- Volume 67, Issue 6, 2017
Volume 67, Issue 6, 2017
- Notification List
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- New Taxa
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- Actinobacteria
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Mangrovihabitans endophyticus gen. nov., sp. nov., a new member of the family Micromonosporaceae isolated from Bruguiera sexangula
A novel endophytic actinobacterium, designated strain S3Cf-2T, was isolated from a surface-sterilized bark of Bruguiera sexangula collected from Dongzhaigang National Nature Reserve in Hainan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain S3Cf-2T fell within the family Micromonosporaceae and formed a distinct clade in the Micromonosporaceae phylogenetic tree. The 16S rRNA gene sequence similarity values between strain S3Cf-2T and the type species of 30 genera in the family Micromonosporaceae were 91.55–97.45 %. Strain S3Cf-2T formed extensively branched substrate mycelia without fragmentation. An oval or rod-like spore with a smooth surface was borne singly at the end of substrate mycelium. The novel isolate possessed meso-diaminopimelic acid as the diamino acid of the peptidoglycan, and glucose, galactose, mannose, arabinose, xylose and ribose as whole-cell sugars. The acyl type of the cell-wall peptidoglycan was glycolyl and mycolic acids were absent. The major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown aminolipid, corresponding to phospholipid type PII. The major menaquinones were MK-9(H6) and MK-9(H8). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 71.4 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, strain S3Cf-2T represents a novel species of a new genus within the family Micromonosporaceae , for which the name Mangrovihabitans endophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is S3Cf-2T (=DSM 100693T=CGMCC 4.7299T).
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Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil
A novel strain, G25T, was isolated from desert soil collected near Jeddah in Saudi Arabia. The strain could accumulate nearly 65 % of its cell dry weight as fatty acids, grow on a broad range of carbon sources and tolerate temperatures of up to 50 °C. With respect to to its 16S rRNA gene sequence, G25T is most closely related to Streptomyces massasporeus DSM 40035T, Streptomyces hawaiiensis DSM 40042T, Streptomyces indiaensis DSM 43803T, Streptomyces luteogriseus DSM 40483T and Streptomyces purpurascens DSM 40310T. Conventional DNA–DNA hybridization (DDH) values ranged from 18.7 to 46.9 % when G25T was compared with these reference strains. Furthermore, digital DDH values between the draft genome sequence of G25T and the genome sequences of other species of the genus Streptomyces were also significantly below the threshold of 70 %. The DNA G+C content of the draft genome sequence, consisting of 8.46 Mbp, was 70.3 %. The prevalent cellular fatty acids of G25T comprised anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The polar lipids profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides as well as unidentified phospholipids and phosphoaminolipids. The cell wall contained ll-diaminopimelic acid. Whole-cell sugars were predominantly glucose with small traces of ribose and mannose. The results of the polyphasic approach confirmed that this isolate represents a novel species of the genus Streptomyces , for which the name Streptomyces jeddahensis sp. nov. is proposed. The type strain of this species is G25T (=DSM 101878T =LMG 29545T =NCCB 100603T).
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Nonomuraea rhodomycinica sp. nov., isolated from peat swamp forest soil
The taxonomic position of an actinomycete, strain NR4-ASC07T, isolated from a soil sample collected from Sirindhorn peat swamp forest, Narathiwat Province, Thailand, was clarified using a polyphasic approach. On the basis of morphological and chemotaxonomic characteristics, it was classified among the members of the genus Nonomuraea . It produced tightly closed spiral spore chains on aerial mycelium as well as forming a pseudosporangium. Whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, ribose, madurose and mannose. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, unknown ninhydrin-positive phosphoglycolipids and unknown glycolipid. Menaquiones were MK-9(H4), MK-9(H0), MK-9(H2), MK-10(H4) and MK-9(H6). Predominant cellular fatty acids were iso-C16 : 0, C17 : 0 10-methyl, C16 : 0, C17 : 1ω8c, C16 : 0 2-OH and iso-C15 : 0. The phylogenetic tree reconstructed on the basis of 16S rRNA gene sequences showed that the strain fell within the clade containing Nonomuraea muscovyensis FMN03T, Nonomuraea roseoviolacea subsp. roseoviolacea NBRC 14098T and Nonomuraea roseoviolacea subsp. carminata NBRC 15903T. The DNA–DNA relatedness and phenotypic data supported that strain NR4-ASC07T was clearly distinguished from the closely related species and represents a novel species of the genus Nonomuraea for which the name Nonomuraea rhodomycinica sp. nov. is proposed. The type strain is NR4-ASC07T (=NBRC 112327T=TISTR 2465T).
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Pseudonocardia profundimaris sp. nov., isolated from marine sediment
More LessA novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated GY0556T, was isolated from deep-sea sediment collected from the western Pacific Ocean at a depth of 7118 m. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this strain belongs to the genus Pseudonocardia , being most closely related to Pseudonocardia hydrocarbonoxydans IMSNU 22140T (97.6 % similarity), Pseudonocardia sulfidoxydans DSM 44248T (97.6 %) and Pseudonocardia alaniniphila Y-16303T (97.6 %); similarity to other type strains of the genus Pseudonocardia was less than 97.5 %. Strain GY0556T contained MK-8(H4) as the predominant menaquinone and iso-C16 : 0 and iso H-C16 : 1 as the major fatty acids. The polar lipids detected in strain GY0556T were phosphatidylcholine, phosphatidylinositol, one unknown glycolipid, one unknown phospholipid and two unknown lipids. The whole organism hydrolysates mainly consisted of meso-diaminopimelic acid, xylose, galactose and arabinose. The DNA G+C content of strain GY0556T was 76.9 mol%. The results of DNA–DNA hybridizations and phylogenetic analysis, together with the phenotypic and biochemical tests, allowed the differentiation of strain GY0556T from established members of the genus Pseudonocardia . Therefore, it is proposed that strain GY0556T represents a novel species of the genus Pseudonocardia , for which the name Pseudonocardia profundimaris sp. nov. is proposed. The type strain is GY0556T (=MCCC 1A10574T=KCTC 39641T).
