KCTC 22460 = JCM 16243) as a reference strain.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Sewage; Ubiquinone; Xanthomonadaceae

A Gram-negative, aerobic and non-motile rod, designated Y4(T), was isolated from a cucumber leaf from Pinggu District, east Beijing, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Y4(T) was most closely related to Luteimonas aquatica RIB1-20(T) (96.7% 16S rRNA gene sequence similarity). DNA-DNA relatedness between strain Y4(T) and L. aquatica RIB1-20(T) was 42.5 ± 3.9%. The predominant fatty acids were iso-C(15:0), iso-C(17:1)ω9c, iso-C(16:0) and iso-C(17:0). The major ubiquinone was Q-8. The DNA G+C content of the type strain was 69.9 mol%. Based on the evidence above, strain Y4(T) represents a novel species of the genus Luteimonas, for which the name Luteimonas cucumeris sp. nov. is proposed. The type strain is Y4(T) ( = CGMCC 1.10821(T) = KCTC 23627(T)).

Topics: Bacterial Typing Techniques; Base Composition; China; Cucumis sativus; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Xanthomonadaceae

The bacterial strain LH2-2(T) was isolated from freshwater of Longhu Lake, a slightly alkaline lake (pH 8.8) in north-east China. Cells of strain LH2-2(T) were Gram-staining-negative, non-spore-forming rods, 0.3-0.5 µm wide and 2.0-4.0 µm long. Cells were motile by means of a single polar flagellum. The strain was strictly aerobic and heterotrophic and oxidase- and catalase-positive. Growth occurred at 0-36 °C (optimum, 26-34 °C), pH 6.5-11 (optimum, pH 8.0-8.6) and in the presence of 0-2 % (w/v) NaCl (optimum, 1%). Strain LH2-2(T) contained Q-8 as the major respiratory quinone. The major fatty acids were summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH; 21.9%), C(17:1)ω8c (18.9%), C(18:1)ω7c (16.4%) and C(16:0) (12.7%) after growth on marine agar 2216. The DNA G+C content was 47 mol% (T(m)). The 16S rRNA gene and a conserved portion of the gyrB gene were sequenced and used for phylogenetic analyses. Phylogenetic trees based on 16S rRNA gene and gyrB sequences showed that strain LH2-2(T) was associated with the genus Rheinheimera and closely related to the type strains of Rheinheimera species, and showed the highest 16S rRNA gene sequence similarity to Rheinheimera pacifica KMM 1406(T) (97.4%), R. aquimaris SW-353(T) (97.1%) and R. chironomi K19414(T) (96.5%). The DNA-DNA relatedness of strain LH2-2(T) to R. pacifica NBRC 103167(T), R. aquimaris JCM 14331(T) and R. chironomi LMG 23818(T) was 39, 31 and 23%, respectively. Based on these results, it is concluded that strain LH2-2(T) represents a novel species of the genus Rheinheimera, for which the name Rheinheimera longhuensis sp. nov. is proposed. The type strain is LH2-2(T) ( = CGMCC 1.7003(T)  = NBRC 105632(T)). An emended description of the genus Rheinheimera is also provided.

Topics: Bacterial Typing Techniques; Base Composition; China; Chromatiaceae; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Lakes; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone; Water Microbiology

The Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) is the prototype of a novel class of flavoproteins carrying a riboflavin phosphate bound to serine or threonine by a phosphodiester bond to the ribityl side chain. This membrane-bound, respiratory complex also contains one non-covalently bound FAD, one non-covalently bound riboflavin, ubiquinone-8 and a [2Fe-2S] cluster. Here, we report the quantitative analysis of the full set of flavin cofactors in the Na(+)-NQR and characterize the mode of linkage of the riboflavin phosphate to the membrane-bound NqrB and NqrC subunits. Release of the flavin by β-elimination and analysis of the cofactor demonstrates that the phosphate group is attached at the 5'-position of the ribityl as in authentic FMN and that the Na(+)-NQR contains approximately 1.7mol covalently bound FMN per mol non-covalently bound FAD. Therefore, each of the single NqrB and NqrC subunits in the Na(+)-NQR carries a single FMN. Elimination of the phosphodiester bond yields a dehydro-2-aminobutyrate residue, which is modified with β-mercaptoethanol by Michael addition. Proteolytic digestion followed by mass determination of peptide fragments reveals exclusive modification of threonine residues, which carry FMN in the native enzyme. The described reactions allow quantification and localization of the covalently attached FMNs in the Na(+)-NQR and in related proteins belonging to the Rhodobacter nitrogen fixation (RNF) family of enzymes. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).

Topics: Bacterial Proteins; Catalytic Domain; Flavin Mononucleotide; Ion Transport; NADH, NADPH Oxidoreductases; Peptides; Proteolysis; Sodium; Ubiquinone; Vibrio cholerae

A yellow-pigmented bacterial strain, designated RCML-52(T), was isolated from an abandoned gold mine in the desert in Xinjiang, China. Strain RCML-52(T) was Gram-negative, aerobic and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RCML-52(T) was affiliated with the genus Lysobacter. Strain RCML-52(T) exhibited <95.6 % 16S rRNA gene sequence similarity to the type strains of all species of the genus Lysobacter. The major fatty acids were iso-C(16 : 0) (27.6 %), iso-C(15 : 0) (19.1 %), iso-C(17 : 1)ω9c (16.4 %), iso-C(11 : 0) 3-OH (6.5 %) and iso-C(11 : 0) (5.3 %). The DNA G+C content was 69.7 mol%. The major isoprenoid quinone was Q-8. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain RCML-52(T) should be assigned to a novel species of the genus Lysobacter, for which the name Lysobacter xinjiangensis sp. nov. is proposed. The type strain is RCML-52(T) (=CCTCC AB 208194(T) =KCTC 22558(T)).

Topics: Bacterial Typing Techniques; Base Composition; Desert Climate; DNA, Bacterial; Fatty Acids; Gamma Rays; Lysobacter; Mining; Molecular Sequence Data; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium originating from a human clinical specimen was studied for its taxonomic position. 16S rRNA gene sequence similarity studies clearly allocated this strain (CCUG 58010(T)) to the class Betaproteobacteria, closely related to members of the genera Massilia and Naxibacter. Naxibacter varians was shown to be the most closely related species on the basis of 16S rRNA gene sequence similarity (97.5 %), followed by Massilia niastensis (96.8 %) and Massilia aerilata (96.4 %). Similarities to all other species of the genera Naxibacter and Massilia were in the range 93.9-96.2 %. Chemotaxonomic data (major ubiquinone: Q-8; major polar lipids: phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; and major fatty acids: summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH), C(16 : 0), C(18 : 1)ω7c and C(12 : 0), with C(10 : 0) 3-OH as hydroxylated fatty acid) supported the affiliation of the isolate to these genera, which share these chemotaxonomic traits. DNA-DNA hybridization of strain CCUG 58010(T) with the type strain of N. varians CCUG 35299(T) resulted in a relatedness value of 39.2 % (reciprocal, 50 %) and physiological and biochemical tests also allowed phenotypic differentiation of the isolate from the most closely related species. There is currently no justification for a division of the genera Massilia and Naxibacter and for this reason a proposal is made to transfer all species of the genus Naxibacter to the genus Massilia, as Massilia alkalitolerans comb. nov., Massilia varians comb. nov., Massilia haematophila comb. nov. and Massilia suwonensis comb. nov. Strain CCUG 58010(T) represents a novel species, for which the name Massilia consociata sp. nov. is proposed, with the type strain CCUG 58010(T) ( = CCM 7792(T)).

Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Humans; Molecular Sequence Data; Nucleic Acid Hybridization; Oxalobacteraceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

A novel aerobic, gram-negative bacterial strain, designated 17X/A02/237(T), was isolated from waters of the coastal north-western Mediterranean Sea. Cells were motile straight rods and formed dark-grey colonies on marine agar medium. Strain 17X/A02/237(T) contained ubiquinone Q-8 and its major fatty acids were C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(18 : 1)ω7c, C(16 : 0), C(18 : 0) and C(10 : 0) 3-OH. The G+C content of the genomic DNA was 47.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. Based on 16S rRNA gene sequence data, as well as physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name of Eionea nigra gen. nov., sp. nov. is proposed. The type strain is 17X/A02/237(T) ( = DSM 19752(T) = CIP 109759(T) = MOLA 288(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Mediterranean Sea; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

Coenzyme Q (ubiquinone or Q) is a lipid electron and proton carrier in the electron transport chain. In yeast Saccharomyces cerevisiae eleven genes, designated COQ1 through COQ9, YAH1 and ARH1, have been identified as being required for Q biosynthesis. One of these genes, COQ8 (ABC1), encodes an atypical protein kinase, containing six (I, II, III, VIB, VII, and VIII) of the twelve motifs characteristically present in canonical protein kinases. Here we characterize seven distinct Q-less coq8 yeast mutants and show that unlike the coq8 null mutant, each maintained normal steady-state levels of the Coq8 polypeptide. The phosphorylation states of Coq polypeptides were determined with two-dimensional gel analyses. Coq3p, Coq5p, and Coq7p were phosphorylated in a Coq8p-dependent manner. Expression of a human homolog of Coq8p, ADCK3(CABC1) bearing an amino-terminal yeast mitochondrial leader sequence, rescued growth of yeast coq8 mutants on medium containing a nonfermentable carbon source and partially restored biosynthesis of Q(6). The phosphorylation state of several of the yeast Coq polypeptides was also rescued, indicating a profound conservation of yeast Coq8p and human ADCK3 protein kinase function in Q biosynthesis.

