menaquinone-6 and sym-homospermidine

A yellow-pigmented bacterial strain, designated T13

Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fabaceae; Fatty Acids; Flavobacterium; Phosphatidylethanolamines; Phospholipids; Phylogeny; Pigmentation; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

A Gram-stain-negative, yellowish-orange pigmented, rod-shaped, motile bacterium, designated strain ARC111

Topics: Arctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Geologic Sediments; Ice Cover; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Svalbard; Vitamin K 2

A novel Gram-stain-negative, rod-shaped, strictly aerobic, and orange-yellow pigmented bacterium, designated strain AFPH31

Topics: Animals; Anthozoa; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Germany; Phosphatidylethanolamines; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

Four rod-shaped and Gram-stain-negative bacterial strains, CCM 8647, CCM 8649T, CCM 8643T and CCM 8648T, were isolated from rock samples collected on James Ross Island, Antarctica. Extensive biotyping, fatty acid profiling, chemotaxonomy, 16S rRNA gene sequencing and whole-genome sequencing was applied to isolates to clarify their taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that all four isolates belonged to the genus Hymenobacter. Strains CCM 8649T and CCM 8647 were most closely related to Hymenobacter arizonensis OR362-8T (94.4 % 16S rRNA gene sequence similarity), strain CCM 8643T to Hymenobacter terrae DG7AT (96.3 %) and strain CCM 8648T to Hymenobacter glaciei VUG-A130T (96.3 %). The predominant fatty acids of CCM 8649T and CCM 8647 were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 1ω5c and iso-C15 : 0, whereas those of CCM 8643T and CCM 8648T were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 1ω5c. The quinone systems contained exclusively menaquinone MK-7. The major polyamine was sym-homospermidine. All four strains contained the major polar lipid phosphatidylethanolamine. The G+C content of genomic DNA ranged from 60-63 mol%. Whole-genome sequencing data supported the finding that isolates represented distinct species of the genus Hymenobacter. On the basis of the results obtained, three novel species are proposed for which the names Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov. are suggested, with the type strains CCM 8649T (=LMG 29441T=P5239T), CCM 8643T (=LMG 29435T=P3150T) and CCM 8648T (=LMG 29440T=P5086T), respectively.

Topics: Antarctic Regions; Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Phosphatidylethanolamines; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A non-motile, red-pink-coloured, rod-shaped bacterium, designated strain POB6T, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The strain contained menaquinone MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 61 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain POB6T forms a distinct evolutionary lineage within the radiation enclosing the members of the genus Hymenobacter, sharing the highest similarity with Hymenobacterrigui WPCP131T (97.5 %) followed by Hymenobacter xinjiangensis X2-1gT (97.2 %), Hymenobacter perfusus A1-12T (97.2 %) and Hymenobacter gelipurpurascens Txg-1T (97.1 %). A number of phenotypic characteristics distinguished strain POB6T from related members of the genus Hymenobacter. On the basis of the evidence presented in this study, a novel species, Hymenobacter tenuis sp. nov., is proposed, with POB6T (=KCTC 52271T=JCM 31659T) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Phosphatidylethanolamines; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2; Wastewater

Strain P4487AT was isolated during investigation of cultivable bacterial populations of environmental materials sampled at James Ross Island, Antarctica. It revealed Gram-stain-negative short rod-shaped cells producing a pink pigment. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain P4487AT to the genus Pedobacter but showed that the strain represents a distinct intrageneric phylogenetic lineage clearly separated from remaining Pedobacter species. Phylogenetically, strain P4487AT formed a common branch with the Pedobacter arcticus and Pedobacter lignilitoris cluster while the highest value of 94.4 % 16S rRNA gene sequence similarity suggested that Pedobacter lentus is the most closely related species. Biochemical and physiological test results enabled the differentiation of strain P4487AT from all phylogenetically closely related species. Chemotaxonomic analyses of strain P4487AT showed MK-7 as the respiratory menaquinone, sym-homospermidine as the major polyamine, phosphatidylethanolamine and two unidentified lipids as the major polar lipids, presence of sphingolipids, and C16 : 1ω7c/C16 : 1ω6c (summed feature 3), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids, all of which corresponded with characteristics of the genus Pedobacter. The results showed that strain P4487AT represents a novel species within the genus Pedobacter, for which the name Pedobacter psychrophilus sp. nov. is proposed. The type strain is P4487AT (=CCM 8644T=LMG 29436T).

Topics: Antarctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Pedobacter; Phosphatidylethanolamines; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Sphingolipids; Vitamin K 2

A polyphasic approach was used to characterize a Gram-staining negative bacterium (designated strain CC-YHH650T) isolated from agarwood chips. Strain CC-YHH650T was aerobic and rod-shaped, able to grow at 15-37 °C (optimal 30 °С), pH 6.0-8.0 (optimal 7.0) and 0-1 % (w/v) NaCl (optimal 0 %). Phylogenetic analysis based on 16S rRNA genes revealed that strain CC-YHH650T shared highest sequence similarities with Filimonas lacunae (97.5 %), F. zeae (97.4 %), F. endophytica (97.3 %) and F. aurantiibacter (93.0 %), and lower sequence similarity with other genera (less than 93.0 %). The levels of DNA-DNA relatedness between strain CC-YTH209T, F. lacunae, F. endophytica and F. zeae were estimated to be 18.3, 6.1, 24.7 % (the reciprocal values were 9.8, 8.8, 18.3 %). The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, C16 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 1ω7c/C16 : 1ω6c. The polar lipid profile contained phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminophospholipids, three unidentified aminolipids and three unidentified lipids. The DNA G+C content was 46.6 mol% and the predominant quinone was menaquinone-7 (MK-7). The major polyamine was sym-homospermidine. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-YHH650T is considered to represent a novel species of the genus Filimonas, for which the name Filimonas aquilariae sp. nov. is proposed. The type strain is CC-YHH650T (=BCRC 80935T=JCM 31197T).

Topics: Bacterial Typing Techniques; Bacteroidetes; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Taiwan; Thymelaeaceae; Vitamin K 2; Wood

A yellow-pigmented bacterial strain, JM-222T, isolated from the root tissue of field-grown cotton (Gossypium hirsutum) in Auburn, Alabama, USA, was studied for its taxonomic allocation. Cells of the isolate were rod-shaped and Gram-stain-negative. A blast analysis using the EzTaxon database showed that strain JM-222T shared highest 16S rRNA gene sequence similarity with the type strain of Flavobacterium endophyticum (98.9 %) followed by Flavobacterium qiangtangense (96.7 %). 16S rRNA gene sequence similarities to all other Flavobacterium species were below 95 %. The fatty acid profile of strain JM-222T consisted of the major fatty acids C15 : 0, iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. Major compounds in the polar lipid profile were phosphatidylethanolamine and several unidentified lipids. The quinone system consisted predominantly of menaquinone MK-6. The polyamine pattern consisted of the major compound sym-homospermidine and only minor amounts of other polyamines. These data and the differential biochemical and chemotaxonomic properties showed that the isolate JM-222T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium gossypii sp. nov. is proposed. The type strain is JM-222T (LMG 28821T=CCM 8610T).

Topics: Alabama; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Flavobacterium; Gossypium; Phosphatidylethanolamines; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A yellow-pigmented, Gram-stain-negative, motile and rod-shaped bacterium, strain M1A16

Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Haliclona; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A novel Gram-staining-negative, aerobic, non-motile by gliding and rod-shaped strain, designated 22T, was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, PR China. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter suwonensis 15-52T (97.5 %), Pedobacter terrae DS-57T (97.1 %) and Pedobacter alluvionis NWER-II11T (97.0 %). Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain 22T is a member of the genus Pedobacter. The isolate exhibited relatively low levels of DNA-DNA relatedness with respect to P. suwonensis DSM 18130T (21.3±2.0 %), P. alluvionis DSM 19624T (38.1±1.8 %) and P. terrae DSM 17933T (17.1±1.4 %). The DNA G+C content was 41.2±0.5 mol%. The major isoprenoid quinone was menaquinone-7 (MK-7). The major component in the polyamine pattern was sym-homospermidine. The major polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids and one unidentified lipid. The major fatty acids were identified as iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The results of the physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 22T from the related species with high 16S rRNA gene sequence similarity, P. suwonensis DSM 18130T, P. alluvionis DSM 19624T and P. terrae DSM 17933T. Strain 22T represents a novel species within the genus Pedobacter, for which the name Pedobacter zeae sp. nov. is proposed, with the type strain 22T (=CGMCC 1.15287T=DSM 100774T).