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Actinomyces vulturis sp. nov., isolated from Gyps himalayensis
Two strains of Gram-stain-positive, facultatively anaerobic, non-spore-forming short rods (VUL7T and VUL8) were isolated from rectal swabs of Old World vultures, namely Gyps himalayensis, in Tibet-Qinghai Plateau, China. Optimal growth occurred at 37 °C, pH 6–7, with 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences classified the two strains to the genus Actinomyces , with highest 16S rRNA gene sequence similarity (95 %) to type strains of Actinomyces haliotis , Actinomyces radicidentis and Actinomyces urogenitalis . The major cellular fatty acids were C18 : 1ω9c and C16 : 0. MK-10(H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 54.4 mol%. DNA–DNA hybridization values with the most closely related species of the genus Actinomyces was 24.6 %. The two strains can be differentiated from the most closely related species such as A. haliotis , A. radicidentis, A. graevenitzii and A. urogenitalis by a list of carbohydrate fermentations and enzyme activities. On the basis of physiological, biochemical and phylogenetic analysis, strains VUL7T and VUL8 represent novel species of the genus Actinomyces , for which the name Actinomyces vulturis sp. nov. is proposed. The type strain is VUL7T (=CGMCC 4.7366T=DSM 103437T).
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Micromonospora fulva sp. nov., isolated from forest soil
More LessA novel actinobacterium, designated strain UDF-1T, was isolated from forest soil in Chungnam, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain UDF-1T formed a branched brownish-orange substrate mycelium with spherical or oval spores. No aerial mycelium was formed. Comparative 16S rRNA gene sequence analysis indicated that strain UDF-1T belongs to the genus Micromonospora , showing the highest sequence similarity to Micromonospora palomenae NEAU-CX1T (99.2 % 16S rRNA gene sequence similarity), ‘ Micromonospora maoerensis ’ NEAU-MES19 (99.0 %), Micromonospora endolithica DSM 44398T (98.8 %) and Micromonospora matsumotoense IMSNU 22003T (98.8 %). The predominant menaquinones of strain UDF-1T were MK-10 (H4) and MK-10 (H6). The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 73.1 mol%. DNA–DNA relatedness between strain UDF-1T and closely related type strains in the genus Micromonospora was below 30 %. On the basis of the polyphasic analysis conducted in this study, strain UDF-1T represents a novel species of the genus Micromonospora , for which the name Micromonospora fulva sp. nov. is proposed. The type strain is UDF-1T (=KACC 18696T=NBRC 111826T).
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Three novel species of the genus Kibdelosporangium; Kibdelosporangium kanagawaense sp. nov., Kibdelosporangium rhizosphaerae sp. nov. and Kibdelosporangium rhizovicinum sp. nov.
More LessThe taxonomic positions of three actinomycete isolates, K08-0175T, K10-0543T and K12-0791T, which were isolated from plant root and rhizospheric soil samples were subjected to a polyphasic taxonomic study. On the basis of the results of phylogenetic analysis and morphological and chemotaxonomic characteristics, these three strains were classified as representing members of the genus Kibdelosporangium . These strains were observed to produce both long chains of rod-shaped spores and sporangium-like structures with well-defined walls on aerial hyphae. Phylogenetic position, DNA–DNA hybridization and comparison of the phylogenetically closest relatives revealed that these three strains were clearly distinguishable from each other and from their closest phylogenetic relatives. Therefore, three novel species are proposed as Kibdelosporangium kanagawaense sp. nov. [type strain K08-0175T (=NBRC 112388T=TBRC 6786T)], Kibdelosporangium rhizosphaerae sp. nov. [type strain K10-0543T (=NBRC 112389T=TBRC 6787T)] and Kibdelosporangium rhizovicinum sp. nov. [type strain K12-0791T (=NBRC 112390T=TBRC 6788T)].
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Mycobacterium persicum sp. nov., a novel species closely related to Mycobacterium kansasii and Mycobacterium gastri
Four strains isolated in Iran from pulmonary specimens of unrelated patients are proposed as representative of a novel Mycobacterium species. Similarity, at the phenotypic level, with Mycobacterium kansasii is remarkable with the photochromogenic yellow pigmentation of the colonies being the salient feature. They differ, however, genotypically from this species and present unique sequences in 16S rRNA, hsp65 and rpoB genes. The average nucleotide identity and the genome-to-genome distance fully support the status of an independent species. The name proposed for this species is Mycobacterium persicum sp. nov. with AFPC-000227T (=DSM 104278T=CIP 111197T) as the type strain.
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Microbacterium tumbae sp. nov., an actinobacterium isolated from the stone chamber of ancient tumulus
Eight strains characterised as Gram-stain-positive, non-spore-forming and non-motile rods were isolated from samples collected from stone chambers of the Takamatsuzuka and Kitora tumuli in Asuka village, Nara Prefecture, Japan. Among them, one strain, T7528-3-6bT, was shown to form a novel lineage within the genus Microbacterium . The most closely phylogenetically related species to T7528-3-6bT was Microbacterium panaciterrae , with 97.8 % sequence similarity. The major isoprenoid quinones of T7528-3-6bT were MK-12, MK-13 and MK-11. The predominant cellular fatty acids for this isolate were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The diagnostic diamino acid of the peptidoglycan of this isolate was ornithine. Major polar lipids of the isolate were phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The G+C content of the genomic DNA of this isolate was 70.1 mol%. On the basis of the results of physiological, biochemical and chemotaxonomic tests and molecular phylogenetic analysis, T7528-3-6bT is considered to represent a novel species of the genus Microbacterium , for which the name M. tumbae sp. nov. has been proposed. The type strain is T7528-3-6bT (=JCM 28836T=NCIMB 15039T). The results of comparisons of both phenotypic and genotypic (16S rRNA gene sequence) characteristics indicated that the remaining seven isolates were very closely related to Microbacterium shaanxiense . Although the sequence similarity between the two was 99.2 %, further detailed multifaceted comparisons are needed to determine their accurate taxonomic assignment.
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Nesterenkonia cremea sp. nov., a bacterium isolated from a soda lake
A Gram-stain-positive, aerobic, non-motile, rod-shaped, non-endospore-forming bacterial strain, 10CT, was isolated from Lonar soda lake in India. Based on the 16S rRNA gene sequence analysis, this strain was identified as belonging to the genus Nesterenkonia and was most closely related to the type strains of Nesterenkonia lacusekhoensis (99.1 %, sequence similarity), Nesterenkonia aethiopica (96.9 %), Nesterenkonia flava (96.9 %) and related of the genus Nesterenkonia (<96.6 %, sequence similarity). However, the DNA–DNA relatedness of strain 10CT with N. lacusekhoensis KCTC 19283T was only 34.6±0.9. The DNA G+C content of strain 10CT was 68.6 mol%. Strain 10CT was an aerobic microbe with optimal growth at 37 °C, pH 7.5–8.0 and 5–6 % (w/v) NaCl. The cell-wall peptidoglycan of strain 10CT was of the type A4α (l-Lys–l-Glu). The major polar lipids present were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The major isoprenoid quinones were MK-7, MK-8 and MK-9. Major fatty acids of strain 10CT were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain 10CT, which represents a novel member of the genus Nesterenkonia for which the name Nesterenkonia cremea sp. nov. is proposed. The type strain is 10CT (=LMG 29100T=KCTC 39636T=CGMCC 1.15388T).