Topics: Amino Acid Sequence; Humans; Mitochondria; Mitochondrial Proteins; Molecular Sequence Data; Mutation; Peptides; Phosphorylation; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Sequence Alignment; Ubiquinone

Ubiquinone (Coenzyme Q) plays an important role in the mitochondrial respiratory chain and also acts as an antioxidant in its reduced form, protecting cellular membranes from peroxidation. De novo disulfide bond generation in the E. coli periplasm involves a transient complex consisting of DsbA, DsbB, and ubiquinone (UQ). It is hypothesized that a charge-transfer complex intermediate is formed between the UQ ring and the DsbB-C44 thiolate during the reoxidation of DsbA, which gives a distinctive ~500 nm absorbance band. No enzymological precedent exists for an UQ-protein thiolate charge-transfer complex, and definitive evidence of this unique reaction pathway for DsbB has not been fully demonstrated. In order to study the UQ-8-DsbB complex in the presence of native lipids, we have prepared isotopically labeled samples of precipitated DsbB (WT and C41S) with endogenous UQ-8 and lipids, and we have applied advanced multidimensional solid-state NMR methods. Double-quantum filter and dipolar dephasing experiments facilitated assignments of UQ isoprenoid chain resonances not previously observed and headgroup sites important for the characterization of the UQ redox states: methyls (~20 ppm), methoxys (~60 ppm), olefin carbons (120-140 ppm), and carbonyls (150-160 ppm). Upon increasing the DsbB(C41S) pH from 5.5 to 8.0, we observed a 10.8 ppm upfield shift for the UQ C1 and C4 carbonyls indicating an increase of electron density on the carbonyls. This observation is consistent with the deprotonation of the DsbB-C44 thiolate at pH 8.0 and provides direct evidence of the charge-transfer complex formation. A similar trend was noted for the UQ chemical shifts of the DsbA(C33S)-DsbB(WT) heterodimer, confirming that the charge-transfer complex is unperturbed by the DsbB(C41S) mutant used to mimic the intermediate state of the disulfide bond generating reaction pathway.

Topics: Bacterial Proteins; Disulfides; Magnetic Resonance Spectroscopy; Membrane Proteins; Molecular Structure; Reference Standards; Ubiquinone

We studied ubiquinone (Q), Q homologue ratio, and steady-state levels of mCOQ transcripts in tissues from mice fed ad libitum or under calorie restriction. Maximum ubiquinone levels on a protein basis were found in kidney and heart, followed by liver, brain, and skeletal muscle. Liver and skeletal muscle showed the highest Q(9)/Q(10) ratios with significant interindividual variability. Heart, kidney, and particularly brain exhibited lower Q(9)/Q(10) ratios and interindividual variability. In skeletal muscle and heart, the most abundant mCOQ transcript was mCOQ7, followed by mCOQ8, mCOQ2, mPDSS2, mPDSS1, and mCOQ3. In nonmuscular tissues (liver, kidney, and brain) the most abundant mCOQ transcript was mCOQ2, followed by mCOQ7, mCOQ8, mPDSS1, mPDSS2, and mCOQ3. Calorie restriction increased both ubiquinone homologues and mPDSS2 mRNA in skeletal muscle, but mCOQ7 was decreased. In contrast, Q(9) and most mCOQ transcripts were decreased in heart. Calorie restriction also modified the Q(9)/Q(10) ratio, which was increased in kidney and decreased in heart without alterations in mPDSS1 or mPDSS2 transcripts. We demonstrate for the first time that unique patterns of mCOQ transcripts exist in muscular and nonmuscular tissues and that Q and COQ genes are targets of calorie restriction in a tissue-specific way.

Topics: Animals; Brain; Caloric Restriction; Free Radicals; Kidney; Liver; Mice; Muscle, Skeletal; Myocardium; Organ Specificity; RNA, Messenger; Ubiquinone

The abc1(-)/coq8(-) gene deletion respiratory-deficient mutant NBp17 of fission yeast Schizosaccharomyces pombe displayed a phenotypic fermentation pattern with enhanced production of glycerol and acetate, and also possessed oxidative stress-sensitive phenotypes to H(2)O(2), menadione, tBuOOH, Cd(2+), and chromate in comparison with its parental respiratory-competent strain HNT. As a consequence of internal stress-inducing mutation, adaptation processes to restore the redox homeostasis of mutant NBp17 cells were detected in minimal glucose medium. Mutant NBp17 produced significantly increased amounts of O(2)•- and H(2)O(2) as a result of the decreased internal glutathione concentration and the only slightly increased glutathione reductase activity. The Cr(VI) reduction capacity and hence the •OH production ability were decreased. The mutant cells demonstrated increased specific activities of superoxide dismutases and glutathione reductase (but not catalase) to detoxify at least partially the overproduction of reactive oxygen species. All these features may be explained by the decreased redox capacity of the mutant cells. Most notably, mutant NBp17 hyperaccumulated yellow CdS.

Topics: ATP-Binding Cassette Transporters; Cadmium; Gene Deletion; Glutathione; Microbial Sensitivity Tests; Oxidants; Oxidation-Reduction; Peroxides; Phenotype; Schizosaccharomyces; Schizosaccharomyces pombe Proteins; Ubiquinone

Na(+) is the second major coupling ion at membranes after protons, and many pathogenic bacteria use the sodium-motive force to their advantage. A prominent example is Vibrio cholerae, which relies on the Na(+)-pumping NADH:quinone oxidoreductase (Na(+)-NQR) as the first complex in its respiratory chain. The Na(+)-NQR is a multisubunit, membrane-embedded NADH dehydrogenase that oxidizes NADH and reduces quinone to quinol. Existing models describing redox-driven Na(+) translocation by the Na(+)-NQR are based on the assumption that the pump contains four flavins and one FeS cluster. Here we show that the large, peripheral NqrA subunit of the Na(+)-NQR binds one molecule of ubiquinone-8. Investigations of the dynamic interaction of NqrA with quinones by surface plasmon resonance and saturation transfer difference NMR reveal a high affinity, which is determined by the methoxy groups at the C-2 and C-3 positions of the quinone headgroup. Using photoactivatable quinone derivatives, it is demonstrated that ubiquinone-8 bound to NqrA occupies a functional site. A novel scheme of electron transfer in Na(+)-NQR is proposed that is initiated by NADH oxidation on subunit NqrF and leads to quinol formation on subunit NqrA.

Topics: Bacterial Proteins; Binding Sites; Electron Transport Complex I; Nuclear Magnetic Resonance, Biomolecular; Oxidation-Reduction; Sodium-Potassium-Exchanging ATPase; Ubiquinone; Vibrio cholerae

Two bacterial strains, II-B4(T) and II-D5(T), isolated from the meso-eutrophic freshwater Římov reservoir (Czech Republic), were characterized phenotypically, phylogenetically and chemotaxonomically. Both strains were chemo-organotrophic, facultatively anaerobic, non-motile rods, with identical DNA G+C contents of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and their major fatty acids were C(16 : 1)ω7c/C(16 : 1)ω6c, C(16 : 0), C(18 : 1)ω7c/C(18 : 1)ω6c and C(12 : 0). Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA gene sequences of the two strains possessed 99.1 % similarity; however, the level of DNA-DNA reassociation was only 26.7 %. The strains can also be discriminated from each other by several chemotaxonomic and biochemical traits. Phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent the first isolated members of a narrow phylogenetic cluster (the so-called R-BT065 cluster) formed by a large number of environmental sequences and abundant populations detected in the pelagic zones of various freshwater habitats. We propose to place the two strains in separate novel species within the genus Limnohabitans, Limnohabitans planktonicus sp. nov., with the type strain II-D5(T) (=DSM 21594(T) =CIP 109844(T)), and Limnohabitans parvus sp. nov., with the type strain II-B4(T) (=DSM 21592(T) =CIP 109845(T)). The description of the genus Limnohabitans is emended accordingly.

Topics: Bacterial Typing Techniques; Base Composition; Comamonadaceae; Czech Republic; DNA, Bacterial; Fatty Acids; Fresh Water; Molecular Sequence Data; Phenotype; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Two Gram-negative, non-motile, non-pigmented and curved rod-shaped bacterial strains, designated IMCC4489(T) and IMCC4451, were isolated from a tidal flat sediment of the Yellow Sea. Strains IMCC4489(T) and IMCC4451 shared 99.9 % 16S rRNA gene sequence similarity and 78.5 % DNA-DNA relatedness, which suggested that they belonged to the same species. The isolates were most closely related to Reinekea blandensis MED297(T) (98.7-98.8 % 16S rRNA gene sequence similarity) and Reinekea marinisedimentorum DSM 15388(T) (95.3-95.4 %). DNA-DNA relatedness between the strains and R. blandensis CCUG 52066(T) was 31-34 %. Strains IMCC4489(T) and IMCC4451 could also be differentiated from the type strains of the two recognized Reinekea species by several phenotypic properties. The DNA G+C content was 51.3-51.5 mol% and the major isoprenoid quinone was Q-8. On the basis of the data obtained in this study, it is proposed that strains IMCC4489(T) and IMCC4451 represent a novel species, Reinekea aestuarii sp. nov. The type strain is IMCC4489(T) (=KCTC 22813(T) =KCCM 42938(T) =NBRC 106079(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Molecular Sequence Data; Nucleic Acid Hybridization; Oceanospirillaceae; Oceans and Seas; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Ubiquinone

A chemo-organotrophic, aerobic, non-motile strain, MWH-BRAZ-DAM2D(T), isolated from a freshwater pond in Brazil, was characterized phenotypically, phylogenetically and chemotaxonomically. Phylogenetic analysis of 16S rRNA gene sequences indicated affiliation of the strain with the genus Limnohabitans (Comamonadaceae, Betaproteobacteria). 16S rRNA gene sequence similarities between the isolate and Limnohabitans curvus MWH-C5(T), representing the type species of the genus, and the type strains of Limnohabitans parvus and Limnohabitans planktonicus were 98.2, 96.5 and 97.0 %, respectively. DNA-DNA reassociation analyses with DNA of the type strains of all three previously described Limnohabitans species revealed similarity values in the range 26.2-44.6 %. The predominant fatty acids of the isolate were C(16 : 1)ω7c/ω6c, C(16 : 0), C(12 : 0) and C(8 : 0) 3-OH, the major quinone was ubiquinone Q-8 and the DNA G+C content was 55.8 mol%. The isolate could be discriminated from the type strains of the three Limnohabitans species by several phenotypic traits including differences in the utilization of several carbon sources. Based on the phylogeny of the isolate and its differences from the three most closely related species, the isolate represents a novel species for which the name Limnohabitans australis sp. nov. is proposed. The type strain is MWH-BRAZ-DAM2D(T) (=DSM 21646(T)=CCUG 56719(T)).