Topics: Bacterial Typing Techniques; Base Composition; Beijing; DNA, Bacterial; Endophytes; Fatty Acids; Pedobacter; Phosphatidylethanolamines; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2; Zea mays

A taxonomic study performed on 17 Gram-stain-negative rod-shaped bacterial strains originating from the Antarctic environment is described. Initial phylogenetic analysis using 16S rRNA gene sequencing differentiated the strains into four groups belonging to the genus Pedobacter but they were separated from all hitherto described Pedobacter species. Group I (n=8) was closest to Pedobacter aquatilis (97.8 % 16S rRNA gene sequence similarity). Group II (n=2) and group III (n=4) were closely related (98.8 % 16S rRNA gene sequence similarity) and had Pedobacter jejuensis as their common nearest neighbour. Group IV (n=3) was distantly delineated from the remaining Pedobacter species. Differentiation of the analysed strains into four clusters was further confirmed by repetitive sequence-based PCR fingerprinting, ribotyping, DNA-DNA hybridization and phenotypic traits. Common to representative strains for the four groups were the presence of major menaquinone MK-7, sym-homospermidine as the major polyamine, phosphatidylethanolamine, two unidentified lipids (L2, L5) and an unidentified aminolipid (AL2) as the major polar lipids, presence of an alkali-stable lipid, and C16:1ω7c/C16:1ω6c (summed feature 3), iso-C15:0 and iso-C 17:0 3-OH as the major fatty acids, which corresponded to characteristics of the genus Pedobacter. The obtained results showed that the strains analysed represent four novel species of the genus Pedobacter, for which the names Pedobacter jamesrossensis sp. nov. (type strain CCM 8689T=LMG 29684T), Pedobacter lithocola sp. nov. (CCM 8691T=LMG 29685T), Pedobacter mendelii sp. nov. (CCM 8685T=LMG 29688T) and Pedobacter petrophilus sp. nov. (CCM 8687T=LMG 29686T) are proposed.

Topics: Antarctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Pedobacter; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A pale-pink-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterial strain, PP-F2F-G47T, was isolated from the phyllosphere of the herbaceous plant Galium album. Phylogenetic analysis based on the nearly full-length 16S rRNA gene sequence revealed highest sequence similarity to the type strains of Mucilaginibacter daejeonensis (96.2 %), Mucilaginibacter dorajii (95.7 %) and Mucilaginibacter phyllosphaerae (95.5 %). 16S rRNA gene sequence similarities to all other type strains were below 95.5 %. The predominant cellular fatty acids of the strain were C16 : 1ω7c/iso-C15 : 0 2-OH (measured as summed feature 3) and iso-C15 : 0. The major compound in the polyamine pattern was sym-homospermidine and major quinone was menaquinone MK-7. The polar lipid profile was composed of phosphatidylethanolamine and several unidentified aminolipipids, phospholipids, aminophospholipids and lipids without a functional group. A sphingophospholipid could not be detected but a ninhydrin-positive alkaline-stable lipid was visible. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Based on phylogenetic, chemotaxonomic and phenotypic analyses a novel species is proposed, Mucilaginibacter galii sp. nov., with PP-F2F-G47T (=CCM 8711T=CIP 111182T=LMG 29767T) as the type strain.

Topics: Bacterial Typing Techniques; Bacteroidetes; Base Composition; Diaminopimelic Acid; DNA, Bacterial; Fatty Acids; Galium; Germany; Phospholipids; Phylogeny; Plant Leaves; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

Strain NP1T, a Gram-stain-negative, orange, rod-shaped bacterium was isolated from hexacholorocyclohexane (HCH)-contaminated soil sediment samples collected from Ummari village, Lucknow, Uttar Pradesh, India. The results of 16S rRNA gene sequence analysis indicated that NP1T clustered with members of the genus Pontibacter of the order Cytophagales, family Cytophagaceae and phylum Bacteriodetes. The 16S rRNA gene sequence similarity with type strains of members of the genus Pontibacter ranged from 98.57 to 93.95 % with Pontibacter odishensis JC-130T (98.57 %), Pontibacter korlensis X14-1T (97.82 %), Pontibacter litorisediminisYKTF-7T (97.42 %) and Pontibacter virosus W-14T (97.01 %) as the closest neighbours. Cells of NP1T were aerobic, motile and oxidase- and catalase-positive. NP1T was capable of hydrolysis of gelatin, aesculin and starch and reduced nitrates to nitrogen. The major fatty acids of NP1T were summed feature 4 and iso-C15 : 0. The polar lipid profile of NP1T showed the presence of phosphatidylethanolamine (PE), unknown glycolipids and unknown aminolipids. Menaquinone-7 (MK-7) was the predominant respiratory quinone and sym-homospermidine was found to be the predominant polyamine in NP1T. The DNA G+C content of NP1T was 52.1±0.7 mol%. The levels of DNA-DNA relatedness of NP1T to P. odishensis JC-130T, P. korlensis X14-1T, P. litorisediminis YKTF-7T and P. virosus W14T were 44.9±0.6 %, 40.5±0.4 %, 34.4±0.7 % and 33.4±0.5 % respectively. Based on the phenotypic, chemotaxonomic, physiological and biochemical evidence and DNA-DNA hybridization results, it is proposed that NP1T represents a novel species of the genus Pontibacter, for which the name Pontibacter aurantiacus sp. nov. is proposed. The type strain is NP1T (KCTC 42943T=CCM 8697T=MCC 2931T).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Glycolipids; Hexachlorocyclohexane; India; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants; Spermidine; Vitamin K 2

A Gram-stain-negative, non-motile, aerobic and rod-shaped bacterium, strain Ra1T, was isolated from the gut of a wood-feeding lower termite, Reticulitermes aculabialis. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain was closely related to Chryseobacterium rigui JCM 18078T (96.7 % similarity). Growth was observed at 15-45 °C (optimum 30 °C), at pH 6.0-9.0 (optimum pH 8.0) and in the presence of 0-2 % (w/v) NaCl (optimum 0 %). The DNA G+C content of strain Ra1T was 39.9 mol%. Cells contained menaquinone MK-6 as the sole respiratory quinone and the major fatty acids were iso-C15 : 0, iso-C17 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 9 (comprising C16 : 0 10-methyl and/or iso-C17 : 1ω9c). The predominant polyamine was sym-homospermidine. The cellular polar lipids consisted of one phosphatidylethanolamine, three unidentified aminolipids, one unidentified phospholipid and one unidentified lipid. Based on phenotypic, genotypic and phylogenetic studies, it is concluded that strain Ra1T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium reticulitermitis sp. nov. is proposed. The type strain is Ra1T (=CCTCC AB 2015431T=KCTC 52230T).

Topics: Animals; Bacterial Typing Techniques; Base Composition; China; Chryseobacterium; DNA, Bacterial; Fatty Acids; Isoptera; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A polyphasic approach was used to characterize a presumably novel bacterium, designated strain CC-KYC063T, isolated from a compost sample collected at a greenhouse facility within Taiwan. Strain CC-KYC063T was Gram-stain-negative and aerobic, able to grow at 15-37 °C (optimal 30 °C), at pH 7.0-9.0 (optimal pH 7.0) and with 0-2 % (w/v) NaCl. The 16S rRNA gene sequence of strain CC-KYC063T showed highest similarity to Olivibacter ginsengisoli Gsoil 060T (96.2 %) and Olivibacter terrae Jip13T (95.5 %). The DNA G+C content was 43.0 mol% and the predominant quinone system was menaquinone-7 (MK-7). The polyamine pattern showed a predominance of sym-homospermidine. The major fatty acids found in strain CC-KYC063T were iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω6c/C16 : 1ω7c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-KYC063T is considered to represent a novel species of the genus Olivibacter, for which the name Olivibacter composti sp. nov. is proposed. The type strain is CC-KYC063T (=BCRC 80939T=JCM 31198T).

Topics: Bacterial Typing Techniques; Bacteroidetes; Base Composition; DNA, Bacterial; Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Taiwan; Vitamin K 2

A Gram-stain-negative, motile by gliding, yellow-pigmented bacterial strain, designated KNUS1T, was isolated from Lake Paro in Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain KNUS1T formed a distinct lineage within the genus Flavobacterium. Strain KNUS1T was closely related to Flavobacterium cheonhonense ARSA-15T (96.8 %16S rRNA gene sequence similarity), Flavobacterium pectinovorum DSM 6368T (96.3 %) and Flavobacterium dankookense ARSA-19T (96.1 %). The major fatty acids of strain KNUS1T were iso-C15 : 0 and iso-C15 : 1 G. The major polyamine was sym-homospermidine. The major polar lipids of strain KNUS1T were phosphatidylethanolamine, five unidentified aminolipids and three unidentified polar lipids. The major respiratory'quinone was menaquinone 6 (MK-6). The DNA G+C content of strain KNUS1T was 34.2 mol%. On the basis of the evidence presented in this study, strain KNUS1T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium paronense sp. nov. is proposed. The type strain is KNUS1T ( = KACC 17692T = CECT 8460T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacterium; Fresh Water; Islands; Molecular Sequence Data; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A Gram-stain-negative, aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG S15-2T, was isolated from playground soil in Sindorim-dong, Guro-gu, Seoul, South Korea. According to 16S rRNA gene sequence comparisons, strain THG S15-2T was found to be related most closely to Pedobacter ginsengisoli Gsoil 104T (97.5 % similarity), Pedobacter panaciterrae Gsoil 042T (97.4 %), Pedobacter seoulensis THG-G12T (97.1 %) and Pedobacter caeni LMG 22862T (97.1 %). The level of DNA-DNA relatedness between strain THG S15-2T and its phylogenetically closest neighbours was below 30.0 %. The only isoprenoid quinone detected in strain THG S15-2T was menaquinone-7. The DNA G+C content was 45.9 mol%. The major polar lipid was phosphatidylethanolamine. The major component in the polyamine pattern was sym-homospermidine. The major fatty acids were identified as summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0 and C16:0. These data supported the affiliation of strain THG S15-2T to the genus Pedobacter. Strain THG S15-2T was distinguished from related Pedobacter species by physiological and biochemical tests. Therefore, strain THG S15-2T represents a novel species, for which the name Pedobacter humi sp. nov. is proposed. The type strain is THG S15-2T (= KCTC 42735T = CCTCC AB 2015293T).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Pedobacter; Phosphatidylethanolamines; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