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Naumannella huperziae sp. nov., an endophytic actinobacterium isolated from Huperzia serrata (Thunb.)
More LessAn endophytic, short rod-shaped, non-motile and non-spore-forming actinobacterium, designated strain CPCC 204135T, was isolated from a surface-sterilized medicinal plant, Huperzia serrata (Thunb.), collected from Sichuan Province, south-west China. Strain CPCC 204135T was observed to grow at temperatures between 20 and 37 °C (optimum, 28–32 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and in the presence of 0–9.0 % (w/v) NaCl (optimum, 0–3 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204135T belonged to the genus Naumannella , showing the highest level of 16S rRNA gene sequence similarity with Naumannella halotolerans DSM 24323T (97.2 %), the only species of the genus Naumannella in the family Propionibacteriaceae with a validly published name. The DNA–DNA hybridization value between strain CPCC 204135T and N. halotolerans DSM 24323T was 20.1±1.8 %, which is far below the accepted 70 % threshold for species delineation. The cell-wall hydrolysates contained ll-diaminopimelic acid, alanine, glycine and glutamic acid, with the peptidoglycan type of A3γ. Diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid, one unidentified aminolipid, one unidentified polar lipid and several kinds of glycolipids were detected in the polar lipids profile. MK-9(H4) was identified as the predominant menaquinone. The major cellular fatty acids (>10 %) were anteiso-C15 : 0 and iso-C16 : 0. The G+C content of the genomic DNA of strain CPCC 204135T was determined to be 71.8 mol%. On the basis of phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, we concluded that strain CPCC 204135T represents a novel species of the genus Naumannella , for which the name Naumannella huperziae sp. nov. is proposed, with strain CPCC 204135T (=DSM 101717T=NBRC 111773T) as the type strain.
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Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus
More LessTwo strains (VUL4_1T and VUL4_2) of Gram-staining-positive, catalase-negative, non-spore-forming short rods were isolated from rectal swabs of Old World vultures (Gypaetus barbatus) in the Tibet-Qinghai Plateau, China. Analysis of morphological characteristics and biochemical tests indicated that the two strains closely resembled each other but were distinct from other species of the genus Actinomyces previously described. Based on the results of 16S rRNA gene sequence comparison and genome analysis, strains were determined to be members of the genus Actinomyces , closely related to the type strains of Actinomyces marimammalium (96.4 % 16S rRNA gene sequence similarity), Actinomyces hongkongensis (92.4 %), Actinomyces hordeovulneris (92.3 %) and Actinomyces nasicola (92.2 %), respectively. Optimal growth conditions were 37 °C, pH 6–7, with 1 % (w/v) NaCl. Strain VUL4_1T contained C18 : 1ω9c and C16 : 0 as the major cellular fatty acids and diphosphatidylglycerol as the major component of the polar lipids. The genomic DNA G+C content of VUL4_1T was 54.9 mol%. Strain VUL4_1T showed less than 70 % DNA–DNA relatedness with other species of the genus Actinomyces , further supporting strain VUL4_1T as a representative of a novel species. Based on the phenotypic data and phylogenetic inference, a novel species, Actinomyces liubingyangii sp. nov., is proposed with VUL4_1T (=CGMCC 4.7370T=DSM 104050T) as the type strain.
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Calidifontibacter terrae sp. nov., an actinomycete isolated from soil, with potential applications in cosmetics
More LessAn aerobic, Gram-stain-positive, oxidase- and catalase-positive, non-motile, non-spore-forming, coccoid, creamish-white-coloured bacterium, designated strain R161T, was isolated from soil in Hwaseong, South Korea. The cell-wall peptidoglycan contained glycine, glutamic acid, alanine, aspartic acid, serine and lysine, and whole-cell sugars were galactose, rhamnose, glucose and ribose. Strain R161T showed antibacterial and enzyme inhibitory activities. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain R161T formed a lineage within the family Dermacoccaceae , and showed highest sequence similarity with type strains of Calidifontibacter indicus PC IW02T (97.71 % sequence similarity) and Yimella lutea YIM 45900T (97.58 %). The sequence similarity of strain R161T with type strains of members of the genus Dermacoccus was less than 96.5 %. The major menaquinone was MK-8(H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The DNA G+C content of strain R161T was 73.9 mol%. The DNA–DNA hybridization value between strain R161T and C. indicus JCM 16038T was 52.1 %. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strain R161T represents a novel species of genus Calidifontibacter , for which the name Calidifontibacter terrae sp. nov. is proposed. The type strain of Calidifontibacter terrae sp. nov. is R161T (=KEMB 9005-404T=KACC 18906T=JCM 31558T).
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Tessaracoccus arenae sp. nov., isolated from sea sand
More LessA Gram-stain positive, non-spore-forming, non-motile, facultatively anaerobic bacterial strain, designated CAU 1319T, was isolated from sea sand and the strain’s taxonomic position was investigated using a polyphasic approach. Strain CAU 1319T grew optimally at 30 °C and at pH 7.5 in the presence of 2 % (w/v) NaCl. Phylogenetic analysis, based on the 16S rRNA gene sequence, revealed that strain CAU 1319T belongs to the genus Tessaracoccus , and is closely related to Tessaracoccus lapidicaptus IPBSL-7T (similarity 97.69 %), Tessaracoccus bendigoensis Ben 106T (similarity 95.64 %) and Tessaracoccus flavescens SST-39T (similarity 95.84 %). Strain CAU 1319T had ll-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-9 (H4) as the predominant menaquinone, and anteiso-C15 : 0 as the major fatty acid. The polar lipids consisted of phosphatidylglycerol, phosphatidylinositol, two unidentified aminolipids, three unidentified phospholipids and one unidentified glycolipid. Predominant polyamines were spermine and spermidine. The DNA–DNA hybridization value between strain CAU 1319T and T. lapidicaptus IPBSL-7T was 24 %±0.2. The DNA G+C content of the novel strain was 69.5 mol%. On the basis of phenotypic and chemotaxonomic properties, as well as phylogenetic relatedness, strain CAU 1319Tshould be classified as a novel species of the genus Tessaracoccus , for which the name Tessaracoccus arenae sp. nov. is proposed. The type strain is CAU 1319T(=KCTC 39760T=NBRC 111973T).