Topics: Bacterial Typing Techniques; Base Composition; Brazil; Comamonadaceae; DNA, Bacterial; Fatty Acids; Fresh Water; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Ponds; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

COQ10 deletion in Saccharomyces cerevisiae elicits a defect in mitochondrial respiration correctable by addition of coenzyme Q(2). Rescue of respiration by Q(2) is a characteristic of mutants blocked in coenzyme Q(6) synthesis. Unlike Q(6) deficient mutants, mitochondria of the coq10 null mutant have wild-type concentrations of Q(6). The physiological significance of earlier observations that purified Coq10p contains bound Q(6) was examined in the present study by testing the in vivo effect of over-expression of Coq10p on respiration. Mitochondria with elevated levels of Coq10p display reduced respiration in the bc1 span of the electron transport chain, which can be restored with exogenous Q(2). This suggests that in vivo binding of Q(6) by excess Coq10p reduces the pool of this redox carrier available for its normal function in providing electrons to the bc1 complex. This is confirmed by observing that extra Coq8p relieves the inhibitory effect of excess Coq10p. Coq8p is a putative kinase, and a high-copy suppressor of the coq10 null mutant. As shown here, when over-produced in coq mutants, Coq8p counteracts turnover of Coq3p and Coq4p subunits of the Q-biosynthetic complex. This can account for the observed rescue by COQ8 of the respiratory defect in strains over-producing Coq10p.

Topics: Cell Respiration; Electron Transport; Gene Deletion; Mitochondria; Saccharomyces cerevisiae; Ubiquinone

Coenzyme Q (Q) regulates aging in Caenorhabditis elegans, and its deficiency leads to a variety of pathologies in humans. We used a coq-8 deleted strain to study the role of Q in C. elegans development and how it influences life span. Endogenous Q(9) content of coq-8(ok840) knockouts was demonstrated to be about 7% of that found in the wild-type, indicating the basal biosynthesis rate is reduced in this strain. Knockouts abnormally developed both gonads and hypodermis, showed reduced fertility and shortened life span, and this was partially recovered by ingestion of exogenous Q. Knockouts produced embryos that showed arrested development at the time of initial expression of coq-8 in embryo. Uridine, whose biosynthesis depends on mitochondrial Q, improved both egg production and progeny under Q-rich dietary conditions. COQ-8 is a candidate protein for post-translational regulation of Q biosynthesis rate and its expression correlates with Q content during the life cycle in C. elegans. We show for the first time that a critical level of Q is necessary to support embryo development and fertility in C. elegans. These results suggest that extra-mitochondrial function of Q is a key factor linking development and bioenergetics in C. elegans.

Topics: Aging; Animals; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Fertility; Gene Expression Regulation, Developmental; Gene Expression Regulation, Enzymologic; Gene Knockout Techniques; Genotype; Gonads; Larva; Longevity; Phenotype; Ubiquinone; Uridine

To provide insight into effects of UV pretreatment on microorganisms in subsequent biofilters, the changes of microbial community structure and metabolic characteristics of biofilters with (UV-BF) and without (BF) UV pretreatment were studied. The respiratory quinone and BIOLOG methods were used to analyze microbial community structure and metabolic characteristics, respectively. The results indicated the quinone profiles, the species of dominant quinone and its molar fraction of the biofilm in both biofilters showed different behaviors. Ubiquinones-8 and menaquinone-9(H(2)) was the dominant quinones in BF and UV-BF processes, respectively. The dissimilarity index of two biofilters markedly increased to nearly 60 after turning on the UV lamp. The microbial samples from UV-BF process showed higher metabolic activities of 0.040 cm(-1) h(-1) than 0.028 cm(-1) h(-1) in BF process. Moreover, the microorganisms in both biofilters demonstrated distinct metabolic characteristics. Further, the performance of biofilters showed good correlation with microbial community structure and metabolic characteristics.

Topics: Biodegradation, Environmental; Biofilms; Biotechnology; Chlorobenzenes; Filtration; Gases; Models, Statistical; Principal Component Analysis; Quinones; Ubiquinone; Ultraviolet Rays; Vitamin K 2; Waste Disposal, Fluid; Water Microbiology; Water Purification

A Gram-negative, motile bacterium, designated DCY36T, was isolated from soil of a ginseng field in South Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain DCY36T belongs to genus Castellaniella in the family Alcaligenaceae of the class Betaproteobacteria. The 16S rRNA gene sequence similarities between strain DCY36T and the three recognized representatives of the genus, Castellaniella caeni Ho-11T, Castellaniella defragrans 54PinT and Castellaniella denitrificans NKNTAUT, were 98.4, 97.5 and 98.1%, respectively. Strain DCY36T exhibited relatively low levels of DNA-DNA relatedness with respect to these three species. The G+C content of the genomic DNA was 63.7 mol%. Strain DCY36T contained ubiquinone Q-8. The major fatty acids were C16:0 (27.4%), C18:1omega7c (16.9%) and summed feature 4 (C16:1omega7c and C15:0 iso 2-OH, 32.5%). On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain DCY36T (=KCTC 22398T=JCM 15515T) should be classified in the genus Castellaniella as the type strain of a novel species, for which the name Castellaniella ginsengisoli sp. nov. is proposed.

Topics: Alcaligenaceae; Bacterial Typing Techniques; Base Composition; beta-Glucosidase; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Korea; Locomotion; Molecular Sequence Data; Nucleic Acid Hybridization; Panax; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone

Coenzyme Q is a redox-active lipid that functions as an electron carrier in the mitochondrial respiratory chain. Q-biosynthesis in Saccharomyces cerevisiae requires at least nine proteins (Coq1p-Coq9p). The molecular function of Coq8p is still unknown; however, lack of Q and the concomitant accumulation of the intermediate 3-hexaprenyl-4-hydroxybenzoic acid in the absence of Coq8p suggest an essential role in Q-biosynthesis. Localization studies identify Coq8p as a soluble mitochondrial protein, with characteristics of a protein of the matrix or associated with the inner mitochondrial membrane. Coq8p forms homomeric structure(s) as revealed by two-hybrid analysis and tandem affinity purification. Two-dimensional (2D)-Blue Native/sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis suggests that Coq8p - together with Coq2p and Coq10p - is predominantly associated with a complex of about 500 kDa, whereas Coq3p, Coq5p and Coq9p are mainly organized in a 1.3 MDa Q-biosynthesis complex that is not associated with the complex III and IV supracomplexes of the respiratory chain. Loss of Coq8p is accompanied by destabilization of Coq3p, but not of Coq9p from the 1.3 MDa Q-biosynthesis complex. This effect cannot be reversed by Q(6) supplementation. The detection of Coq3p isoforms by 2D-isoelectric focusing is in line with the proposed function of Coq8p as a kinase, with Coq3p as a target.

Topics: Gene Expression Regulation, Fungal; Methyltransferases; Mitochondria; Mitochondrial Proteins; Phosphorylation; Phosphotransferases; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Ubiquinone

Two Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from a hexane-treated, full-scale biofilter from an oil mill. The strains were cultivated with hexane as the sole carbon source. One strain, MN154.3(T), showed a fatty acid profile that contained 16 : 0, 18 : 1cis11 and 19 : 0 cyclo11-12 as major compounds, while the second strain, isolate MN28(T), contained 14 : 0 3-OH, 16 : 0 and 18 : 1cis11 as the predominant fatty acids. On the basis of almost-complete 16S rRNA gene sequences, both strains could be allocated to the Nevskia branch of the class Gammaproteobacteria. The sequence similarities for strains MN154.3(T) and MN28(T) with respect to the most closely related type strains of this branch were 90.5 and 94.1 %, respectively. The sequence similarity between strains MN154.3(T) and MN28(T) was 90.6 %. The DNA G+C content of strain MN154.3(T) was 62.8 mol% and that for strain MN28(T) was 64.9 mol%. Both strains possessed ubiquinone-8 as the major quinone. On the basis of the 16S rRNA gene sequences of these two new isolates and several phenotypic differences exhibited with respect to known species of the Nevskia branch, strains MN154.3(T) and MN28(T) represent two novel genera and species, for which the names Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov. are proposed. The type strain of Alkanibacter difficilis gen. nov., sp. nov. is MN154.3(T) (=DSM 14804(T)=LMG 22842(T)) and that of Singularimonas variicoloris gen. nov., sp. nov. is MN28(T) (=DSM 15731(T)=LMG 22844(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gammaproteobacteria; Genes, Bacterial; Genes, rRNA; Hexanes; Industrial Waste; Molecular Sequence Data; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone

Membrane-bound glucose dehydrogenase (mGDH) is a single integral protein in the respiratory chain in Escherichia coli which oxidizes D-glucose and feeds electrons to ubiquinol oxidase via bulk ubiquinone (UQ). mGDH contains a bound UQ, CoQ8, for its intramolecular electron transfer in addition to pyrroloquinoline quinone (PQQ) as a coenzyme. Pulse radiolysis analysis revealed that the bound UQ exists very close to PQQ at a distance of 11-13 angstroms. Studies on mGDH mutants with substitutions for amino acid residues around PQQ showed that Asp-466 and Lys-493, which are crucial for catalytic activity, interact with bound UQ. Based on these findings, we propose that the bound UQ is involved in the catalytic reaction in addition to the intramolecular electron transfer in mGDH.