A Gram-stain-negative, rod-shaped bacterium, strain 784B1_12E-Caso

Topics: Bacterial Typing Techniques; Biofuels; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Germany; Manure; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A polyphasic approach was used to characterize an endospore-forming bacterium, designated strain CC-RT-ET, isolated from resin fragments. Strain CC-RT-ET was Gram-stain-variable and facultatively anaerobic, able to grow at 20-37 °C (optimal 30 °C) and pH6.0-9.0 (optimal pH 7.0). Ellipsoidal and terminal endospores were observed. The 16S rRNA gene sequence analysis of strain CC-RT-ET showed highest sequence similarity to Ammoniphilus oxalivorans RAOx-FST (97.8 %) and Ammoniphilus oxalaticus RAOx-1T (97.7 %). According to the DNA-DNA hybridization, the relatedness values of strain CC-RT-ET with Ammoniphilus oxalivorans RAOx-FST and Ammoniphilus oxalaticus RAOx-1T were 21 % and 29 %, respectively. The DNA G+C content was 39.2 mol% and the predominant quinone system was menaquinone-7 (MK-7). The major polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmethylethanolamine. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The polyamine pattern showed predominance of sym-homospermidine and putrescine. The major fatty acids found in strain CC-RT-ET were C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and C16 : 1ω7c/C16 : 1ω6c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-RT-ET is considered to represent a novel species of the genus Ammoniphilus, for which the name Ammoniphilus resinaesp. nov. is proposed. The type strain is CC-RT-ET (=BCRC 80314T=DSM 24738T).

Topics: Bacillales; Bacterial Typing Techniques; Base Composition; Diaminopimelic Acid; DNA, Bacterial; Fatty Acids; Indonesia; Nucleic Acid Hybridization; Peptidoglycan; Phospholipids; Phylogeny; Resins, Plant; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Spores, Bacterial; Vitamin K 2

A non-motile and rod-shaped bacterium, designated strain WW84T, was isolated from freshwater collected from the Woopo wetland (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were C16 : 0, C18 : 0, iso-C15 : 0 and iso-C17 : 1I and/or anteiso-C17 : 1B. The strain contained MK-7 as the major isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 59 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WW84T forms an evolutionary lineage within the radiation including the members of the genus Hymenobacter with Hymenobactero cellatus Myx 2105T (96.96 % sequence similarity) as its nearest neighbor. A number of phenotypic characteristics distinguished strain WW84T from the related members of the genus Hymenobacter. On the basis of the evidence presented in this study, a novel species, Hymenobacter coalescens sp. nov. is proposed with strain WW84T (=KCTC 32530T=JCM 19493T) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Fresh Water; Phosphatidylethanolamines; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2; Wetlands

A Gram-stain-negative bacterium was isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1458T had a sequence similarity to Filimonas lacunae YT21T, Sediminibacterium goheungense HME7863T, Parasegetibacter terrae SGM2-10T, Sediminibacterium ginsengisoli DCY13T, Terrimonas ferruginea DSM 30193T, Lacibacter cauensis NJ-8T, Flavihumibacter solisilvae 3-3T, Parasegetibacter luojieneis RHYL-37T, Vibrionimonas magnilacihabitans MU-2T and Parafilimonas terrae 5GHs7-2T with values of 93.4, 92.3, 91.9, 91.9, 91.8, 91.6, 91.6, 91.6, 91.5 and 90.4 %, respectively. The primary cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1G and summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c). The primary polar lipids were phosphatidylethanolamine and an unidentified polar lipid only detectable after total polar lipid staining. The quinone system was menaquinone MK-7, and in the polyamine pattern, sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 15 to 40 °C and pH 5.0 to 8.0, a salt tolerance range of 0 to 2.0 % (w/v), production of orange cell-bound pigment flexirubin, and gliding motility. After phenotypic, chemotaxonomic and molecular analyses, strain 1458T was identified as a novel species of the genus Filimonas, for which the name Filimonas aurantiibacter sp. nov. is proposed. The type strain is 1458T (=NRRL B-65305T=LMG 29039T). An emended description of the genus Filimonas is also provided.

Topics: Bacterial Typing Techniques; Bacteroidetes; Base Composition; DNA, Bacterial; Fatty Acids; Lakes; Michigan; Phosphatidylethanolamines; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A pink-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterial strain, PP-F2F-G21T, was isolated from the phyllosphere of Galium album. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence of strain PP-F2F-G21T showed the closest relationship to type strains of the species Mucilaginibacter lutimaris (97.7 %), Mucilaginibacter soli (97.3 %) and Mucilaginibacter rigui (97.1 %). Sequence similarities to all other type strains were below 97 %. The predominant cellular fatty acids of strain PP-F2F-G21T are C16 : 1 ω7c/iso-C15 : 0 2-OH (measured as summed feature 3 fatty acids) and iso-C15 : 0 followed by iso-C17 : 0 3-OH, C16 : 1 ω5c and C16 : 0. The major compound in the polyamine pattern was sym-homospermidine and the diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system was exclusively composed of menaquinone MK-7. The polar lipid profile contained the major lipid phosphatidylethanolamine and in addition 18 unidentified lipids. Based on phylogenetic, chemotaxonomic and phenotypic analyses, we propose a novel species of the genus Mucilaginibacter named Mucilaginibacter phyllosphaeraesp. nov. The type strain is PP-F2F-G21T (=CCM 8625T=CIP 110921T=LMG 29118T).

Topics: Bacterial Typing Techniques; Bacteroidetes; Diaminopimelic Acid; DNA, Bacterial; Fatty Acids; Galium; Germany; Phosphatidylethanolamines; Phylogeny; Pigmentation; Plant Leaves; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A motile and rod-shaped bacterium, designated strain KYW1030T, was isolated from seawater collected from the Gwangyang bay (Republic of Korea). Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), iso-C15 : 0 and iso-C17 : 0 3-OH. The strain contained MK-7 as the major isoprenoid quinone, phosphatidylethanolamine and diphosphatidylglycerol as the major polar lipids and sym-homospermidine as the major polyamine. The DNA G+C content was 46 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW1030T forms an evolutionary lineage within the radiation enclosing the members of the genus Pontibacter, with Pontibacterakesuensis AKS 1T (97.9 % 16S rRNA gene sequence similarity) as its nearest neighbour. A number of phenotypic characteristics distinguished strain KYW1030T from the related members of the genus Pontibacter. On the basis of the evidence presented in this study, a novel species, Pontibacter rugosus sp. nov., is proposed for strain KYW1030T (=KACC 18739T=JCM 31319T).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A Gram-stain-negative, short rod-shaped and light-red-pigmented bacterium, designated XAAS-1T, was isolated from the soil of Aydingkol Lake near the Turpan City, Xinjiang, China. The isolate was positive for oxidase, catalase and hydrolysis of starch, casein, gelatin and aesculin. The sole respiratory quinone was MK-7 and the principal cellular fatty acids were iso-C15 : 0 and C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid and two unidentified polar lipids. The polyamine pattern was found to contain mainly sym-homospermidine. 16S rRNA gene sequence analysis indicated that strain XAAS-1T belongs to the genus Pontibacter in the family Cytophagaceae, with sequence similarities ranging from 93.8 to 96.7 % with other type species of the genus Pontibacter. On the basis of phenotypic and genotypic data, strain XAAS-1T represents a novel species of the genus Pontibacter, for which the name Pontibacter aydingkolensis sp. nov. (type strain XAAS-1T=CCTCC AB 2016134T=JCM 31442T) is proposed.

Topics: Bacterial Typing Techniques; Base Composition; China; Cytophagaceae; DNA, Bacterial; Fatty Acids; Lakes; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Sodium Chloride; Soil; Soil Microbiology; Spermidine; Vitamin K 2

A novel Gram-staining-negative, rod-shaped bacterium, designated DCY78(T), was isolated from soil of a ginseng field in Yeon-cheon province (38° 04' 00″ N 126° 57' 00″ E), Republic of Korea. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY78(T) belonged to the genus Epilithonimonas and was most closely related to Epilithonimonas lactis DSM 19921(T) (98.5 % sequence similarity) and Epilithonimonas tenax DSM 16811(T) (97.8 %). Growth occurred at 10-30 °C with an optimum temperature of 28 °C. The pH range for growth was pH 5.5-8.0. The major polar lipids were found to be phosphatidylethanolamine three unidentified amino lipids and one unidentified polar lipid. The only predominant quinone was MK-6. The major polyamines were sym-homospermidine and spermidine. The major fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content was 37.9 mol%. On the basis of the phenotypic and genotypic analysis, the isolate is classified as representative of a novel species in the genus Epilithonimonas, for which the name Epilithonimonas ginsengisoli is proposed. The type strain is DCY78(T) ( = KCTC 32174(T) = JCM 19896(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Molecular Sequence Data; Panax; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