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Saccharopolyspora spongiae sp. nov., a novel actinomycete isolated from the marine sponge Scopalina ruetzleri (Wiedenmayer, 1977)
A novel marine actinomycete, designated strain CMAA 1452T, was isolated from the sponge Scopalina ruetzleri collected from Saint Peter and Saint Paul Archipelago, in Brazil, and subjected to a polyphasic taxonomic investigation. The organism formed a distinct phyletic line in the Saccharopolyspora 16S rRNA gene tree and had chemotaxonomic and morphological properties consistent with its classification in this genus. It was found to be closely related to Saccharopolyspora dendranthemae KLBMP 1305T (99.5% 16S rRNA gene sequence similarity) and shared similarities of 99.3, 99.2 and 99.0 % with ‘ Saccharopolyspora endophytica’ YIM 61095, Saccharopolyspora tripterygii YIM 65359T and ‘ Saccharopolyspora pathumthaniensis’ S582, respectively. DNA–DNA relatedness values between the isolate and its closest phylogenetic neighbours, namely S. dendranthemae KLBMP 1305T, ‘ S. endophytica ’ YIM 61095 and S. tripterygii YIM 65359T, were 53.5, 25.8 and 53.2 %, respectively. Strain CMAA 1452T was also distinguished from the type strains of these species using a range of phenotypic features. On the basis of these results, it is proposed that strain CMAA 1452T (=DSM 103218T=NRRL B-65384T) merits recognition as the type strain of a novel Saccharopolyspora species, Saccharopolyspora spongiae sp. nov.
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- Archaea
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Pyrobaculum igneiluti sp. nov., a novel anaerobic hyperthermophilic archaeon that reduces thiosulfate and ferric iron
More LessA novel anaerobic, hyperthermophilic archaeon was isolated from a mud volcano in the Salton Sea geothermal system in southern California, USA. The isolate, named strain 521T, grew optimally at 90 °C, at pH 5.5–7.3 and with 0–2.0 % (w/v) NaCl, with a generation time of 10 h under optimal conditions. Cells were rod-shaped and non-motile, ranging from 2 to 7 µm in length. Strain 521T grew only in the presence of thiosulfate and/or Fe(III) (ferrihydrite) as terminal electron acceptors under strictly anaerobic conditions, and preferred protein-rich compounds as energy sources, although the isolate was capable of chemolithoautotrophic growth. 16S rRNA gene sequence analysis places this isolate within the crenarchaeal genus Pyrobaculum . To our knowledge, this is the first Pyrobaculum strain to be isolated from an anaerobic mud volcano and to reduce only either thiosulfate or ferric iron. An in silico genome-to-genome distance calculator reported <25 % DNA–DNA hybridization between strain 521T and eight other Pyrobaculum species. Due to its genotypic and phenotypic differences, we conclude that strain 521T represents a novel species, for which the name Pyrobaculum igneiluti sp. nov. is proposed. The type strain is 521T (=DSM 103086T=ATCC TSD-56T).
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Sulfodiicoccus acidiphilus gen. nov., sp. nov., a sulfur-inhibited thermoacidophilic archaeon belonging to the order Sulfolobales isolated from a terrestrial acidic hot spring
More LessA novel thermoacidophilic archaeon, strain HS-1T, was isolated from the Hakone Ohwaku-dani hot spring in Japan. Cells of strain HS-1T in exponential phase were cocci to irregular cocci with a diameter of 0.8–1.5 µm. The strain grew within a temperature range of 50–70 °C (optimal: 65–70 °C), a pH range of pH 1.4–5.5 (optimal: pH 3.0–3.5) and a NaCl concentration range of 0–2.5 % (w/v). The novel strain grew in aerobic conditions but did not grow anaerobically. Moreover, this strain utilized various complex substrates (beef extract, casamino acids, peptone, tryptone and yeast extract) and sugars (arabinose, xylose, galactose, glucose, maltose, sucrose, raffinose and lactose) as sole carbon sources. No chemolithoautotrophic growth occurred on elemental sulfur, pyrite, K2S4O6, Na2S2O3 or FeSO4 . 7H2O; however, growth by the oxidation of hydrogen occurred weakly. The core lipids were calditoglycerocaldarchaeol (CGTE) and caldarchaeol (DGTE). The DNA G+C content of the strain was 52.0 mol%, which was remarkably higher than those of known species of the order Sulfolobales (31–46.2 %). The growth of the strain was significantly inhibited in the presence of elemental sulfur. Analyses of 16S rRNA and 23S rRNA gene sequences showed that HS-1T belonged to the order Sulfolobales ; however, it was distantly related to all known species of the order Sulfolobales (less than 89 % sequence similarity). On the basis of these results, we propose the novel genus, Sulfodiicoccus, in the order Sulfolobales (in the family Sulfolobaceae ). The type species of the genus is Sulfodiicoccus acidiphilus sp. nov., and the type strain of the species is HS-1T (=JCM 31740T=InaCC Ar79T).
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- Bacteroidetes
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Cloacibacterium caeni sp. nov., isolated from activated sludge
More LessA Gram-stain-negative, facultatively anaerobic bacterium, designated B6T, was isolated from activated sludge of a wastewater treatment plant in South Korea. Cells were oxidase- and catalase-positive and non-motile rods producing yellow carotenoid-type pigments. Growth of B6T was observed at 20–40 °C (optimum, 37 °C) and pH 6.6–8.2 (optimum, pH 7.0) and in R2A broth supplemented with 0–1 % (w/v) NaCl (optimum, 0 %). B6T contained iso-C15 : 0 as the major fatty acid. Menaquinone-6 was detected as the sole respiratory quinone. The G+C content of the genomic DNA of B6T was 31.5 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that B6T formed a tight phylogenetic lineage with members of the genus Cloacibacterium . B6T was most closely related to Cloacibacterium rupense R2A-16T (99.0 %), Cloacibacterium normanense NRS1T (98.7 %) and Cloacibacterium haliotis WB5T (97.4 %), but their DNA–DNA relatedness levels were less than 42.0 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that B6T represents a novel species of the genus Cloacibacterium , for which the name Cloacibacterium caeni sp. nov. is proposed. The type strain is B6T (=KACC 18988T=JCM 31714T).
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Chryseobacterium reticulitermitis sp. nov., isolated from the gut of Reticulitermes aculabialis
Yun Zhao, Yu Wang, Dan Hong Li, Yu Deng and Hong YangA 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).