Topics: Amino Acid Substitution; Calcium; Catalytic Domain; Escherichia coli; Glucose Dehydrogenases; Magnesium; Ubiquinone

Flux Balance Analysis (FBA) has been successfully applied to facilitate the understanding of cellular metabolism in model organisms. Standard formulations of FBA can be applied to large systems, but the accuracy of predictions may vary significantly depending on environmental conditions, genetic perturbations, or complex unknown regulatory constraints. Here we present an FBA-based approach to infer the biomass compositions that best describe multiple physiological states of a cell. Specifically, we seek to use experimental data (such as flux measurements, or mRNA expression levels) to infer best matching stoichiometrically balanced fluxes and metabolite sinks. Our algorithm is designed to provide predictions based on the comparative analysis of two metabolic states (e.g. wild-type and knockout, or two different time points), so as to be independent from possible arbitrary scaling factors. We test our algorithm using experimental data for metabolic fluxes in wild type and gene deletion strains of E. coli. In addition to demonstrating the capacity of our approach to correctly identify known exchange fluxes and biomass compositions, we analyze E. coli central carbon metabolism to show the changes of metabolic objectives and potential compensation for reducing power due to single enzyme gene deletion in pentose phosphate pathway.

Topics: Adenosine Triphosphate; Algorithms; Biomass; Carbon Dioxide; Escherichia coli; Glycolysis; Kinetics; Metabolism; Models, Biological; Models, Genetic; NADH Dehydrogenase; Pentose Phosphate Pathway; Succinate Dehydrogenase; Ubiquinone

Coenzyme Q(10) (CoQ(10)) plays a pivotal role in oxidative phosphorylation (OXPHOS) in that it distributes electrons between the various dehydrogenases and the cytochrome segments of the respiratory chain. Primary coenzyme Q(10) deficiency represents a clinically heterogeneous condition suggestive of genetic heterogeneity, and several disease genes have been previously identified. The CABC1 gene, also called COQ8 or ADCK3, is the human homolog of the yeast ABC1/COQ8 gene, one of the numerous genes involved in the ubiquinone biosynthesis pathway. The exact function of the Abc1/Coq8 protein is as yet unknown, but this protein is classified as a putative protein kinase. We report here CABC1 gene mutations in four ubiquinone-deficient patients in three distinct families. These patients presented a similar progressive neurological disorder with cerebellar atrophy and seizures. In all cases, enzymological studies pointed to ubiquinone deficiency. CoQ(10) deficiency was confirmed by decreased content of ubiquinone in muscle. Various missense mutations (R213W, G272V, G272D, and E551K) modifying highly conserved amino acids of the protein and a 1 bp frameshift insertion c.[1812_1813insG] were identified. The missense mutations were introduced into the yeast ABC1/COQ8 gene and expressed in a Saccharomyces cerevisiae strain in which the ABC1/COQ8 gene was deleted. All the missense mutations resulted in a respiratory phenotype with no or decreased growth on glycerol medium and a severe reduction in ubiquinone synthesis, demonstrating that these mutations alter the protein function.

Topics: Adolescent; Adult; Amino Acid Sequence; Benzoquinones; Brain; Cerebellar Ataxia; Female; Haplotypes; Humans; Magnetic Resonance Imaging; Male; Molecular Sequence Data; Muscle, Skeletal; Mutation, Missense; Pedigree; Seizures; Ubiquinone

Muscle coenzyme Q(10) (CoQ(10) or ubiquinone) deficiency has been identified in more than 20 patients with presumed autosomal-recessive ataxia. However, mutations in genes required for CoQ(10) biosynthetic pathway have been identified only in patients with infantile-onset multisystemic diseases or isolated nephropathy. Our SNP-based genome-wide scan in a large consanguineous family revealed a locus for autosomal-recessive ataxia at chromosome 1q41. The causative mutation is a homozygous splice-site mutation in the aarF-domain-containing kinase 3 gene (ADCK3). Five additional mutations in ADCK3 were found in three patients with sporadic ataxia, including one known to have CoQ(10) deficiency in muscle. All of the patients have childhood-onset cerebellar ataxia with slow progression, and three of six have mildly elevated lactate levels. ADCK3 is a mitochondrial protein homologous to the yeast COQ8 and the bacterial UbiB proteins, which are required for CoQ biosynthesis. Three out of four patients tested showed a low endogenous pool of CoQ(10) in their fibroblasts or lymphoblasts, and two out of three patients showed impaired ubiquinone synthesis, strongly suggesting that ADCK3 is also involved in CoQ(10) biosynthesis. The deleterious nature of the three identified missense changes was confirmed by the introduction of them at the corresponding positions of the yeast COQ8 gene. Finally, a phylogenetic analysis shows that ADCK3 belongs to the family of atypical kinases, which includes phosphoinositide and choline kinases, suggesting that ADCK3 plays an indirect regulatory role in ubiquinone biosynthesis possibly as part of a feedback loop that regulates ATP production.

Topics: Amino Acid Sequence; Brain; Cerebellar Ataxia; Coenzymes; Female; Genes, Recessive; Humans; Magnetic Resonance Imaging; Male; Molecular Sequence Data; Mutation; Pedigree; Phosphotransferases; Sequence Analysis, DNA; Ubiquinone; Yeasts

A Gram-negative, rod-shaped bacterium (CC-JY-1(T)) was isolated on nutrient agar from a soil sample collected from an oil-contaminated site located in Chyai county, Taiwan. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing 96.7 % sequence similarity to the type strain of Arenimonas donghaensis and similarities of 93.0-93.8 % to species of the genera Thermomonas, Lysobacter and Silanimonas. The presence of ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and the fatty acid profile were in accordance with the phylogenetic affiliation of CC-JY-1(T). DNA-DNA reassociation experiments between CC-JY-1(T) and A. donghaensis KACC 11381(T) resulted in a mean relatedness value of 32 %, indicating that strain CC-JY1(T) represents a novel species in the genus Arenimonas, for which we propose the name Arenimonas malthae sp. nov. The type strain is CC-JY-1(T) (=CCUG 53596(T) =CIP 109310(T)).

Topics: Bacterial Typing Techniques; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Genes, rRNA; Molecular Sequence Data; Petroleum; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Soil Microbiology; Taiwan; Ubiquinone; Xanthomonadaceae

Coenzyme Q (Q) and the genes involved in its biosynthesis are involved in aging and development of Caenorhabditis elegans. Q is synthesized by at least eight highly conserved nuclear coq genes, but this biosynthesis pathway and its regulation is not known. The coq-8 gene sequence has homology to the ABC-1 family kinases and is the only known candidate for a possible regulation of this pathway. To study coq-8 expression pattern, we have developed a C. elegans transgenic strain expressing ubiquinone biosynthesis coq-8 gene promoter and GFP construct. We show here an age-dependent specific pattern from embryo to senescence for COQ-8 protein expression. Expression in embryo was triggered by a defined group of blastomers before morphogenesis. In elderly nematodes expression was only observed in nervous system, whilst expression in larvae was also detected in hypodermis, muscles and coelomocytes. Global expression provide a regulated pattern during life cycle of the nematode.

Topics: Aging; Animals; Animals, Genetically Modified; Caenorhabditis elegans; Embryo, Nonmammalian; Gene Expression Regulation, Developmental; Genes, Helminth; Green Fluorescent Proteins; Larva; Tissue Distribution; Ubiquinone

A procedure was developed to isolate fractions enriched in plasma membrane from Caenorhabditis elegans. Coenzyme Q9 (Q9) was found in plasma membrane isolated from either wild-type or long-lived qm30 and qm51 clk-1 mutant strains of Caenorhabditis elegans, along with dietary coenzyme Q8 (Q8) and the biosynthetic intermediate demethoxy-Q9 (DMQ9). NADH was able to reduce both Q8 and Q9, but not DMQ9. Our results indicate that DMQ9 cannot achieve the same redox role of Q9 in plasma membrane, suggesting that proportion of all these Q isoforms in plasma membrane must be an important factor in establishing the clk-1 mutant phenotype.

Topics: Animals; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Cell Membrane; NAD; Oxidation-Reduction; Ubiquinone

The chromosomal ispA gene encoding farnesyl diphosphate synthase of Escherichia coli was disrupted by inserting a neo gene cassette. The null ispA mutants were viable. The growth yield of the mutants was 70% to 80% of that of the wild-type strain under aerobic conditions, and was almost the same as the wild-type under anaerobic conditions. The levels of ubiquinone-8 and menaquinone-8 were both significantly lower (less than 13% and 18% of normal, respectively) in the mutants than in the wild-type. The undecaprenyl phosphate level in the mutants was modestly lower (40% to 70% of normal) than in the wild-type strain. Thus the synthesis of all-E-octaprenyl diphosphate, the precursor of ubiquinone-8 and menaquinone-8, was decreased more severely than that of Z,E-mixed undecaprenyl diphosphate, the precursor of undecaprenyl monophosphates, under the conditions where the synthesis of farnesyl diphosphate was decreased. The condensation of isopentenyl diphosphate with dimethylallyl diphosphate was detected in the cell-free extracts of the mutants, although it was 5% of that in the wild-type strain. A low level of farnesyl diphosphate seems to be synthesized in the mutants by other prenyltransferases such as octaprenyl diphosphate synthase or undecaprenyl diphosphate synthase.