A Gram-staining-negative, catalase- and oxidase-positive, obligately aerobic, motile by gliding, bright yellow and rod-shaped bacterial strain was isolated from soil of Daemo Mountain (Daemosan) in Seoul, Republic of Korea. Its taxonomic position was investigated by using a polyphasic study. On the basis of 16S rRNA gene sequence comparisons, strain THG-DJ7(T) was found to be most closely related to Flavobacterium denitrificans ED5(T) (97.9 % sequence similarity), Flavobacterium ginsenosidimutans THG 01(T) (97.6 %), Flavobacterium kyungheensis THG-107(T) (97.5 %), Flavobacterium anhuiense D3(T) (97.1 %) and Flavobacterium ginsengisoli DCY54(T) (97.0 %). The DNA-DNA relatedness between strain THG-DJ7(T) and its phylogenetically closest neighbours was below 40.0 %. The G+C content of the genomic DNA was determined to be 32.6 mol%. The only isoprenoid quinone detected in strain THG-DJ7(T) was menaquinone-6 (MK-6). The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were found to be phosphatidylethanolamine, phosphatidyldimethylethanolamine, an unidentified aminophosphoglycolipid, phosphatidylserine and an unidentified lipid. The major fatty acids were identified as iso-C15 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). These data support the affiliation of strain THG-DJ7(T) to the genus Flavobacterium. We report the phenotypic, genotypic and phylogenetic characterization of strain THG-DJ7(T). Based on the findings presented, a novel species of the genus Flavobacterium, Flavobacterium daemonensis sp. nov. is proposed, with THG-DJ7(T) ( = KACC 17651(T) = JCM 19455(T)) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacterium; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

A Gram-stain-negative, strictly aerobic, rod-shaped and pinkish-yellow bacterium, which was motile by gliding and designated strain THG-T11(T), was isolated from tomato rhizosphere soil in Gyeonggi province, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-T11(T) was found to be most closely related to 'Pedobacter zeaxanthinifaciens' TDMA-5 (95.9 % sequence similarity), Pedobacter agri PB92(T) (94.9 %), Pedobacter rhizosphaerae 01-96(T) (94.6 %) and Pedobacter alluvionis NWER-II11(T) (94.5 %). The DNA G+C content was 38.4 mol%. The only isoprenoid quinone detected in strain THG-T11(T) was menaquinone-7 (MK-7). The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylethanolamine, an unidentified phosphoglycolipid, an unidentified glycolipid, an unidentified lipid, unidentified aminophospholipids and unidentified aminolipids. The major ceramide was found to be ceramide phosphorylethanolamine. The major fatty acids were identified as iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. These data support the affiliation of strain THG-T11(T) to the genus Pedobacter. Based on phenotypic, chemotaxonomic and phylogenetic analysis, it is proposed that strain THG-T11(T) represents a novel species of the genus Pedobacter for which the name Pedobacter ureilyticus sp. nov. is proposed, with THG-T11(T) as the type strain ( = KACC 17660(T) = JCM 19461(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Pedobacter; Phylogeny; Republic of Korea; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Solanum lycopersicum; Spermidine; Vitamin K 2

YF-3T is a Gram-stain-negative, non-motile, non-spore-forming, yellow-orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis, on the basis of the 16S rRNA gene sequence, showed that strain YF-3T was closely related to the strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine pattern with sym-homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain YF-3T was 37 mol%. The DNA-DNA relatedness levels between strain YF-3T and the most closely related strains, C. hispalense AG13T and C. taiwanense Soil-3-27T, were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named Chryseobacterium shandongense sp. nov. is proposed. The type strain is YF-3T ( = CCTCC AB 2014060T = JCM 30154T).

Topics: Bacterial Typing Techniques; Base Composition; China; Chryseobacterium; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

A non-motile and rod-shaped bacterium, designated strain WM78T, was isolated from freshwater collected from the Woopo wetland (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:1ω7c and/or C16:1ω6c and iso-C17:1 I and/or anteiso-C17:1 B. The strain contained MK-7 as the major isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The genomic DNA G+C content was 62 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WM78T forms evolutionary lineage within the radiation comprising members of the genus Hymenobacter with Hymenobacter gelipurpurascens Txg1T (97.7 % sequence similarity) as its nearest neighbour. A number of phenotypic characteristics distinguished strain WM78T from related members of the genus Hymenobacter. The evidence presented in this study support the designation of strain WM78T as a representative of a novel species in the genus Hymenobacter for which the name Hymenbactor wooponensis sp. nov. is proposed. The type strain is WM78T ( = KCTC 32528T = JCM 19491T).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Fresh Water; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2; Wetlands

A slightly yellow bacterial strain (JM-87(T)), isolated from the stem of healthy 10 day-old sweet corn (Zea mays), was studied for its taxonomic allocation. The isolate revealed Gram-stain-negative, rod-shaped cells. A comparison of the 16S rRNA gene sequence of the isolate showed 99.1, 97.8, and 97.4% similarity to the 16S rRNA gene sequences of the type strains of Elizabethkingia anophelis, Elizabethkingia meningoseptica and Elizabethkingia miricola, respectively. The fatty acid profile of strain JM-87(T) consisted mainly of the major fatty acids C15:0 iso, C17:0 iso 3-OH, and C15:0 iso 2-OH/C16:1ω7c/t. The quinone system of strain JM-87(T) contained, exclusively, menaquinone MK-6. The major polyamine was sym-homospermidine. The polar lipid profile consisted of the major lipid phosphatidylethanolamine plus several unidentified aminolipids and other unidentified lipids. DNA-DNA hybridization experiments with E. meningoseptica CCUG 214(T) ( = ATCC 13253(T)), E. miricola KCTC 12492(T) ( = GTC 862(T)) and E. anophelis R26(T) resulted in relatedness values of 17% (reciprocal 16%), 30% (reciprocal 19%), and 51% (reciprocal 54%), respectively. These DNA-DNA hybridization results, in addition to some differentiating biochemical properties, clearly indicate that strain JM-87(T) is a representative of a novel species, for which the name Elizabethkingia endophytica sp. nov. is proposed. The type strain is JM-87(T) ( = CIP 110885(T) = LMG 28604(T) = CCM 8570(T)).

Topics: Alabama; Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Plant Stems; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2; Zea mays

A novel bacterial strain, designated GCR0105(T), was isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment, located in JEOLlabuk-do, South Korea. Cells of strain GCR0105(T) were Gram-stain-negative, non-motile and rod-shaped. Colonies of strain GCR0105(T) were pale yellow-pigmented on R2A agar and nutrient agar media, and were able to grow at 15-30 °C (optimum 25 °C) and pH 6.5-8.5 (optimum pH 7.5). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GCR0105(T) was related most closely to Flavisolibacter ginsengisoli Gsoil 643(T) (93.14% similarity). The polar lipid profile of strain GCR0105(T) comprised phosphatidylethanolamine, two unknown aminolipids, an unknown aminophospholipid and four unknown lipids. The DNA G+C content of strain GCR0105(T) was 42.9 mol% and the respiratory quinone was MK-7.On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain GCR0105(T) represents a novel species in a new genus within the family Chitinophagaceae, for which the name Flaviaesturariibacter amylovorans gen. nov., sp. nov. is proposed. The type strain of Flaviaesturariibacter amylovorans is GCR0105(T) ( = KACC 16454(T) = JCM 17919(T)).

Topics: Bacterial Typing Techniques; Bacteroidetes; Base Composition; DNA, Bacterial; Estuaries; Fatty Acids; Molecular Sequence Data; Phosphatidylethanolamines; Phylogeny; Pigmentation; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Starch; Vitamin K 2; Water Microbiology

A yellow-pigmented bacterial strain, 91A-612(T), isolated from the geocarposphere (soil around the peanut) of very immature peanuts (Arachis hypogaea) in Alabama, USA, was studied for its taxonomic position. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Chryseobacterium, showing the highest sequence similarities to the type strains of Chryseobacterium molle (98.4%), C. pallidum (98.3%) and C. hominis (97.8%). The 16S rRNA gene sequence similarities to the type strains of all other species of the genus Chryseobacterium were below 97.0%. The fatty acid profile of strain 91A-612(T) consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c) and iso-C17 : 0 3-OH. Major compounds in the polar lipid profile were phosphatidylethanolamine and several unidentified lipids, including two lipids that did not contain a sugar moiety, an amino group or a phosphate group (L3, L8), and an aminolipid (AL1). The quinone system was composed mainly of MK-6. The polyamine pattern contained sym-homospermidine as the major compound and moderate amounts of spermidine and spermine. DNA-DNA hybridizations between strain 91A-612(T) and the type strains of C. molle, C. pallidum and C. hominis resulted in relatedness values well below 70%. These data and the differentiating biochemical and chemotaxonomic properties showed that isolate 91A-612(T) represents a novel species of the genus Chryseobacterium, for which we propose the name Chryseobacterium arachidiradicis sp. nov. (type strain 91A-612(T) = LMG 27814(T)= CCM 8490(T) = CIP 110647(T)).

Topics: Alabama; Arachis; Bacterial Typing Techniques; Chryseobacterium; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Pigmentation; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

An orange-pigmented, Gram-staining-negative, rod-shaped bacterium, designated 96_Hippo_TS_3/13(T) was isolated from the brood pouch of a diseased seahorse male of the species Hippocampus barbouri from the animal facility of the University of Giessen, Germany. Phylogenetic analyses based on the nearly full-length 16S rRNA gene sequence placed strain 96_Hippo_TS_3/13(T) into the monophyletic cluster of the genus Mesonia within the family Flavobacteriaceae. However, the strain shared only 92.2-93.8% sequence similarity to type strains of species of the genus Mesonia, with highest sequence similarity to the type strain of Mesonia aquimarina. Cellular fatty acid analysis showed a Mesonia-typical fatty acid profile including several branched and hydroxyl fatty acids with highest amounts of iso-C15 : 0 (40.9%) followed by iso-C17 : 0 3-OH (14.8%). In the polyamine pattern, sym-homospermidine was predominant. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system contained exclusively menaquinone MK-6. The only identified compound in the polar lipid profile was phosphatidylethanolamine present in major amounts. Additionally, major amounts of an unidentified aminolipid and two unidentified lipids not containing a phosphate group, an amino group or a sugar residue were detected. The genomic G+C content of strain 96_Hippo_TS_3/13(T) was 30 mol%. Based on genotypic, chemotaxonomic and physiological characterizations we propose a novel species of the genus Mesonia, Mesonia hippocampi sp. nov., with strain 96_Hippo_TS_3/13(T) ( = CIP 110839T =  LMG 28572(T) = CCM 8557(T)) as the type strain. An emended description of the genus Mesonia is also provided.