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Emticicia aquatilis sp. nov., isolated from a freshwater sample
A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG-DN6.14T, was isolated from a freshwater sample near Donghaksa temple in Daejeon, South Korea. On the basis of the results of 16S rRNA gene sequence comparisons, THG-DN6.14T was found to be most closely related to Emticicia sediminis JBR12T (99.1 % sequence similarity), Emticicia oligotrophica DSM 17448T (97.6 %), Emticicia aquatica HMF2925T (96.5 %), and Emticicia ginsengisoli Gsoil 085T (94.4 %). The DNA–DNA relatedness between THG-DN6.14T and its phylogenetically closest neighbours was below 65.0 %. The DNA G+C content was 43.3 mol%. The major polar lipids were found to be phosphatidylethanolamine, an unidentified glycolipid and an unidentified aminoglycolipid. The major fatty acids were identified as C16 : 0, iso-C15 : 0, iso-C17 : 0 3-OH, and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The respiratory quinone was menaquinone MK-7. These data supported the affiliation of THG-DN6.14T to the genus Emticicia . THG-DN6.14Tcould be distinguished from related species of the genus Emticicia by physiological and biochemical tests. Therefore, the novel isolate represents a novel species, for which the name Emticicia aquatilis sp. nov. is proposed, with THG-DN6.14T (=KACC 18540T=CGMCC 1.15958T) as the type strain.
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Flaviaesturariibacter luteus sp. nov., isolated from an agricultural floodplain soil, and emended description of the genus Flaviaesturariibacter
More LessA novel slow-growing bacterial strain designated as AW305T was isolated from an agricultural floodplain soil located in Mashare, Kavango region, Namibia. Cells stained Gram-negative, were non-motile, non-spore-forming, coccoid to rod-shaped and did not form a capsule. Colonies were yellow-pigmented, but flexirubin-type pigments were not detected. AW305T had an aerobic chemo-organoheterotrophic metabolism, using a narrow spectrum of carbon sources for growth, with preference for complex protein substrates, organic acids and amino acids. AW305T was able to grow at 15–40 °C, pH 5.3–8.3 and in the presence of up to 0.25 % (w/v) NaCl. 16S rRNA gene sequence comparison showed that AW305T belonged to the genus Flaviaesturariibacter (family Chitinophagaceae ). Its closest relatives were Flaviaesturariibacter amylovorans GCR0105T (97.0 %), Flavisolibacter ginsengiterrae Gsoil 492T (93.6 %) and Flavisolibacter ginsengisoli Gsoil 643T (93.2 %). DNA–DNA hybridization experiments corroborated that AW305T represents an independent genomospecies. The genomic DNA G+C content was 57.6 mol%. Major fatty acids were iso-C15 : 1 G, iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The predominant respiratory quinone was MK-7, albeit minor amounts of MK-6 were also detected. The polar lipids comprised major amounts of phosphatidylethanolamine and minor amounts of two unidentified lipids, an unidentified phospholipid, an unidentified glycolipid and an unidentified aminoglycophospholipid. On the basis of the polyphasic characterization, strain AW305T represents a novel species of the genus Flaviaesturariibacter for which the name Flaviaesturariibacter luteus sp. nov. is proposed, with the type strain AW305T (=DSM 100282T=LMG 29416T).
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Salibacter halophilus gen. nov., sp. nov., isolated from a saltern
More LessA Gram-stain-negative and facultatively anaerobic bacterium, JZ3C34T, was isolated from a saltern in Feicheng, China (36° 8′ 24.45″ E 116° 49′ 22.46″ N). Cells of strain JZ3C34T were 0.3–0.4 µm wide and 1.5–2.0 µm long, catalase-positive and oxidase-negative. Colonies on modified marine agar 2216 were orange, circular, convex, translucent and approximately 1 mm in diameter after incubation for 96 h at 33 °C. Growth occurred at 20–50 °C (optimally at 33 °C), at pH 6.5–8.5 (optimally at 7.0–8.0) and in the presence of 2–18 % (w/v) NaCl (optimally in 6 % NaCl). Phylogenetic analysis of the 16S rRNA gene indicated that strain JZ3C34T was a member of the family Cryomorphaceae within the order Flavobacteriales and the most closely related species was Owenweeksia hongkongensis DSM 17368T (89.2 % 16S rRNA gene sequence similarity). The major respiratory quinone of strain JZ3C34T was menaquinone MK-7, and the dominant fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The major polar lipids were two unidentified lipids and phosphatidylethanolamine, and the genomic DNA G+C content was 39.6 mol%. Polyphasic taxonomy clearly places the new strain as a novel species within a new genus of the family Cryomorphaceae , for which the name Salibacter halophilus gen. nov., sp. nov. The type strain of Salibacter halophilus is JZ3C34T (=KCTC 52047T=MCCC 1K02288T).
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Aquimarina rubra sp. nov., isolated from sediment of a sea cucumber culture pond
More LessA Gram-stain-negative, non-motile, rod-shaped, red-pigmented, facultatively anaerobic bacterium, designated SS2-9T, was isolated from sediment collected from a sea cucumber culture pond located in Rongcheng, Shandong province, China. Cells of strain SS2-9T were approximately 0.3–0.5 µm in width and 1.5–6.0 µm in length. The strain was able to grow at 10–37 °C, at pH 6.5–8.5 and in the presence of 0.5–6.0 % (w/v) NaCl. It grew optimally at 28 °C and in the presence of 2.0 % (w/v) NaCl. The DNA G+C content was 34.5 mol% and the sole respiratory quinone was menaquinone 6 (MK-6). The predominant cellular fatty acids were C15 : 0, iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SS2-9T was phylogenetically related to members of the genus Aquimarina and was closely related to Aquimarina amphilecti 92VT (97.29 % similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SS2-9T was considered to represent a novel species of the genus Aquimarina , for which the name Aquimarina rubra sp. nov. is proposed. The type strain is SS2-9T (=KCTC 52274T=MCCC 1H00142T).
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Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae
More LessFlexibacter tractuosa [Lewin, 1969] was reclassified as Marivirga tractuosa . Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic, Gram-stain-negative, slender rods, which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0, iso-G-C15 : 1, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine, several unidentified aminolipids, glycolipids and five unidentified polar lipids. The G+C content of the genomic DNA was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NBRC 15981T clustered with members of the genus Marivirga in the family Flammeovirgaceae of the phylum Bacteroidetes . Levels of DNA–DNA relatedness were less than 16 % between strain NBRC 15981T and the two closely related species, Marivirga sericea NBRC 15983T and Marivirga tractuosa NBRC 15989T. Strain NBRC 15981T could be differentiated from these type strains in the genus Marivirga based on the polar lipid pattern and the activity of α-chymotrypsin, as well as by α-glucosidase and β-glucosidase activity. On the basis of these results, NBRC 15981T is proposed as representing a novel species of the genus Marivirga , named Marivirga harenae sp. nov. The type strain is JK11T (=NBRC 15981T=NCIMB 1429T).