Topics: Alkyl and Aryl Transferases; Escherichia coli; Genes, Bacterial; Geranyltranstransferase; Plasmids; Polyisoprenyl Phosphates; Ubiquinone; Vitamin K 2

A new obligately methylotrophic bacterium (strain MTT) with the ribulose monophosphate pathway of carbon assimilation is described. The isolate, utilizing only methanol, is an aerobic, Gram-negative, asporogenous, non-motile short rod multiplying by binary fission. Its cellular fatty acids profile consists primarily of straight-chain saturated C16:0 and unsaturated C16:l acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol (cardiolipin) is absent. Optimal growth conditions are 25-29 degree C, pH 6.5 - 7.5, 0.5% CH3OH and 0.05% NaCl. Strain MTT lacks alpha-ketoglutarate dehydrogenase, the glyoxylate shunt enzymes, and glutamate dehydrogenase. Ammonium is assimilated by the operation of the glutamate cycle enzymes: glutamine synthetase and glutamate synthase. An exopolysaccharide consisting of rhamnose, glucose and galactose is formed under nitrogen limitation. The G + C content of the DNA is 54.0 mol%. Based on 16S rDNA sequence analysis and DNA-DNA relatedness (29-34%) with type strains of the genus Methylophilus, the novel isolate was classified as a new species of this genus and named Methylophilus quaylei MTT (VKM B-2338T, DSMZ, etc.).

Topics: Aerobiosis; Base Composition; DNA, Bacterial; DNA, Ribosomal; Environmental Microbiology; Genes, rRNA; Glutamate Dehydrogenase; Glutamate Synthase; Glutamate-Ammonia Ligase; Hydrogen-Ion Concentration; Ketoglutarate Dehydrogenase Complex; Lipids; Methanol; Methylophilus; Molecular Sequence Data; Phylogeny; Polysaccharides, Bacterial; Quaternary Ammonium Compounds; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Temperature; Ubiquinone

Dehalococcoides species have a highly restricted lifestyle and are only known to derive energy from reductive dehalogenation reactions. The lipid fraction of two Dehalococcoides isolates, strains BAV1 and FL2, and a tetrachloroethene-to-ethene-dechlorinating Dehalococcoides-containing consortium were analyzed for neutral lipids and phospholipid fatty acids. Unusual phospholipid modifications, including the replacement of unsaturated fatty acids with furan fatty acids, were detected in both Dehalococcoides isolates and the mixed culture. The following three furan fatty acids are reported as present in bacterial phospholipids for the first time: 9-(5-pentyl-2-furyl)-nonanoate (Fu18:2omega6), 9-(5-butyl-2-furyl)-nonanoate (Fu17:2omega5), and 8-(5-pentyl-2-furyl)-octanoate (Fu17:2omega6). The neutral lipids of the Dehalococcoides cultures contained unusually large amounts of benzoquinones (i.e., ubiquinones [UQ]), which is unusual for anaerobes. In particular, the UQ-8 content of Dehalococcoides was 5- to 20-fold greater than that generated in aerobically grown Escherichia coli cultures relative to the phospholipid fatty acid content. Naphthoquinone isoprenologues (MK), which are often found in anaerobically grown bacteria and archaea, were also detected. Dehalococcoides shows a difference in isoprenologue pattern between UQ-8 and MK-5 that is atypical of other bacteria capable of producing both quinone types. The difference in UQ-8 and MK-5 isoprenologue patterns strongly suggests a special function for UQ in Dehalococcoides, and Dehalococcoides may utilize structural modifications in its lipid armamentarium to protect against free radicals that are generated in the process of reductive dechlorination.

Topics: Biofilms; Biomass; Chloroflexi; Culture Media; Fatty Acids; Free Radicals; Linoleic Acids; Mass Spectrometry; Phospholipids; Quinones; Ubiquinone

Ubiquinone is an essential molecule in aerobic organisms to achieve both, ATP synthesis and antioxidant defence. Mutants in genes responsible of ubiquinone biosynthesis lead to non-respiring petite yeast. In C. elegans, coq-7/clk-1 but not coq-3 mutants live longer than wild type showing a 'slowed' phenotype. In this paper we demonstrate that absence in ubiquinone in coq-1, coq-2 or coq-8 mutants lead to larval development arrest, slowed pharyngeal pumping, eventual paralysis and cell death. All these features emerge during larval development, whereas embryo development appeared similar to that of wild type individuals. Dietary coenzyme Q did not restore any of the alterations found in these coq mutants. These phenomena suggest that coenzyme Q mutants unable to synthesize this molecule develop a deleterious phenotype leading to lethality. On the contrary, phenotype of C. elegans coq-7/clk-1 mutants may be a unique phenotype than can not generalize to mutants in ubiquinone biosynthesis. This particular phenotype may not be based on the absence of endogenous coenzyme Q, but to the simultaneous presence of dietary coenzyme Q and the its biosynthesis intermediate demethoxy-coenzyme Q.

Topics: Aging; Animals; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Gene Deletion; Heterozygote; Larva; Longevity; Pharynx; Phenotype; Ubiquinone

The mechanism of the dioxygen (O(2)) reduction conducted by cytochrome bo-type quinol oxidase was investigated using submillisecond-resolved freeze-quench EPR spectroscopy. The fully reduced form of the wild-type enzyme (WT) with the bound ubiquinone-8 at the high-affinity quinone-binding site was mixed with an O(2)-saturated solution, and the subsequent reaction was quenched at different time intervals from 0.2 to 50 ms. The EPR signals derived from the binuclear center and heme b were weak in the time domain from 0.2 to 0.5 ms. The signals derived from the ferric heme b and hydroxide-bound ferric heme o increased simultaneously after 1 ms, indicating that the oxidation of heme b is coupled to the formation of hydroxy heme o. In contrast, the enzyme without the bound ubiquinone-8 (Delta UbiA) showed the faster oxidation of heme b and the slower formation of hydroxy heme o than WT. It is interpreted that the F(I) intermediate possessing ferryl-oxo heme o, cupric Cu(B), and ferric heme b is converted to the F(II) intermediate within 0.2 ms by an electron transfer from the bound ubiquinonol-8 to ferric heme b. The conversion of the F(II) intermediate to the hydroxy intermediate occurred after 1 ms and was accompanied by the one-electron transfer from heme b to the binuclear center. Finally, it is suggested that the hydroxy intermediate possesses no bridging ligand between heme o and Cu(B) and is the final intermediate in the turnover cycle of cytochrome bo under steady-state conditions.

Topics: Binding Sites; Coenzymes; Cytochrome b Group; Electron Spin Resonance Spectroscopy; Escherichia coli Proteins; Free Radicals; Freezing; Heme; Nanotechnology; Oxidation-Reduction; Oxidoreductases; Oxygen; Spectrophotometry; Ubiquinone

The Saccharomyces cerevisiae gene ABC1 was originally isolated as a multicopy suppressor of a yeast strain harboring a mutation in a cytochrome b translational activator (cbs2-223). Based on this identification, Abc1p was postulated to activate the bc1 complex and function as a chaperone of cytochrome b. ABC1 was subsequently identified as COQ8 and found to be necessary for yeast coenzyme Q synthesis. In this work we show that a segment of yeast genomic DNA containing ABC1/COQ8 and neighboring genes suppresses the respiratory and Q-deficient phenotypes of the coq6 mutant, coq6-1. COQ6 is essential for yeast coenzyme Q biosynthesis. We show that a tRNA(TRP) gene located downstream of ABC1/COQ8 mediates suppression of the cbs2-223 and coq6-1 mutations, and each is identified here as containing UGA nonsense codons. The inability of ABC1/COQ8 to suppress the cbs2-223 allele in multicopy indicates it may not be a chaperone as previously reported.

Topics: Gene Expression Regulation, Fungal; Molecular Chaperones; Mutagenesis, Site-Directed; RNA, Transfer, Trp; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Species Specificity; Suppression, Genetic; Trans-Activators; Ubiquinone

A lab-scale-enhanced biological phosphorus removal (EBPR) reactor was operated for 204 days to investigate the correlation between phosphorus removing performance and bacterial community structure. The phosphorus removing performance was good from day 1 to 92 and from day 172 to 204. However, the removal activity was in a deteriorated state from day 93 to 171. From day 69 (2 weeks before the beginning of the deterioration) to 118 (2 weeks after the beginning of the deterioration), sludge P content decreased. The amounts of ubiquinone-8 and menaquinone-8 (H(4)) decreased during this period while the amount of ubiquinone-10 increased. The comparison of these changes and the general attribution of each quinone to the bacterial phylogenetic groups suggested that beta proteobacteria and Actinobacteria contributed to EBPR positively, and that alpha proteobacteria were related to this EBPR deterioration. Glycogen accumulating organisms (GAOs) are considered to detrimentally affect EBPR ability by outcompeting the phosphorus accumulating organisms by using aerobically synthesized glycogen as the energy source to assimilate organic substrates anaerobically to form polyhydroxyalkanoates. However, in this research, there was nearly no substrate uptake during the anaerobic period at the middle of the deteriorated performance period. This suggests that the deterioration observed in this research does not agree with the GAOs inhibition model. In this research, the excess P release at the anaerobic period was concluded to cause the deterioration.