Topics: Animals; Bacterial Typing Techniques; Base Composition; Diaminopimelic Acid; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Germany; Male; Molecular Sequence Data; Peptidoglycan; Phosphatidylethanolamines; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Smegmamorpha; Spermidine; Vitamin K 2

A yellow, nitrogen-fixing bacterial strain, NXU-44(T), isolated from the rhizosphere of switchgrass (Panicum virgatum) in Auburn, Alabama, USA, was studied to determine its taxonomic position. Cells of the isolate were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Flavobacterium with highest sequence similarities to the type strains of Flavobacterium ginsenosidimutans (97.9%), Flavobacterium phragmitis (97.6%) and Flavobacterium anhuiense (97.5%). The 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were below 97.5%. The fatty acid profile of strain NXU-44(T) consisted of the major fatty acids iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. The major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylserine, one aminolipid and two polar lipids. The quinone system was composed exclusively of menaquinone MK-6. The polyamine pattern contained the major compound sym-homospermidine and only minor amounts of other polyamines. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. These data and the differential biochemical and chemotaxonomic properties show that strain NXU-44(T) represents a novel species of the genus Flavobacterium for which the name Flavobacterium nitrogenifigens sp. nov. is proposed. The type strain is NXU-44(T) ( = LMG 28694(T) = CIP 110894(T)).

Topics: Alabama; Bacterial Typing Techniques; Diaminopimelic Acid; DNA, Bacterial; Fatty Acids; Flavobacterium; Molecular Sequence Data; Nitrogen Fixation; Panicum; Peptidoglycan; Phylogeny; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

Two Gram-stain-negative, rod-shaped bacteria, strains 990B6_12ER2AT and 994B6_12ER2A, were isolated during microbiological analysis of a mixed manure sample which was used as input material for a German biogas plant. Phylogenetic identification based on nearly full-length 16S rRNA gene sequences placed the isolates into the family Flavobacteriaceae within the phylum Bacteroidetes. Strains 990B6_12ER2AT and 994B6_12ER2A shared identical 16S rRNA gene sequences and showed highest 16S rRNA gene sequence similarity to the type strains of Empedobacter falsenii (97.3 %) and Empedobacter brevis (96.8 %).The major cellular fatty acids of strains 990B6_12ER2AT and 994B6_12ER2A were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH.The polyamine pattern contained predominantly sym-homospermidine and the quinone system was menaquinone MK-6. Major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified polar lipid not containing an amino residue, a phosphate residue or a sugar moiety. In addition, moderate to minor amounts of several unidentified lipids were detected. The DNA G+C content was 31.7 and 29.0 mol%, for strains 990B6_12ER2AT and 994B6_12ER2A, respectively. On the basis of phylogenetic, chemotaxonomic and physiological analysis we propose a novel species of the genus Empedobacter, Empedobacter stercoris sp. nov. (type strain 990B6_12ER2AT = CIP 110833T = LMG 28501T).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Biofuels; Cattle; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Germany; Manure; Molecular Sequence Data; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Swine; Vitamin K 2

A slightly yellow-pigmented strain (IMT-174T) isolated from a river sediment in Guyana was studied in detail for its taxonomic position. Cells of the isolate appeared rod-shaped and stained Gram-negative. Comparative 16S rRNA gene sequence analysis showed that the isolate had the highest sequence similarities to type strains of Chryseobacterium rhizoplanae (99.0 %), Chryseobacterium viscerum (98.9 %), Chryseobacterium lactis (98.8 %) and Chryseobacterium indologenes (98.6 %). The 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98.5 %. Fatty acid analysis of whole-cell hydrolysates of the strain resulted in a pattern typical of members of the genus Chryseobacterium, with fatty acids iso-C15 : 0, iso-C15 : 0 2-OH, iso-C17 : 1ω9c and iso-C17 : 0 3-OH as major compounds. The polyamine pattern contained predominantly sym-homospermidine. The major quinone was menaquinone MK-6 and the only lipid identified in the polar lipid profile was phosphatidylethanolamine. In addition, 13 unidentified lipids were detected in moderate to major amounts. DNA-DNA hybridizations with type strains of C. rhizoplanae, C. viscerum, C. lactis and C. indologenes resulted in values below 70 %. In addition to the genotypic differences, differentiating biochemical and chemotaxonomic properties confirmed that isolate IMT-174T represents a novel species, for which the name Chryseobacterium sediminis sp. nov. (type strain IMT-174T = LMG 28695T = CIP 110895T) is proposed.

Topics: Bacterial Typing Techniques; Base Composition; Chryseobacterium; DNA, Bacterial; Fatty Acids; Geologic Sediments; Guyana; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A Gram-stain-negative, aerobic, non-motile, rod-shaped, flexirubin-producing bacterium, designated strain CC-CZW010T, was isolated from the edible sea urchin Tripneustes gratilla in Penghu Island, Taiwan. The isolate grew optimally at pH 7.0 and 30 °C in the presence of 2 % (w/v) NaCl. The most closely related strains in terms of 16S rRNA gene sequence similarity were Chryseobacterium taihuense NBRC 108747T (97.6 %) and Chryseobacterium aquaticum KCTC 12483T (96.7 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed a distinct taxonomic position attained by strain CC-CZW010T with respect to other species of the genus Chryseobacterium. Strain CC-CZW010T possessed iso-C15 : 0, anteiso-C15 : 0, iso-C17 :  0 3-OH, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) and summed feature 9 (comprising C16 :  0 10-methyl/iso-C17 : 1ω9c) as predominant fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, two unidentified lipids and five aminolipids. The polyamine pattern contained the major compound sym-homospermidine. Menaquinone 6 (MK-6) was the predominant respiratory quinone, and the G+C content of the genomic DNA was 36.4 mol%. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-CZW010T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium echinoideorum sp. nov. is proposed. The type strain is CC-CZW010T ( = BCRC 80786T = JCM 30470T).

Topics: Animals; Bacterial Typing Techniques; Base Composition; Chryseobacterium; DNA, Bacterial; Fatty Acids; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sea Urchins; Sequence Analysis, DNA; Spermidine; Taiwan; Vitamin K 2

A Gram-stain-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming and gliding marine bacterium, designated strain CC-AMZ-304(T), was isolated from coastal surface seawater near Taichung harbour, Taiwan. Strain CC-AMZ-304(T) predominantly synthesized zeaxanthin and thus formed yellow colonies on marine agar. The novel strain showed an unstable phylogenetic position, although sharing high pairwise 16S rRNA gene sequence similarities of 95.9-94.9, 95.7 and 95.1-93.9 % with Gaetbulibacter species (n = 4), Aestuariibaculum suncheonense SC17(T) and Bizionia species (n = 7), respectively. The polar lipid profile of strain CC-AMZ-304(T) consisted of phosphatidylethanolamine, five unidentified lipids, one unidentified phospholipid, two unidentified aminolipids and one unidentified glycolipid. The major (>5 % of the total) fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and C15 : 1ω5c. The DNA G+C content was 36.0 mol%. Menaquinone-6 (MK-6) was the sole respiratory quinone and the major polyamine was triamine sym-homospermidine. Phylogenetic distinctiveness, unique polar lipid composition, presence of significant amounts of branched hydroxyl fatty acids (iso-C17 : 0 3-OH and iso-C15 : 0 3-OH) and a low amount of anteiso-C15 : 0, and several additional distinguishing biochemical features clearly discriminated strain CC-AMZ-304(T) from the type species of the genera Aestuariibaculum and Gaetbulibacter. Thus, based on data from the present polyphasic study, strain CC-AMZ-304(T) is considered to represent a novel species of a new genus within the family Flavobacteriaceae, for which the name Aquibacter zeaxanthinifaciens gen. nov., sp. nov. is proposed; the type strain of Aquibacter zeaxanthinifaciens is CC-AMZ-304(T) ( = JCM 18557(T) = BCRC 80463(T)). Emended descriptions of the genera Aestuariibaculum and Gaetbulibacter are also proposed.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Molecular Sequence Data; Phosphatidylethanolamines; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Spermidine; Taiwan; Vitamin K 2; Xanthophylls; Zeaxanthins

An orange-pigmented bacterial strain, designated LP100(T), was isolated from hexachlorocyclohexane-contaminated soil (Lucknow, India). A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LP100(T) occupied a distinct phylogenetic position in the Pontibacter species cluster, showing highest similarity with Pontibacter lucknowensis DM9(T) (97.4 %). Levels of similarity to strains of other Pontibacter species ranged between 94.0 and 96.8 %. Strain LP100(T) contained MK-7 as the predominant menaquinone and sym-homospermidine was the major polyamine in the cell. The major cellular fatty acids of strain LP100(T) were anteiso-C17 : 0 A, iso-C15 : 0 and iso-C18 : 1 H. The polar lipid profile of strain LP100(T) showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and two unknown polar lipids. The G+C content of strain LP100(T) was 58.2 mol%. The results of DNA-DNA hybridization, biochemical and physiological tests clearly distinguish the novel strain from closely related species of the genus Pontibacter. Therefore, strain LP100(T) represents a novel species of the genus Pontibacter for which the name Pontibacter indicus is proposed. The type strain is LP100(T) ( = CCM8435(T) = MCC2027(T)).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Hexachlorocyclohexane; India; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants; Spermidine; Vitamin K 2