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Sphingobacterium alkalisoli sp. nov., isolated from a saline-alkaline soil
More LessA Gram-staining-negative, non-motile, non-spore-forming bacterium designated Y3L14T was isolated from the saline-alkaline soil of a farmland, Inner Mongolia, northern China. Strain Y3L14T could grow at 10–40 °C (optimally at 30 °C), pH 6.0–10.0 (optimally at pH 8.0), and in the presence of 0–6.0 % (w/v) NaCl (optimally with 0–2.0 %). Phylogenetic analysis based on the 16S rRNA gene and DNA gyrase subunit B (gyrB) gene sequences revealed that strain Y3L14T clustered with strains belonging to the genus Sphingobacterium , sharing the highest 16S rRNA gene sequence similarity with Sphingobacterium lactis WCC 4512T (94.99 %). Its major cellular fatty acids contained iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone-7 (MK-7) was the only isoprenoid quinone. Strain Y3L14T contained phosphatidylethanolamine, sphingophospholipid, two unknown phospholipids and three unknown lipids as the major polar lipids. The genomic DNA G+C content of strain Y3L14T was 36.0 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y3L14T represents a novel species within the genus Sphingobacterium , for which Sphingobacterium alkalisoli sp. nov. is proposed; the type strain is Y3L14T (=CGMCC 1.15782T=KCTC 52379T).
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Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica
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.
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Polaribacter litorisediminis sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated OITF-11T, was isolated from a tidal flat in Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-11T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OITF-11T belonged to the genus Polaribacter . Strain OITF-11T exhibited 16S rRNA gene sequence similarity values of 97.4–98.1 % to Polaribacter haliotis RA4-7T, Polaribacter atrinae KACC 17473T, Polaribacter dokdonensis DSW-5T and Polaribacter marinaquae KCTC 42664T, and of 94.1–96.9 % to the type strains of the other Polaribacter species. Strain OITF-11T contained menaquinone MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and C15 : 1ω6c as the major fatty acids. The major polar lipids detected in strain OITF-11T were phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified lipid. The DNA G+C content of strain OITF-11T was 32.2 mol% and its DNA–DNA relatedness values with the type strains of P. haliotis , P. atrinae , P. dokdonensis and P. marinaquae were 14–33 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain OITF-11T is separated from recognized species of the genus Polaribacter . On the basis of the data presented, strain OITF-11T is considered to represent a novel species of the genus Polaribacter , for which the name Polaribacter litorisediminis sp. nov. is proposed. The type strain is OITF-11T (=KCTC 52500T=NBRC 112457T).
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- Firmicutes and Related Organisms
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Marinisporobacter balticus gen. nov., sp. nov., Desulfosporosinus nitroreducens sp. nov. and Desulfosporosinus fructosivorans sp. nov., new spore-forming bacteria isolated from subsurface sediments of the Baltic Sea
More LessFour novel Gram-stain-positive, endospore-forming bacteria of the order Clostridiales were isolated from subsurface sediments sampled during International Ocean Discovery Program Expedition 347 to the Baltic Sea. One strain (59.4MT) grew as an obligate heterotroph by aerobic respiration and anaerobically by fermentation. Optimum growth was observed with 0.5 % NaCl at 25 °C and pH 7.0–7.3. Analysis of 16S rRNA gene sequences of 59.4MT revealed Alkaliphilus transvaalensis (92.3 % identity), Candidatus Geosporobacter ferrireducens (92.2 %), Geosporobacter subterraneus (91.9 %) and Alkaliphilus peptidifermentans (91.7 %) to be the closest relatives. On the basis of the results of phenotypic and genotypic analyses, we propose that strain 59.4MT represents a novel species within a novel genus, Marinisporobacter balticus gen. nov., sp. nov., with the type strain 59.4MT (=DSM 102940T=JCM 31103T). Three other strains, 59.4F, 59.4BT and 63.6FT, were affiliated with the genus Desulfosporosinus and grew as strictly anaerobic sulfate reducers. These strains additionally used thiosulfate, elemental sulfur, sulfite and DMSO as electron acceptors and hydrogen as an electron donor. Strains 59.4F and 59.4BT had identical 16S rRNA gene sequences, which were most similar to those of Desulfosporosinus lacus (97.8 %), Desulfosporosinus hippei (97.3 %) and Desulfosporosinus orientis (97.3 %). Strain 63.6FT was closely related to D. lacus (97.7 %), Desulfosporosinus meridiei (96.6 %) and D. hippei (96.5 %). The similarity of 16S rRNA gene sequences of strains 59.4BT and 63.6FT was 96.6 %. We propose the new names Desulfosporosinus nitroreducens sp. nov., incorporating strain 59.4F (=DSM 101562=JCM 31104) and the type strain 59.4BT (=DSM 101608T=JCM 31105T), and Desulfosporosinus fructosivorans sp. nov., with the type strain 63.6FT (=DSM 101609T=JCM 31106T).
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Paenibacillus apis sp. nov. and Paenibacillus intestini sp. nov., isolated from the intestine of the honey bee Apis mellifera
More LessThree strains, CBM1T, CBH23 and LAH16T, belonging to the genus Paenibacillus were isolated from the midgut and hindgut of Apis mellifera. Based on 16S rRNA gene sequence analyses and phenotypic characteristics, the three strains represent two novel species. Strains CBM1T and CBH23 formed a group with Paenibacillus puldeungensis CAU 9324T, and strain LAH16T belonged to the Paenibacillus amylolyticus NRRL NRS-290T subgroup of the genus Paenibacillus . The DNA G+C contents of strains CBM1T, CBH23 and LAH16T were 47.7, 48.1 and 46.1 mol%, respectively. The three strains possessed diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as polar lipids. The predominant quinone in the three strains was MK-7, but strains CBM1T and CBH23 contained an additional major quinone, MK-8(H2). While strain LAH16T and most species of the genus Paenibacillus possessed anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 as major cellular fatty acids, strains CBM1T and CBH23 possessed C16 : 0, anteiso-C15 : 0, C18 : 1ω7c and C19 : 0cyclo ω8c. Based on phenotypic, chemotaxonomic and phylogenetic data, strains CBM1T and CBH23 and the strain LAH16T represent novel species in the genus Paenibacillus , for which the names Paenibacillus apis sp. nov. and Paenibacillus intestini sp. nov. are proposed, with CBM1T (=KCTC 33844T=JCM 31620T) and LAH16T (=KCTC 33832T=JCM 31621T) as the type strains, respectively.