Topics: Actinobacteria; Betaproteobacteria; Bioreactors; Carbon; Glycogen; Microscopy, Electron; Organic Chemicals; Phosphorus; Sewage; Time Factors; Ubiquinone; Vitamin K 2; Waste Disposal, Fluid

Two Gram-negative, non-motile, non-spore-forming, rod-shaped organisms, strains SW-125T and SW-154T, were isolated from tidal flat sediment of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strains SW-125T and SW-154T grew optimally at 30-37 degrees C and in the presence of 2-3 % (w/v) NaCl. They contained ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and iso-C(15 : 0) as the major fatty acid. The DNA G + C contents of strains SW-125T and SW-154T were 44 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that the two strains form deep evolutionary lineages of descent within the gamma-Proteobacteria. Strains SW-125T and SW-154T exhibited 16S rRNA gene sequence similarity levels of less than 90 % to members of the gamma-Proteobacteria used in this analysis. Strains SW-125T and SW-154T showed a 16S rRNA gene sequence similarity level of 98.5 % and a mean DNA-DNA relatedness level of 9.4 %. Therefore, on the basis of phenotypic, phylogenetic and genomic data, a new genus, Kangiella gen. nov., is proposed to accommodate the novel strains, comprising two novel species, Kangiella koreensis sp. nov. (type strain, SW-125T = KCTC 12182T = DSM 16069T) and Kangiella aquimarina sp. nov. (type strain, SW-154T = KCTC 12183T = DSM 16071T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Gammaproteobacteria; Genes, rRNA; Growth Inhibitors; Korea; Molecular Sequence Data; Movement; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Saline Solution, Hypertonic; Seawater; Sequence Analysis, DNA; Spores, Bacterial; Temperature; Ubiquinone; Water Microbiology

A novel analytical method was applied for identification of isoprenoid quinones in Escherichia coli by liquid chromatography atmospheric press chemical ionization mass spectrometry in negative mode (LC-NI-APCI-MS). Extraction and clean-up of sample were carried out on Sep-Pak Plus Silica solid-phase extraction cartridges. Ubiquinone-7 (UQ-7), Ubiquinone-8 (UQ-8) and Mequinone-8 (MK-8) were determined directly using combined information on retention time, molecular ion mass, fragment ion masses and UV characteristic spectrometry without any standard reagent. It was found that UQ-8 was the major component of isoprenoid quinones in Escherichia coli under aerobic condition. Compared with UQ-8, the relative abundance of UQ-7 and MK-8 is only 15% and 14%, respectively. The average recoveries of UQ-6, UQ-10 and vitamin K(1) in Escherichia coli were investigated by standard spiking experiment. The recoveries were achieved in the range from 94 to 106%, and the relative standard deviations (RSD) of the triplicate analysis of the spiked samples (UQ-6, UQ-10 and vitamin K(1)) ranged from 3 to 8%. The detection limits of LC-NI-APCI-MS were estimated to be 5, 40 and 0.8 microg/g dry cell for UQ-6, UQ-10 and vitamin K(1), respectively.

Topics: Chromatography, Liquid; Escherichia coli; Mass Spectrometry; Quinones; Sensitivity and Specificity; Terpenes; Ubiquinone; Vitamin K 1; Vitamin K 2

Ubiquinone (coenzyme Q; Q) is a key factor in the mitochondria electron transport chain, but it also functions as an antioxidant and as a cofactor of mitochondrial uncoupling proteins. Furthermore, Q isoforms balance in Caenorhabditis elegans is determined by both dietary intake and endogenous biosynthesis. In the absence of synthesis, withdrawal of dietary Q8 in adulthood extends life span. Thus, Q plays an important role in the aging process and understanding its synthesis acquires a new impetus. We have identified by RNA interference (RNAi) eight genes, including clk-1, involved in ubiquinone biosynthesis in C. elegans feeding animals with dsRNA-containing Escherichia coli HT115 strains. Silenced C. elegans showed lower levels of both endogenous Q9 and Q8 provided by diet, produced less superoxide without a significant modification of mitochondrial electron chain, and extended life span compared with non-interfered animals. E. coli strains harboring dsRNA also interfered with their own Q8 biosynthesis. These findings suggest that more efficient electron transport between a lower amount of Q and electron transport capacity of the mitochondrial complexes leads to less production of reactive oxygen species that contributes to extension of life span in the nematode C. elegans.

Topics: Animals; Caenorhabditis elegans; Electron Transport; Escherichia coli; Longevity; Mitochondria; Models, Biological; RNA Interference; Superoxides; Transformation, Bacterial; Ubiquinone

We previously constructed two Schizosaccahromyces pombe ubiquinone-10 (or Coenzyme Q10) less mutants, which are either defective for decaprenyl diphosphate synthase or p-hydroxybenzoate polyprenyl diphosphate transferase. To further confirm the roles of ubiquinone in S. pombe, we examined the phenotype of the abc1Sp (coq8Sp) mutant, which is highly speculated to be defective in ubiquinone biosynthesis. We show here that the abc1Sp defective strain did not produce UQ-10 and could not grow on minimal medium. The abc1Sp-deficient strain required supplementation with antioxidants such as cysteine or glutathione to grow on minimal medium. In support of the antioxidant function of ubiquinone, the abc1Sp-deficient strain is sensitive to H2O2 and Cu2+. In addition, expression of the stress inducible ctt1 gene was much induced in the ubiquinone less mutant than wild type. Interestingly, we also found that the abc1-deficient strain as well as other ubiquinone less mutants produced a significant amount of H2S, which suggests that oxidation of sulfide by ubiquinone may be an important pathway for sulfur metabolism in S. pombe. Thus, analysis of the phenotypes of S. pombe ubiquinone less mutants clearly demonstrate that ubiquinone has multiple functions in the cell apart from being an integral component of the electron transfer system.

Topics: Antioxidants; Copper; Cysteine; Glutathione; Hydrogen Peroxide; Hydrogen Sulfide; Mutation; Oxidative Stress; Phenotype; Schizosaccharomyces; Ubiquinone

The Caenorhabditis elegans clk-1 mutants lack coenzyme Q(9) and instead accumulate the biosynthetic intermediate demethoxy-Q(9) (DMQ(9)). clk-1 animals grow to reproductive adults, albeit slowly, if supplied with Q(8)-containing Escherichia coli. However, if Q is withdrawn from the diet, clk-1 animals either arrest development as young larvae or become sterile adults depending upon the stage at the time of the withdrawal. To understand this stage-dependent response to a Q-less diet, the quinone content was determined during development of wild-type animals. The quinone content varies in the different developmental stages in wild-type fed Q(8)-replete E. coli. The amounts peak at the second larval stage, which coincides with the stage of arrest of clk-1 larvae fed a Q-less diet from hatching. Levels of the endogenously synthesized DMQ(9) are high in the clk-1(qm30)-arrested larvae and sterile adults fed Q-less food. Comparison of quinones from animals fed a Q-replete or a Q-less diet establishes that the Q(8) present is assimilated from the E. coli. Furthermore, this E. coli-specific Q(8) is present in mitochondria isolated from fertile clk-1(qm30) adults fed a Q-replete diet. These results suggest that the uptake and transport of dietary Q(8) to mitochondria prevent the arrest and sterility phenotypes of clk-1 mutants and that DMQ is not functionally equivalent to Q.

Topics: Animals; Biological Transport; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Diet; Genes, Helminth; Helminth Proteins; Larva; Mitochondria; Mutation; Quinones; Temperature; Ubiquinone

Topics: Aging; Animals; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Cell Nucleus; Diet; Electron Transport; Energy Metabolism; Escherichia coli; Fermentation; Helminth Proteins; Insulin; Larva; Longevity; Mitochondria; Mutation; Reactive Oxygen Species; Receptor, Insulin; Receptors, Cytoplasmic and Nuclear; Signal Transduction; Ubiquinone

The isoprenylated benzoquinone coenzyme Q is a redox-active lipid essential for electron transport in aerobic respiration. Here, we show that withdrawal of coenzyme Q (Q) from the diet of wild-type nematodes extends adult life-span by approximately 60%. The longevity of clk-1, daf-2, daf-12, and daf-16 mutants is also extended by a Q-less diet. These results establish the importance of Q in life-span determination. The findings suggest that Q and the daf-2 pathway intersect at the mitochondria and imply that a concerted production coupled with enhanced scavenging of reactive oxygen species contributes to the substantial life-span extension.

Topics: Aging; Animals; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Diet; Escherichia coli; Fermentation; Forkhead Transcription Factors; Genes, Helminth; Helminth Proteins; Larva; Longevity; Mitochondria; Models, Biological; Mutation; Oxidation-Reduction; Oxygen Consumption; Phenotype; Reactive Oxygen Species; Receptor, Insulin; Receptors, Cytoplasmic and Nuclear; Signal Transduction; Transcription Factors; Ubiquinone

A new helical, alkaliphilic, gram-negative, chemoorganotrophic bacterium designated strain Z4T was isolated from Haoji soda lake in Inner Mongolia Autonomous Region, China. The isolate grows at salinities between 0.2% and 5.0% (w/v) NaCl and pH range 7.0-11.0, with an optimum at 2.0% (w/v) NaCl and pH 9.5. Its growth temperature ranges from 8 degrees to 49 degrees C with an optimum at 37 degrees C. The G+C content of the DNA is 46.8 mol%. The major isoprenoid quinone is ubiquinone 8 (Q-8). Phylogenetic analyses based on 16S rDNA sequence comparison indicates that strain Z4T is a member of the genus Marinospirillum. Phenotypic features and DNA-DNA homology of less than 20% with the described species of Marinospirillum support the view that strain Z4T represents a new species of the genus Marinospirillum. Strain Z4T (= AS 1.2746) is proposed as the type strain of a new species, named Marinospirillum alkaliphilum sp. nov.