An aerobic, Gram-stain-negative, rod-shaped bacterium (strain CC-ALB-1(T)) was isolated from the rhizosphere of Arabidopsis thaliana. Strain CC-ALB-1(T) was able to grow at 20-30 °C, pH 5.0-8.0 and with up to 1.0% (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain CC-ALB-1(T) had the highest sequence similarity to Chitinophaga ginsengisegetis Gsoil 040(T) (96.9%) and Chitinophaga niastensis JS16-4(T) (96.7%); lower levels of similarity (<97.0%) were observed to strains of all other species of the genus Chitinophaga. The fatty acid profile consisted of iso-C(15 : 0), iso-C(17 : 0) 3-OH, C(15 : 1)ω5c, C(16 : 1)ω5c and summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c). The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The predominant quinone system was menaquinone 7 (MK-7). The DNA G+C content was 53.4 ± 0.4 mol%. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-1(T) is proposed to represent a novel species within the genus Chitinophaga, for which the name Chitinophaga taiwanensis sp. nov. is proposed. The type strain is CC-ALB-1(T) ( = BCRC 80570(T) = JCM 18895(T)).

Topics: Arabidopsis; Bacterial Typing Techniques; Bacteroidetes; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phosphatidylethanolamines; Phylogeny; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A Gram-staining-negative, orange-pigmented, strictly aerobic, carotenoid-producing, rod-shaped, non-flagellated, non-spore-forming bacterium, motile by gliding, designated strain CC-AMO-30D(T), was isolated from surface seawater collected near Taichung harbour, Taiwan. Strain CC-AMO-30D(T) shared pairwise 16S rRNA gene sequence similarities of 94.8, 93.7 and 92.5% with the type strains of the type species of the genera Joostella, Pustulibacterium and Galbibacter, respectively, and formed a distinct monophyletic lineage in phylogenetic trees. The major fatty acids (≥ 5% of total) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile consisted of phosphatidylethanolamine, four unidentified lipids, two unidentified aminolipids and an unidentified phospholipid. The major polyamine was the triamine sym-homospermidine. The DNA G+C content was 47.1 mol% and the predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness and distinguishing phenotypic characteristics, strain CC-AMO-30D(T) represents a novel genus and species of the family Flavobacteriaceae, for which the name Robertkochia marina gen. nov., sp. nov. is proposed; the type strain of the type species Robertkochia marina is CC-AMO-30D(T) ( = JCM 18552(T) = BCRC 80469(T)). Emended descriptions of the genera Joostella and Galbibacter are also proposed.

Topics: Bacterial Typing Techniques; Base Composition; Carotenoids; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Spermidine; Taiwan; Vitamin K 2

A mesophilic bacterium appearing as curved rod-shaped cells was isolated from Lake Michigan water. It exhibited highest similarities with Sediminibacterium ginsengisoli DCY13(T) (94.4%); Sediminibacterium salmoneum NJ-44(T) (93.6%) and Hydrotalea flava CCUG 51397 (T) (93.1%) while similarities with other recognized species were <92.0%. The primary polar lipid was phosphatidylethanolamine, with moderate amounts of two unidentified glycolipids, three unknown polar lipids, one unknown aminophospholipid and one aminolipid. The primary respiratory quinone was MK-7 and sym-homospermidine was the primary polyamine. The major cellular fatty acids were iso-C(15 : 1)G, iso-C(15 : 0), iso-C(16 : 0) 3-OH and iso-C(17 : 0) 3-OH, with moderate amounts of iso-C(16 : 0). The presence of glycolipids differentiated the novel strains from related genera. The DNA mol% G+C content of the type strain MU-2(T) was 45.2. Results for other phenotypic and molecular analyses indicated that strain MU-2(T) is a representative of a novel genus and species for which the name Vibrionimonas magnilacihabitans is proposed. The type strain is MU-2(T) ( = NRRL B-59231 = DSM 22423).

Topics: Bacterial Typing Techniques; Bacteroidetes; Base Composition; DNA, Bacterial; Fatty Acids; Fresh Water; Lakes; Molecular Sequence Data; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2; Wisconsin

A Gram-staining-negative, strictly aerobic, non-motile, rod-shaped and flexirubin-type-pigmented strain, THG C4-1(T), was isolated from green tea leaves in Jangheung-gun, Republic of Korea. Strain THG C4-1(T) grew well at 20-30 °C, at pH 7.0-7.5 and in the absence of NaCl on nutrient agar. Based on 16S rRNA gene sequence comparisons, strain THG C4-1(T) was most closely related to Chryseobacterium taiwanense Soil-3-27(T) (97.7 %), C. hagamense RHA2-9(T) (97.2 %), C. gregarium P 461/12(T) (97.2 %), C. ginsenosidimutans THG 15(T) (97.1 %), C. taeanense PHA3-4(T) (97.0 %) and C. daeguense K105(T) (97.0 %), but DNA-DNA relatedness between strain THG C4-1(T) and its closest phylogenetic neighbours was below 21 %. The DNA G+C content was 41.7 mol%. The only isoprenoid quinone detected in strain THG C4-1(T) was menaquinone 6 (MK-6). The major component of the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminolipids. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. These data supported the affiliation of strain THG C4-1(T) to the genus Chryseobacterium. The results of physiological and biochemical tests enabled strain THG C4-1(T) to be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium. Therefore, the novel isolate represents a novel species, for which the name Chryseobacterium camelliae sp. nov. is proposed, with THG C4-1(T) ( = KACC 16985(T) = JCM 18745(T)) as the type strain.

Topics: Bacterial Typing Techniques; Base Composition; Chryseobacterium; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Pigmentation; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Tea; Vitamin K 2

A taxonomic study using a polyphasic approach was performed on a Gram-stain-negative, aerobic, non-motile, non-spore-forming, rod-shaped bacterium, designated strain PB156(T), isolated from grass soil. Comparative 16S rRNA gene sequence studies showed that the isolate was clearly affiliated with the phylum Bacteroidetes, and most closely related to Hymenobacter soli PB17(T), Hymenobacter antarcticus VUG-A42aa(T) and Hymenobacter glaciei VUG-A130(T), showing 96.4, 96.2 and 95.9 % 16S rRNA gene sequence similarity, respectively, while all other species of the genus shared only 89.3-95.2 % similarity. The main polyamine present was sym-homospermidine. The predominant menaquinone was MK-7. The major fatty acids were C15 : 0 iso, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c/t), C16 : 1ω5c and C15 : 0 anteiso. The G+C content of the genomic DNA of strain PB156(T) was 61.7 mol%. The combined genotypic and phenotypic data supported the conclusion that strain PB156(T) represents a novel species of the genus Hymenobacter, for which the name Hymenobacter ruber sp. nov. is proposed. The type strain is PB156(T) ( = KCTC 32477(T) = JCM 19433(T)).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phylogeny; Poaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

Two yellow-pigmented bacterial strains (100(T) and C26(T)), showing 98.4 % 16S rRNA gene sequence similarity to each other and isolated from a chicken in Germany and as a contaminant from an agar plate of a rhizosphere sample in Alabama, were studied by using a polyphasic taxonomic approach. Cells of both isolates were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequences of the two organisms with the sequences of the type strains of the most closely related species of the genus Chryseobacterium showed the highest sequence similarities of strains 100(T) and C26(T) to the type strains of Chryseobacterium joostei (respectively 97.5 and 98.2 %), C. viscerum (96.6, 97.8 %), C. gleum (97.1, 97.7 %), C. arthrosphaerae (97.3%, 97.7 %), C. indologenes (97.2, 97.7 %), C. tructae (96.6, 97.6 %), C. jejuense (97.0, 97.6 %) and C. oncorhynchi (96.3, 97.5 %); 16S rRNA gene sequence similarities to members of all other species of the genus Chryseobacterium were below 97.5 %. The fatty acid profiles of both strains consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 1ω9c and iso-C17 : 0 3-OH, but also showed slight differences (absence or presence of C16 : 0 3-OH and iso-C15 : 1 F). DNA-DNA hybridizations between the two strains and between the novel strains and the type strains of C. joostei, C. indologenes, C. jejuense, C. tructae and C. viscerum resulted in relatedness values clearly below 70 %. These DNA-DNA hybridization results and the differentiating biochemical and chemotaxonomic properties showed that both strains 100(T) and C26(T) represent novel species, for which the names Chryseobacterium gallinarum sp. nov. (type strain 100(T) = LMG 27808(T) = CCM 8493(T)) and Chryseobacterium contaminans sp. nov. (type strain C26(T) = LMG 27810(T) = CCM 8492(T)) are proposed.