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Enterococcus crotali sp. nov., isolated from faecal material of a timber rattlesnake
A facultatively anaerobic, Gram-stain-positive bacterium, designated ETRF1T, was found in faecal material of a timber rattlesnake (Crotalus horridus). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to the genus Enterococcus . The 16S rRNA gene sequence of strain ETRF1T showed >97 % similarity to that of the type strains of Enterococcus rotai , E. caccae , E. silesiacus , E haemoperoxidus , E. ureasiticus , E. moraviensis , E. plantarum , E. quebecensis , E. ureilyticus , E. termitis , E. rivorum and E. faecalis . The organism could be distinguished from these 12 phylogenetically related enterococci using conventional biochemical testing, the Rapid ID32 Strep system, comparative pheS and rpoA gene sequence analysis, and comparative whole genome sequence analysis. The estimated in silico DNA–DNA hybridization values were <70 %, and average nucleotide identity values were <96 %, when compared to these 12 species, further validating that ETRF1T represents a unique species within the genus Enterococcus . On the basis of these analyses, strain ETRF1T (=CCUG 65857T=LMG 28312T) is proposed as the type strain of a novel species, Enterococcus crotali sp. nov.
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Alkaliphilus namsaraevii sp. nov., an alkaliphilic iron- and sulfur-reducing bacterium isolated from a steppe soda lake
A novel alkaliphilic spore-forming bacterium was isolated from the benthic sediments of the highly mineralized steppe Lake Khilganta (Transbaikal Region, Russia). Cells of the strain, designated Х-07-2T, were straight to slightly curved rods, Gram-stain-positive and motile. Strain Х-07-2T grew in the pH range from 7.0 to 10.7 (optimum pH 9.6–10.3). Growth was observed at 25–47 °C (optimum 30 °C) and at an NaCl concentration from 5 to 150 g l−1 with an optimum at 40 g l−1. Strain Х-07-2T was a chemo-organoheterotroph able to reduce amorphous ferric hydroxide, Fe(III) citrate and elemental sulfur in the presence of yeast extract as the electron donor. It used tryptone, peptone and trypticase with Fe(III) citrate as the electron acceptor. The predominant fatty acids in cell walls were C16:1ω8, iso-C15:0, C14 : 0 3-OH and C16 : 0. The DNA G+C content was 32.6 mol%. 16S rRNA gene sequence analysis revealed that strain Х-07-2T was related most closely to members of the genus Alkaliphilus within the family Clostridiaceae . The closest relative was Alkaliphilus peptidifermentans Z-7036T (96.4 % similarity). On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Х-07-2T represents a novel species in the genus Alkaliphilus , for which the name Alkaliphilus namsaraevii sp. nov. is proposed. The type strain is Х-07-2T (=VKM В-2746Т=DSM 26418Т).
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- Other Bacteria
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Desulfurobacterium indicum sp. nov., a thermophilic sulfur-reducing bacterium from the Indian Ocean
A novel sulfur-reducing bacterium, strain K6013T, was isolated from a sulfide sample collected at a depth of 2771 m from a high-temperature hydrothermal vent in the Indian Ocean. Cells were Gram-stain-negative, anaerobic, motile rods (0.9–2.2×0.4–0.6 µm). The strain grew at NaCl concentrations ranging from 1 to 4.5 % (w/v) (optimum 2.5 %), at pH 5 to 8 (optimum pH 6), and at temperatures between 40 and 75 °C (optimum 65 °C). K6013T was an obligate chemolithoautotroph, using thiosulfate, sulfur and nitrate as terminal electron acceptors in the presence of H2 but not sulfate, sulfite nor nitrite. The major cellular fatty acids were C16 : 0 (17.4 %), C18 : 1ω7c/C18 : 1ω6c (ummed feature 8, 37.91 %), C18 : 0 (18.29 %) and C14 : 0 3-OH/iso-C16: 1I (summed feature 2, 8.56 %). The DNA G+C content was 38.2 mol%. The results of phylogenetic 16S rRNA gene sequence analyses indicated that K6013T represents a member of the genus Desulfurobacterium within the class Aquificae , with highest sequence similarity of 96.93 % to Desulfurobacterium atlanticum SL22T. On the basis of genotypic and phenotypic data, K6013T is considered to represent a novel species of the genus Desulfurobacterium , for which the name Desulfurobacterium indicum sp. nov. is proposed, with the type strain K6013T (=DSM 101677T=MCCC 1A01868T).
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- Proteobacteria
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Salinovum rubellum gen. nov., sp. nov., isolated from sediment of a saltern
More LessAn aerobic, Gram-reaction-negative, oxidase-positive and catalase-positive strain, YCWB25T, was isolated from saltern farm sediment in Jimo-Daqiao of Qingdao, east coast of China. This strain had an absolute requirement for NaCl and was able to grow in the presence of 1–10 % (w/v) NaCl (optimal growth at 3–5 % NaCl). The strain grew at pH 5.0–9.0 (optimal growth at pH 8.0) and 4–42 °C (optimal growth at 30 °C). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YCWB25T belonged to the Roseobacter clade of the family Rhodobacteraceae , and the closest species were members of the genus Pseudooceanicola (similarity lower than 95.58 %). However, the novel strain formed a robust, distinct clade different from other members of the Roseobacter clade. The DNA G+C content of strain YCWB25T was 65.6 mol%. The predominant respiratory quinone was Q-10. The dominant cellular fatty acids were C18 : 1ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The phenotypic, chemotaxonomic and phylogenetic data indicated that strain YCWB25T represents a novel species of a new genus, for which the name Salinovum rubellum gen. nov., sp. nov. is proposed. The type strain of Salinovum rubellum is YCWB25T (=MCCC 1K00272T=LMG 25394T).