Topics: Bacteria; Bacterial Physiological Phenomena; Base Composition; China; Climate; DNA, Bacterial; DNA, Ribosomal; Phylogeny; RNA, Ribosomal, 16S; Temperature; Ubiquinone

A gram-negative, facultatively anaerobic, straight to slightly curved rod-shaped bacterium (RE35F/12T) sensitive to vibriostatic agent O/129 was previously isolated from sea water (Western Mediterranean Sea, Bay of Calvi, Corsica, France) by 0.2 microm-membrane filtration. Strain RE35/F12T (= CIP 107077T = DSM 14347T) was facultatively oligotrophic, halophilic, required Na+ for growth and produced acid but no gas from D-glucose under anaerobic conditions. Comparative 165 rRNA gene-sequence analyses demonstrated that the bacterium is most closely related (94.3%) to Vibrio scophthalmi. Similarities to the sequences of all other established Vibrio species ranged from 93.6% (with Vibrio aestuarianus) to 90.7% (with Vibrio rumoiensis). Strain RE35/F12T occupies a distinct phylogenetic position; this is similar to the case of Vibrio hollisae, because RE35F/12T represents a relatively long subline of descent sharing a branching point with the outskirts species V. hollisae. The G+C content of the DNA was 49.5 mol%. Ubiquinone Q-8 was the main respiratory lipoquinone, and 16:1omega9cis, 16:0 and 18:1trans9, cis11 were the major cellular fatty acids, 16:1omega9cis being predominant. The polyamine pattern was characterized by the presence of the triamine sym-norspermidine. On the basis of the polyphasic information summarized above, a new Vibrio species is described for which the name Vibrio calviensis sp. nov. is proposed.

Topics: Anaerobiosis; Base Composition; DNA, Bacterial; Filtration; France; Genes, rRNA; Marine Biology; Mediterranean Sea; Phylogeny; Polyamines; RNA, Ribosomal, 16S; Sequence Homology, Nucleic Acid; Ubiquinone; Vibrio

The functionality of the membrane-bound, ubiquinone-dependent pyruvate oxidase from the respiratory chain of Escherichia coli was reconstituted with a supported lipidic structure. The artificial structure was especially designed to allow the electrochemical control of the quinone pool through the lateral mobility of the ubiquinone (Q(8)) molecules. The kinetic coupling of the enzyme bound to the lipid structure with the quinone pool was ensured by the regeneration of the oxidized form of ubiquinone at the electrochemical interface. Such an experimental approach enabled us to carry out an unprecedented determination of the kinetic parameters controlling the reaction between the enzyme bound and the electron carrier under conditions taking rigorously into account the fact that the freedom of motion is restricted to two dimensions. The kinetic constants we found show that the activated enzyme can be efficiently regulated by the oxidation level of the quinone pool in natural membranes.

Topics: Carrier Proteins; Catalysis; Electrochemistry; Electrodes; Electron Transport; Escherichia coli; Kinetics; Lipid Bilayers; Membrane Proteins; Models, Chemical; Models, Molecular; Pyruvate Oxidase; Solubility; Surface Plasmon Resonance; Ubiquinone; Water

The cattle filarial parasite Setaria digitata is reported to have two ubiquinones, Q6 and Q8. These quinones are synthesized within the parasite itself and are not of host origin. Maximum concentration is found in the mitochondria of the parasite. When both Q6 and Q8 are formed and present in the adult stage, the microfilarial stage is now shown to contain only one quinone, namely Q6. Both in the adult and the mf stage, Q6 is associated with the process of electron transport. Though reduction of oxygen in S. digitata results in the generation of high concentrations of oxidants, antioxidants such as catalase and tocopherol are present in relatively lower concentrations. Hence it is proposed that the higher ubiquinone Q8 which is not involved in the electron transport process, is functioning as an antioxidant compensating for the reduced levels of classical antioxidants.

Topics: Animals; Cattle; Kinetics; Oxidoreductases; Setaria Nematode; Ubiquinone; Vitamin E

The Arc two-component signal transduction system mediates adaptive responses of Escherichia coli to changing respiratory conditions of growth. Under anaerobic conditions, the ArcB sensor kinase autophosphorylates and then transphosphorylates ArcA, a global transcriptional regulator that controls the expression of numerous operons involved in respiratory or fermentative metabolism. We show that oxidized forms of quinone electron carriers act as direct negative signals that inhibit autophosphorylation of ArcB during aerobiosis. Thus, the Arc signal transduction system provides a link between the electron transport chain and gene expression.

Topics: Aerobiosis; Bacterial Outer Membrane Proteins; Electron Transport; Escherichia coli; Escherichia coli Proteins; Gene Expression Regulation, Bacterial; Membrane Proteins; Mutation; Oxidation-Reduction; Phosphorylation; Protein Kinases; Quinones; Repressor Proteins; Signal Transduction; Ubiquinone; Vitamin K; Vitamin K 2

The filarial parasite Setaria digitata is unique in having two ubiquinones, Q(6) and Q(8), in the adult stage, in place of one, namely Q(10), in the host. However, the microfilariae (mf) as well as the electron transfer complexes from adult mitochondria have been recently shown to contain only Q(6). The second ubiquinone Q(8) is present only in the adult and absent in the mf. Though both Q(6) and Q(8) are present in the adult stage in the ratio 65:35, there is an enrichment of Q(8) in the excretory and secretory (ES) materials released into the incubation medium. The Q(6) level in the ES materials decreased further when the adult parasite was incubated in presence of diethylcarbamazine, a drug which inhibits the release of mf, indicating that the Q(6) detected in ES may be of mf origin. The preferential release of Q(8) into the external medium and its presence in the adult stage without any apparent role in the electron transport process strongly indicate an antioxidant role for the molecule. The inhibitory effect of Q(8) on lipid peroxidation and the presence of other components such as catalase and superoxide dismutase shown to be present in ES materials in earlier studies help the filarial parasite survive for longer periods by overcoming the oxidative reactions of the host generated against it.

Topics: Animals; Antioxidants; Catalase; Cattle; Chromatography, High Pressure Liquid; Diethylcarbamazine; Electron Transport; Filaricides; Hydroquinones; Lipid Peroxidation; Lipoxygenase Inhibitors; Mitochondria; Setaria Nematode; Superoxide Dismutase; Thiobarbituric Acid Reactive Substances; Ubiquinone

A polar multitrichous gram-negative motile rod, EY 3383, originally identified as Burkholderia thailandensis, revealed a DNA-DNA reassociation rate of 36.7%, under stringent conditions, with the type strain of B. thailandensis, despite the 16S rDNA homology value between two type strains being as high as 97.9%. The strain was clearly differentiated from the type strain of B. thailandensis by physiological, bio-chemical, and nutritional characteristics, without significant difference in cellular fatty acid and lipid composition. Based on the results of 16S rDNA sequence analysis, DNA-DNA hybridization and phenotypic characterization, Burkholderia uboniae sp. nov. is herein proposed. The type strain is NCTC 13147=EY 3383, isolated on 8 December 1989 from surface soil along the roadside in Ubon Ratchathani, Thailand. Major respiratory quinone is ubiquinone-8(Q8). G+C content of DNA is 69.71%.

Topics: Anti-Bacterial Agents; Arabinose; Bacterial Typing Techniques; Base Composition; Burkholderia; DNA, Ribosomal; Molecular Sequence Data; Nucleic Acid Hybridization; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Species Specificity; Ubiquinone

Isopentenyl diphosphate (IPP) acts as the common, five-carbon building block in the biosynthesis of all isoprenoids. The first reaction of IPP biosynthesis in Escherichia coli is the formation of 1-deoxy-D-xylulose-5-phosphate, catalysed by 1-deoxy-D-xylulose-5-phosphate synthase (DXPS). E. coli engineered to produce lycopene, was transformed with dxps genes cloned from Bacillus subtilis and Synechocystis sp. 6803. Increases in lycopene levels were observed in strains expressing exogenous DXPS compared to controls. The recombinant strains also exhibited elevated levels of ubiquinone-8. These increases corresponded with enhanced DXP synthase activity in the recombinant E. coli strains.

Topics: Amino Acid Sequence; Carotenoids; Cloning, Molecular; Escherichia coli; Gene Expression; Genes, Bacterial; Lycopene; Molecular Sequence Data; Pentosephosphates; Prokaryotic Cells; Sequence Homology, Amino Acid; Transferases; Ubiquinone

To probe the functional role of a bound ubiquinone-8 in cytochrome bo-type ubiquinol oxidase from Escherichia coli, we examined reactions with ubiquinol-1 and dioxygen. Stopped-flow studies showed that anaerobic reduction of the wild-type and the bound ubiquinone-free (delta UbiA) enzymes with ubiquinol-1 immediately takes place with four kinetic phases. Replacement of the bound ubiquinone with 2,6-dibromo-4-cyanophenol (PC32) suppressed the anaerobic reduction of the hemes with ubiquinol-1 by eliminating the fast phase. Flow-flash studies in the reaction of the fully reduced enzyme with dioxygen showed that the heme b to heme o electron transfer occurs with a rate constant of approximately 10(4) s-1 in all three preparations. These results support our previous proposal that the bound ubiquinone is involved in facile oxidation of substrates in subunit II and subsequent intramolecular electron transfer to low-spin heme b in subunit I.

Topics: Catalysis; Cytochrome b Group; Cytochromes; Escherichia coli; Escherichia coli Proteins; Heme; Oxidation-Reduction; Oxidoreductases; Oxygen; Spectrum Analysis, Raman; Time Factors; Ubiquinone

The coenzyme Q8 (CoQ8) and alpha-tocopherol contents of different mitochondrial fractions were investigated from occipital cerebral cortices of different ages. The highest CoQ8 and vitamin E concentrations were found in non-synaptic free mitochondria (FM) fractions. In several cases heavy mitochondria (HM) fractions displayed the lowest values. Occipital cerebral cortex mitochondria contained higher CoQ9 and lower CoQ10 amounts than those typical for other brain regions.