Topics: Alabama; Animals; Bacterial Typing Techniques; Chickens; Chryseobacterium; DNA, Bacterial; Fatty Acids; Germany; Molecular Sequence Data; Nucleic Acid Hybridization; Pharynx; Phosphatidylethanolamines; Phylogeny; Pigmentation; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain JM-1070T) was isolated as a presumptive endophyte from internal stem tissue of a healthy corn stem. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain JM-1070T in the monophyletic cluster of the genus Mucilaginibacter, with closest affiliation to the type strains of Mucilaginibacter composti (98% similarity) and Mucilaginibacter calamicampi (97.2%). 16S rRNA gene sequence similarity to type strains of other species of the genus Mucilaginibacter was 93.4-96.0%. DNA-DNA hybridizations between strain JM-1070T and the type strains M. composti LMG 23497T and M. calamicampi CCUG 63418T showed low relatedness values of 13% (reciprocal 18%) and 52% (reciprocal 54.4%). Major respiratory quinones were menaquinones MK-6 and MK-7. The predominant fatty acids (>15%) were iso-C15:0, iso-C15:0 2-OH/C16:1ω7c (measured as summed feature 3) and iso-C17:0 3-OH. Several other iso-branched and hydroxylated fatty acids were detected. The polar lipid profile was composed of the major components phosphatidylethanolamine and an unidentified aminophospholipid. The polyamine pattern contained predominantly sym-homospermidine. Characterization by 16S rRNA gene sequencing, physiological parameters and polyamine, ubiquinone, polar lipid and fatty acid compositions revealed that strain JM-1070T represents a novel species of the genus Mucilaginibacter. For this reason, we propose the name Mucilaginibacter auburnensis sp. nov., with the type strain JM-1070T (=CIP 110694T=LMG 28078T).

Topics: Alabama; Bacterial Typing Techniques; Bacteroidetes; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; Pigmentation; Plant Stems; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2; Zea mays

A novel, red-pink-pigmented strain, designated R2-4(T), was isolated from a till sample near Ny-Alesund, Svalbard Archipelago, Norway. Cells were aerobic, Gram-stain-negative and rod-shaped. Growth occurred at 4-30 °C (optimum, 20-22 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0-1% NaCl added to R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R2-4(T) belonged to the genus Hymenobacter. 16S rRNA gene sequence similarity between strain R2-4(T) and the type strains of related species of the genus ranged from 94.51 to 96.05%. Strain R2-4(T) contained iso-C(15 : 0), anteiso-C(15 : 0), summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c), summed feature 4 (C(17 : 1) anteiso B and/or iso I) and C(16 : 1)ω5c as the major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids as the main polar lipids. The polyamine was sym-homospermidine. The DNA G+C content of strain R2-4(T) was 61.6 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R2-4(T) is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter arcticus sp. nov. is proposed. The type strain is R2-4(T) ( = CCTCC AB 2012104(T) = KACC 16881(T)).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Ice Cover; Molecular Sequence Data; Phosphatidylethanolamines; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Svalbard; Vitamin K 2

A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated AG13(T), isolated from a rain water pond at a plant nursery in Spain and characterized as a plant-growth-promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best over a temperature range of 15-40 °C, at pH 5.0-8.0 and with 0-4 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Chryseobacterium. The DNA G+C content of the novel strain was 37.2 mol%. The strain had a polyamine pattern with sym-homospermidine as the major compound and produced flexirubin-type pigments. MK-6 was the dominant menaquinone and the major cellular fatty acids were iso-C15 : 0, C17 : 1ω9c and iso-C17 : 0 3-OH. The main polar lipids were phosphatidylethanolamine, aminolipids and several unidentified lipids. The 16S rRNA gene showed 92.0-97.2 % sequence similarity with those of the members of the genus Chryseobacterium. Based on chemotaxonomic and phenotypic traits, and DNA-DNA hybridizations with the type strains of the most closely related species, the isolate is proposed to represent a novel species, Chryseobacterium hispalense, type strain AG13(T) ( = DSM 25574(T) = CCUG 63019(T)). Emended descriptions of the species Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium are also provided.

Topics: Bacterial Typing Techniques; Base Composition; Chryseobacterium; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Olea; Phosphatidylethanolamines; Phylogeny; Ponds; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spain; Spermidine; Vitamin K 2

Two Gram-reaction-negative, rod-shaped, non-motile and red-pink-pigmented bacterial strains, designated GYR3077(T) and GSR0100(T), were isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment in JEOLlabuk-do, South Korea, and were characterized using a polyphasic approach. 16S rRNA genes of strains GYR3077(T) and GSR0100(T) exhibited sequence similarities of 95.9 % to Hymenobacter deserti ZLB-3(T) and 96.6 % to Hymenobacter soli PB17(T), respectively, and indicated that these isolates belonged to the phylum Bacteroidetes. The major cellular fatty acids present in the two isolates were iso-C15 : 0, C16 : 1ω5c, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major respiratory quinone and polyamine patterns were menaquinone-7 and sym-homospermidine, characteristic of the genus Hymenobacter. Flexirubin-type pigments were absent in both strains. The DNA G+C contents of strains GYR3077(T) and GSR0100(T) were 60.2 mol% and 61.9 mol%, respectively. The major polar lipid of strains GYR3077(T) and GSR0100(T) was phosphatidylethanolamine. Based on the morphological and physiological properties, strains GYR3077(T) and GSR0100(T) were considered to represent two novel species of the genus Hymenobacter, for which the names Hymenobacter koreensis sp. nov. (type strain GYR3077(T) = KACC 16451(T) = JCM 17924(T)) and Hymenobacter saemangeumensis sp. nov. (type strain GSR0100(T) = KACC 16452(T) = JCM 17923(T)) are proposed.

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Estuaries; Fatty Acids; Molecular Sequence Data; Phosphatidylethanolamines; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A Gram-staining-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming and gliding marine bacterium designated strain CC-AMZ-301(T) was isolated from coastal surface seawater near Taichung harbour, Taiwan. Strain CC-AMZ-301(T) predominantly synthesized zeaxanthin and thus formed yellow colonies on marine agar. The novel strain showed high pairwise 16S rRNA gene sequence similarity to Kordia periserrulae IMCC1412(T) (95.0 %), K. algicida KCTC 8814P(T) (94.4 %) and K. antarctica IMCC3317(T) (94.2 %), and formed a phylogenetic lineage tightly associated with species of the genus Kordia. The polar lipid profile of strain CC-AMZ-301(T) consisted of three unidentified lipids, three unidentified aminolipids and one unidentified phospholipid. The major fatty acids (>5 % of total) were iso-C17 : 0 3-OH, iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The DNA G+C content was 36.4 mol%. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The major polyamine was the triamine sym-homospermidine. Based on evidence from the present polyphasic study, strain CC-AMZ-301(T) is proposed to represent a novel species of the genus Kordia, for which the name Kordia aquimaris sp. nov. is proposed; the type strain is CC-AMZ-301(T) ( = JCM 18556(T) = BCRC 80464(T)). An emended description of the genus Kordia is also proposed.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacteriaceae; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Spermidine; Taiwan; Vitamin K 2; Xanthophylls; Zeaxanthins

A Gram-negative, orange-pigmented, rod-shaped, motile and aerobic bacterial strain designated DM9(T) was isolated from hexachlorocyclohexane (HCH)-contaminated soil (Lucknow, India) and its taxonomic position was determined using a polyphasic approach. 16S rRNA gene sequence analysis showed that the isolate belonged to the phylum Bacteroidetes and confirmed its placement in the genus Pontibacter, with sequence similarity ranging from 93.92 to 96.21 % with other members of the genus Pontibacter. The major cellular fatty acids of the novel strain were iso-C(17 : 0) 3-OH (6.00 %), iso-C(15 : 0) (21.54 %) and summed feature 4 (comprising C(17 : 1) iso I/anteiso B; 32.3 %). The polar lipid profile of strain DM9(T) showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, two unknown aminolipids and four unknown polar lipids. Strain DM9(T) contained MK-7 as the predominant menaquinone and its DNA G+C content was 49.2 mol%. sym-Homospermidine was the major polyamine observed in the cell. The results obtained on the basis of phenotypic characteristics, phylogenetic analysis, biochemical and physiological tests clearly distinguished DM9(T) from closely related members of the genus Pontibacter. It is proposed that DM9(T) represents a novel species, Pontibacter lucknowensis sp. nov.; the type strain is DM9(T) (= CCM 7955(T) = MTCC 11079(T)).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Hexachlorocyclohexane; India; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants; Spermidine; Vitamin K 2

A Gram-stain-negative, non-motile, red bacterium, designated DCY57(T), was isolated from soil of a ginseng field in a mountainous region of Chungnam province in South Korea. Strain DCY57(T) grew with 0-1 % (w/v) NaCl and the optimum temperature for growth was 30 °C. Strain DCY57(T) contained MK-7 as the predominant menaquinone. The polyamine was sym-homospermidine. The major fatty acids were C(16:1)ω5c, iso-C(15:0), anteiso-C(15:0) and summed feature 3 (containing C(16:1)ω7c and/or C(16:1)ω6c). The major polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids. The DNA G+C content was 58.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY57(T) was most closely related to members of the genus Hymenobacter. The isolate exhibited 91.7 % 16S rRNA gene sequence similarity with H. soli PB17(T), 94.5 % with H. flocculans A2-50A(T) and 95.8 % with H. metalli A2-91(T). On the basis of the evidence presented in this study, strain DCY57(T) represents a novel species within the genus Hymenobacter, for which the name Hymenobacter ginsengisoli sp. nov. is proposed. The type strain is DCY57(T) ( = KCTC 23674(T) = JCM 17841(T)).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Panax; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spermidine; Vitamin K 2

Bacterial strain THMBM1(T) was isolated from decomposing algal scum that was collected during an algal bloom in Lake Taihu, Wuxi City, Jiangsu Province, China. Cells of strain THMBM1(T) were Gram-negative, facultatively anaerobic, non-motile rods. Colonies on tryptic soy agar were translucent and shiny with entire edges; yellow flexirubin-type pigments were produced. Growth was observed at 15-45 °C (optimum 30-37 °C), at pH 5.0-9.0 (optimum pH 8.0) and in the presence of 0-4.0 % (w/v) NaCl (optimum 0-1.0 %). Strain THMBM1(T) contained MK-6 as the sole respiratory quinone and sym-homospermidine as the predominant polyamine. The predominant cellular fatty acids were iso-C15 : 0 (53.2 %), iso-C17 : 0 3-OH (15.6 %) and iso-C17 : 1ω9c (11.9 %). The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The DNA G+C content was 36.8 mol% (Tm). Strain THMBM1(T) was closely related to members of the genus Chryseobacterium, with 16S rRNA gene sequence similarities ranging from 92.9 to 97.2 %, the highest sequence similarities being with Chryseobacterium taiwanense BCRC 17412(T) (97.2 %) and C. gambrini 5-1St1a(T) (97.1 %). DNA-DNA relatedness between strain THMBM1(T) and C. taiwanense JCM 21767(T) and C. gambrini DSM 18014(T) was 34.1  and 23.0 %, respectively. Based on these results, it is concluded that strain THMBM1(T) represents a novel species, for which the name Chryseobacterium taihuense sp. nov. is proposed. The type strain is THMBM1(T) ( = CGMCC 1.10941(T)  = NBRC 108747(T)). Emended descriptions of the genus Chryseobacterium and C. taiwanense, C. jejuense and C. indoltheticum are also proposed.

Topics: Bacterial Typing Techniques; Base Composition; China; Chryseobacterium; DNA, Bacterial; Eutrophication; Fatty Acids; Lakes; Molecular Sequence Data; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2; Water Microbiology

A psychrophilic, Gram-negative bacterium, designated MOL-1(T), was isolated from water of Lake Michigan. 16S rRNA gene sequence analysis revealed that the sequence of strain MOL-1(T) has sequence similarity of 95.6, 94.8, 94.3, 94.3, 94.2 and 93.9 %, respectively, to the 16S rRNA gene sequences of Sphingobacterium shayense HS39(T), S. lactis WCC 4512(T), S. composti T5-12(T), S. daejeonense TR6-04(T), S. bambusae IBFC2009(T) and S. alimentarium WCC 4521(T). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone MK-7 is the predominant respiratory quinone, while sym-homospermidine is the predominant polyamine. The polar lipid profile is composed of the predominant lipids phosphatidylethanolamine and unidentified polar lipid L2, with moderate amounts of unidentified polar lipids L1, L5 and L6 and unidentified aminophospholipids APL1 and APL2 and minor to trace amounts of unidentified polar lipids L3, L4, L7, L8, L9 and L10, unidentified phospholipid PL4 and unidentified aminophospholipid APL3. After molecular and phenotypic studies, including chemotaxonomic analyses, it was concluded that strain MOL-1(T) represents a novel Sphingobacterium species, for which the name Sphingobacterium psychroaquaticum sp. nov. is proposed. The type strain is MOL-1(T) ( = NRRL B-59232(T)  = DSM 22418(T)).

Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Lakes; Molecular Sequence Data; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Sphingobacterium; Vitamin K 2; Water Microbiology

A bacterium, designated strain CJ16(T), was isolated from the estuarine wetland of the Han River. Cells of the isolate were yellow-pigmented, Gram-stain-negative, non-motile and rod-shaped. Growth of strain CJ16(T) was observed in TSB at 5-37 °C (optimum 30 °C), at pH 5.0-9.0 (optimum pH 6.0) and with 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CJ16(T) was most closely related to Chryseobacterium hagamense KCTC 22545(T) (97.2 % 16S rRNA gene sequence similarity). Genomic relatedness based on DNA-DNA hybridization between strain CJ16(T) and C. hagamense KCTC 22545(T) was 23 % (strain CJ16(T) as probe) and 19 % (strain KCTC 22545(T) as probe). Chemotaxonomic analysis revealed that strain CJ16(T) possessed MK-6 as the major isoprenoid quinone and sym-homospermidine as the predominant polyamine. The predominant fatty acids were iso-C15 : 0 (26.9 %), iso-C17 : 0 3-OH (16.8 %) and summed feature 9 (comprising C16 : 0 10-methyl and/or iso-C17 : 1ω9c; 10.5 %). The DNA G+C content of strain CJ16(T) was 37.9 mol%. Based on phenotypic, genotypic and phylogenetic studies, strain CJ16(T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium rigui sp. nov. is proposed. The type strain is CJ16(T) ( = KACC 16560(T)  = JCM 18078(T)).

Topics: Bacterial Typing Techniques; Base Composition; Chryseobacterium; DNA, Bacterial; Estuaries; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Republic of Korea; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2; Wetlands

A taxonomic study was carried out on a novel bacterial strain, designated MIC3010(T), which was isolated from a freshwater pond in Jeonju, Republic of Korea. Cells of the isolate were Gram-stain-negative, rod-shaped and non-motile. Comparison of the 16S rRNA gene sequences indicated that the isolate belonged to the family Flavobacteriaceae, with Flavobacterium haoranii LQY-7(T) as its closest relative, with a similarity of 94.2 %. The predominant fatty acids of strain MIC3010(T) were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipid profile of strain MIC3010(T) revealed the presence of phosphatidylethanolamine (PE) and one unidentified lipid (L1) as major components. In addition, two aminolipids (AL1, AL2) and one glycolipid were present in small amounts. The DNA G+C content of the strain was 41.0 mol%. The strain contained MK-6 as the major quinone and sym-homospermidine as the predominant polyamine. On the basis of the evidence presented, it is concluded that strain MIC3010(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium fontis sp. nov. is proposed. The type strain is MIC3010(T) ( = KACC 16593(T) = JCM 18212(T)).

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacterium; Fresh Water; Molecular Sequence Data; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A Gram-stain-negative, rod-shaped, non-motile and yellow-pigmented bacterial strain, designated strain JJ013(T), was isolated from an artificial lake in Jeollabuk-do, South Korea, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain JJ013(T) indicated that the isolate belonged to the family Flavobacteriaceae and exhibited similarity levels of 96.6 % to the type strains of Flavobacterium cheonanense and Flavobacterium koreense and 96.5 % to the type strain of Flavobacterium chungnamense. Growth was observed at 20-30 °C and pH 5.0-7.0. The major cellular fatty acids of the novel strain were iso-C15 : 0 (27.5 %), iso-C15 : 1 G (17.8 %), iso-C17 : 0 3-OH (9.4 %) and iso-C15 : 0 3-OH (9.2 %). Flexirubin-type pigments were present. The DNA G+C content of strain JJ013(T) was 33.9 mol%, the major respiratory quinone was menaquinone-6 (MK-6) and the major polyamine was sym-homospermidine. The polar lipid profile of the strain JJ013(T) consisted of a phosphatidylethanolamine (PE), two unknown aminolipids (AL1-2), three unidentified lipid (L1-3) and an unknown glycolipid (GL). On the basis of the morphological and physiological properties and biochemical evidence presented, it is concluded that strain JJ013(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium aciduliphilum sp. nov. is proposed; the type strain is JJ013(T) ( = KACC 16594(T) = JCM 18211(T)). Since C15 : 0, which is known as a predominant fatty acid of the genus Flavobacterium was not detected in the novel strain and other reference strains, we propose an emended description of the genus Flavobacterium.

Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Flavobacterium; Fresh Water; Glycolipids; Molecular Sequence Data; Phylogeny; Polyenes; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spermidine; Vitamin K 2

A Gram-stain-negative, motile, red pigmented, rod-shaped bacterium, designated strain LP43(T), was isolated from hexachlorocyclohexane (HCH)-contaminated soil sediment (Lucknow, India). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate formed a cluster with the genus Pontibacter in the phylum Bacteroidetes with sequence similarities ranging from 92.9 to 97.0 % with species of the genus Pontibacter. The DNA G+C content of strain LP43(T) was 59.1 mol%. The polar lipid profile of strain LP43(T) showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, unknown aminolipids and unknown polar lipids. Strain LP43(T) contained MK-7 as the predominant menaquinone and sym-homospermidine as the major polyamine. The major cellular fatty acids of strain LP43(T) were, iso-C15 : 0 (15.74 %), iso-C15 : 0 3-OH (7.57 %), iso-C17 : 0 3-OH (7.32 %), summed feature 4 (iso-C17 : 1 I/anteiso-C17 : 1 B) (31.22 %) and summed feature 8 (C18 : 1ω7c/ C18 : 1ω6c) (7.60 %). Based on the results of DNA-DNA hybridization and phenotypic and genotypic characteristics, strain LP43(T) represents a novel species of the genus Pontibacter, for which the name Pontibacter ramchanderi is proposed. The type strain is LP43(T) (= CCM 8406(T) = MCC 2019(T)).

Topics: Bacterial Typing Techniques; Base Composition; Cytophagaceae; DNA, Bacterial; Fatty Acids; Geologic Sediments; Hexachlorocyclohexane; India; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Ponds; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Pollutants; Spermidine; Vitamin K 2