Topics: Aging; Animals; Coenzymes; Male; Mitochondria; Occipital Lobe; Oxidative Stress; Rats; Rats, Sprague-Dawley; Synapses; Ubiquinone; Vitamin E

Reaction of ubiquinone in the high-affinity quinone-binding site (QH) in bo-type ubiquinol oxidase from Escherichia coli was revealed by EPR and optical studies. In the QH site, ubiquinol was shown to be oxidized to ubisemiquinone and to ubiquinone, while no semiquinone signal was detected in the oxidase isolated from mutant cells that cannot synthesize ubiquinone. The QH site highly stabilized ubisemiquinone radical with a stability constant of 1-4 at pH 8.5 and the stability became lower at the lower pH. Midpoint potential of QH2/Q couple was -2 mV at pH 8.5 and showed -60 mV/pH dependence indicative of 2H+/2e- reaction. The Em was more negative than that of low-spin heme b above pH 7.0. We conclude that the QH mediates intramolecular electron transfer from ubiquinol in the low-affinity quinol oxidation site (QL) to low-spin heme b. Unique roles of the quinone-binding sites in the bacterial ubiquinol oxidase are discussed.

Topics: Benzoquinones; Binding Sites; Coenzymes; Electron Spin Resonance Spectroscopy; Electron Transport; Electron Transport Complex IV; Enzyme Stability; Escherichia coli; Heme; Hydrogen-Ion Concentration; Oxidation-Reduction; Potentiometry; Spectrum Analysis; Ubiquinone

The incorporation of 2H- and 13C-labelled precursors into ubiquinone-8 (Uq-8) by strains of Escherichia coli was measured in order to define the pathway for the early steps in the biosynthesis of isoprenoids in these eubacteria. Cells grown with DL-[methyl-2H6]valine were found to label both the alpha-oxoisovaleric ('alpha-ketoisovaleric') acid alpha-oxoisohexanoic ('alpha-ketoisocaproic') acid, but not the Uq-8. Since these acids are required for the biosynthesis of isoprenoids by the acetolactate pathway, the operation of this pathway in the biosynthesis of Uq-8 is excluded. Cells grown with [1,2-13C2]acetate and non-labelled glucose readily incorporated 13C2 units into fatty acids, but failed to incorporate any label into the Uq-8. Cells grown with [U-13C6]glucose and non-labelled acetate, however, were found to label both the fatty acids and the Uq-8. Oxidative cleavage with periodate/permanganate of the Uq-8 isolated from cells grown with U-13C6-labelled glucose produced laevulinic acid, which was shown to be derived from two C2 units and one C1 unit of the labelled glucose by mass-spectral analysis of the 4,5-dihydro-6-methyl-2-phenylpyridazin-3(2H)-one derivative. The results of this work indicate that the C-2 and C-3 carbon unit of pyruvate, not acetyl-CoA, is the precursor to isopentenyl pyrophosphate (IPP) in these cells; however, the labelling pattern observed is consistent with the established acetoacetate pathway of isoprenoid biosynthesis. These data, coupled with the observed lack of inhibition of the growth of E. coli by mevinolin, a specific inhibitor of 3-hydroxy-3-methylglutaryl-CoA, can be best rationalized by the biosynthesis of IPP occurring in E. coli through a series of bound intermediates.

Topics: Acetates; Acetic Acid; Bacterial Proteins; Carbon Isotopes; Deuterium; Escherichia coli; Glucose; Hemiterpenes; Isotope Labeling; Lactates; Lactic Acid; Lovastatin; Mass Spectrometry; Organophosphorus Compounds; Ubiquinone

The effect of exogenous ubiquinone-8 (Q8) on IgG- and C3b-mediated phagocytosis of sensitized sheep red blood cells and of opsonized Staphylococcus aureus by macrophages was studied by morphological and quantitative methods. Q8 stimulated the initial events of phagocytosis, that is, attachment and ingestion, in which occupancy of the Fc receptor by IgG was shown to be of critical significance. The kinetics of competitive inhibition of phagocytosis of opsonized bacteria by macrophages by using Fc fragments suggested the intimate role of the kinetics of the Fc receptor in the initial events of phagocytosis and, further, the modulation of the kinetics of the Fc receptor by Q8 as the basis of enhanced phagocytosis by Q8.

Topics: Animals; Blood; Cell Membrane; Erythrocytes; Guinea Pigs; Humans; Immunoglobulin Fc Fragments; Kinetics; Macrophage Activation; Macrophages; Microscopy, Electron; Microscopy, Electron, Scanning; Opsonin Proteins; Organoids; Phagocytosis; Receptors, Fc; Staphylococcus aureus; Ubiquinone

The aerobic respiratory chain of Escherichia coli is branched and contains two terminal oxidases. The chain predominant when the cells are grown with low aeration terminates with the cytochrome d terminal oxidase complex, and the branch present under high aeration ends with the cytochrome o terminal oxidase complex. Previous work has shown that cytochrome d complex functions as a ubiquinol-8 oxidase, and that a minimal respiratory chain can be reconstituted in proteoliposomes with a flavoprotein dehydrogenase (pyruvate oxidase), ubiquinone-8, and the cytochrome d complex. This paper demonstrates that the cytochrome o complex functions as an efficient ubiquinol-8 oxidase in reconstituted proteoliposomes, and that ubiquinone-8 serves as an electron carrier from the flavoprotein to the cytochrome complex. The maximal turnover (per cytochrome o) achieved in reconstituted proteoliposomes is at least as fast as observed in E. coli membrane preparations. Electron flow from the flavoprotein to oxygen in the reconstituted proteoliposomes generates a transmembrane potential of at least 120 mV, negative inside, which is sensitive to ionophore uncouplers and inhibitors of the terminal oxidase. These data demonstrate the minimal composition of this respiratory chain as a flavoprotein dehydrogenase, ubiquinone-8, and the cytochrome o complex. Previous models have suggested that cytochrome b556, also a component of the E. coli inner membrane, is required for electron flow to cytochrome o. This is apparently not the case. It now is clear that both of the E. coli terminal oxidases act as ubiquinol-8 oxidases and, thus, ubiquinone-8 is the branch point between the two respiratory chains.

Topics: Cell Membrane; Cytochrome b Group; Cytochromes; Electron Transport Complex IV; Escherichia coli; Escherichia coli Proteins; Kinetics; Models, Biological; Oxidoreductases; Oxygen Consumption; Pyruvate Oxidase; Spectrometry, Fluorescence; Ubiquinone

Pyruvate oxidase is a flavoprotein dehydrogenase located on the inner surface of the Escherichia coli cytoplasmic membrane and coupled to the E. coli aerobic respiratory chain. In this paper, the role of quinones in the pyruvate oxidase system is investigated, and a minimal respiratory chain is described consisting of only two pure proteins plus ubiquinone 8 incorporated in phospholipid vesicles. The enzymes used in this reconstitution are the flavoprotein and the recently purified E. coli cytochrome d terminal oxidase. The catalytic velocity of the reconstituted liposome system is about 30% of that observed when the flavoprotein is reconstituted with E. coli membranes. It is also shown that electron transport from pyruvate to oxygen in the liposome system generates a transmembrane potential of at least 180 mV (negative inside), which is sensitive to the uncouplers carbonyl cyanide p-(tri-chloromethoxy)phenylhydrazone and valinomycin. A trans-membrane potential is also generated by the oxidation of ubiquinol 1 by the terminal oxidase in the absence of the flavoprotein. It is concluded that (1) the flavoprotein can directly reduce ubiquinone 8 within the phospholipid bilayer, (2) menaquinone 8 will not effectively substitute for ubiquinone 8 in this electron-transfer chain, and (3) the cytochrome d terminal oxidase functions as a ubiquinol 8 oxidase and serves as a "coupling site" in the E. coli aerobic respiratory chain. These investigations suggest a relatively simple organization for the E. coli respiratory chain.

Topics: Cell Membrane; Cytochrome b Group; Cytochromes; Electron Transport; Electron Transport Chain Complex Proteins; Escherichia coli; Escherichia coli Proteins; Kinetics; Lipid Bilayers; Membrane Potentials; Oxidoreductases; Pyruvate Oxidase; Ubiquinone

Extraction with n-heptane abolished over 95% of the NADH oxidase and the hydrogenase activity in membrane preparations from Azotobacter vinelandii. Incorporation of ubiquinone-8 or plastoquinone restored each reaction to about 55% of its original activity.

Topics: Azotobacter; Hydrogen; Multienzyme Complexes; NADH, NADPH Oxidoreductases; Plastoquinone; Ubiquinone

The thermotropic properties of coenzymes Q10, Q9, Q8, and Q7 have been examined by differential scanning calorimetry and wide-angle X-ray diffraction. Typical scanning calorimetry cooling curves of coenzyme Q from the liquid state exhibit a single exothermic phase transition into a crystalline state at a temperature that decreases as the length of the polyisoprenoid side-chain substituent decreases. Upon subsequent heating, the molecules undergo a series of thermal events which precede the main crystalline-to-liquid endothermic phase transition. The temperature of these transitions increases with increasing chain length. The crystallization phase transition temperature depends markedly on the rate at which the sample is cooled and increases with decreasing scan rate; the temperature of the melting endotherm is not markedly affected by the scan rate. Detailed calorimetric studies of coenzyme Q10 indicate that two crystalline states are formed, one at relatively high cooling rates to low temperatures and the other when preparations are cooled slowly from the liquid state to relatively high temperatures. Heating the crystalline phase formed by rapid cooling causes its transformation into the phase observed by cooling slowly. X-ray diffraction analysis confirmed the existence of these two crystal phases in coenzymes Q9 and Q10 and the transformation from the rapidly crystallized form to the more ordered form associated with slower cooling rates. At body temperature (310 K) under equilibrium conditions coenzyme Q10 exists in an ordered crystalline phase; the implications of the thermotropic behavior of coenzyme Q10 on mitochondrial function in vitro and in vivo are discussed.

Topics: Calorimetry, Differential Scanning; Coenzymes; Crystallization; Crystallography, X-Ray; Mitochondria; Thermodynamics; Ubiquinone

Topics: Animals; Anti-Infective Agents; Coenzymes; Female; Immunity, Cellular; Listeriosis; Mice; Spleen; Ubiquinone