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Nitratireductor aestuarii sp. nov., a marine alphaproteobacterium isolated from an estuary
More LessTwo bacterial strains, 2-2-12-1T and 2-2-12-2, were isolated from the estuary of the Jiulong River, south-east China. Cells were Gram-stain-negative, non-motile, short rods without flagella. Growth occurred at 25–45 °C, at pH 5.0–9.0 and with 0.5–2 % (w/v) NaCl. The bacteria were unable to reduce nitrate. The predominant fatty acids were C19 : 0 cyclo ω9c and C18 : 1ω7c. Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belong to the genus Nitratireductor , family Phyllobacteriaceae , class Alphaproteobacteria . Their closest neighbours were ‘ Nitratireductor lucknowense ’ DSM 24322 (96.3 and 96.5 % similarity, respectively) and Nitratireductor pacificus MCCC 1A01024T (96.2 and 96.3 % similarity, respectively). The DNA G+C contents of the two strains were 56.7 mol%. DNA–DNA hybridization between strain 2-2-12-1T and the two most closely related type strains revealed 57.3 and 52.3 % relatedness, respectively. Evidence from genotypic, chemotaxonomic and phenotypic data indicated that strains 2-2-12-1T and 2-2-12-2 represent a novel species of the genus Nitratireductor , for which the name Nitratireductor aestuarii sp. nov. is proposed. The type strain is 2-2-12-1T (=LMG 29090T=CGMCC 1.15320T).
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Campylobacter ornithocola sp. nov., a novel member of the Campylobacter lari group isolated from wild bird faecal samples
More LessDuring a study on the prevalence and diversity of campylobacteria in wild birds faecal samples from the city of Valdivia (southern Chile) 17 Gram-stain-negative, curved-rod-shaped isolates, were initially identified as Campylobacter lari by PCR–RFLP. Further identification by 16S rRNA sequence analysis revealed that they formed a distinct group in the genus Campylobacter . This unique position was confirmed by the results of analysis of rpoB, atpA and cpn60 gene sequences. The average nucleotide identity between the representative strain WBE38T and the type strain of the most closely related taxon C. lari subsp. concheus (LMG 11760) was 90.8 %. The oxidase and urease activity of the novel isolates enabled them to be phenotypically differentiated from species of the genus Campylobacter with validly published names. Therefore, on the basis of phenotypic, genetic and genomic characterizations, the results of this study clearly indicate that these strains represent a novel species within the genus Campylobacter , for which the name Campylobacter ornithocola sp. nov. is proposed, with the type strain WBE38T (=CECT 9147T=LMG 29815T).
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Pararhizobium antarcticum sp. nov., isolated from Antarctic water samples
More LessTwo bacterial strains were isolated from sediments and microbial mats of Kingfisher Pond, Antarctica and characterized in a taxonomic study using a polyphasic approach. Cells were strictly aerobic, Gram-stain-negative, rod-shaped, motile (+50 flagellum-specific genes present in the genome sequence; motility observed under microscope) and formed creamy white, half-transparent colonies. Growth occurred at 4 to 28 °C with an optimum at 20 °C, with 0–5.0 % (w/v) NaCl (optimum at 0–1.0 %) and at pH 4.0–11.0 (optimum pH 7.0–9.0). The major fatty acid was C18 : 1ω7c. The respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C content was 60.7 mol %. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmethanolamine in addition to three unidentified lipids, one unknown glycolipid and five unidentified phospholipids. Comparative analysis of 16S rRNA gene sequences showed highest sequence similarity (98.1 %) to Pararhizobium giardinii H152T, Pararhizobium herbae CCBAU 83011T, and ‘Pararhizobium polonicum’ F5.1. In silico average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC) showed 81.1 % identity (ANI) and 22.6 % identity (GGDC) to the closest relative, ‘P. polonicum’ F5.1. On the basis of phenotypic, phylogenetic, genomic and chemotaxonomic data, the two strains represent a novel species of the genus Pararhizobium , for which the name Pararhizobium antarcticum sp. nov. is proposed. The type strain is NAQVI 59T(=DSM 103442T=LMG 29675T).
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Pseudomonas lactis sp. nov. and Pseudomonas paralactis sp. nov., isolated from bovine raw milk
Five strains, designated WS 4672T, WS 4998, WS 4992T, WS 4997 and WS 5000, isolated from bovine raw milk formed two individual groups in a phylogenetic analysis. The most similar species on the basis of 16S rRNA gene sequences were Pseudomonas azotoformans IAM 1603T, Pseudomonas gessardii CIP 105469T and Pseudomonas libanensis CIP 105460T showing 99.7–99.6 % similarity. Using rpoD gene sequences Pseudomonas veronii LMG 17761T (93.3 %) was most closely related to strain WS 4672T and Pseudomonas libanensis CIP 105460T to strain WS 4992T (93.3 %). The five strains could be differentiated from their closest relatives and from each other by phenotypic and chemotaxonomic characterization and ANIb values calculated from draft genome assemblies. ANIb values of strains WS 4992T and WS4671T to the closest relatives are lower than 90 %. The major cellular polar lipids of both strains are phosphatidylethanolamine, phosphatidylglycerol, a phospholipid and diphosphatidylglycerol, and their major quinone is Q-9. The DNA G+C content of strains WS 4992T and WS 4672T were 60.0 and 59.7 mol%, respectively. Based on these genotypic and phenotypic traits two novel species of the genus Pseudomonas are proposed: Pseudomonas lactis sp. nov. [with type strain WS 4992T (=DSM 29167T=LMG 28435T) and the additional strains WS 4997 and WS 5000], and Pseudomonas paralactis sp. nov. [with type strain WS 4672T (=DSM 29164T=LMG 28439T) and additional strain WS 4998].
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Whole genome sequences reveal Vibrio hemicentroti Kim et al. 2013 as a later heterotypic synonym of Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981
More LessThe synonymy between Vibrio hemicentroti Kim et al. 2013 and Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981 was suggested after a recent multilocus sequence analysis of the Splendidus clade, which included the type strains of both species. To clarify their status, we have determined genomic indexes from whole genome sequences of strains V. hemicentroti CECT 8714T and V. splendidus NCCB 53037T. Average Nucleotide Identities of 96.0–96.7 % and an in silico DNA–DNA hybridization value of 70.2 %, as well as similarity levels of selected housekeeping gene sequences support the consideration of V. hemicentroti as a later heterotypic synonym of V. splendidus .
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Oleiagrimonas citrea sp. nov., a marine bacterium isolated from tidal flat sediment and emended description of the genus Oleiagrimonas Fang et al. 2015 and Oleiagrimonas soli
More LessA Gram-stain-negative, aerobic, rod-shaped (1.4–3.6×0.4–0.6 µm) and motile marine bacterium, designated as MEBiC09124T, was isolated from tidal flat sediment of Suncheon Bay, South Korea. 16S rRNA gene sequence analysis revealed that strain MEBiC09124T showed high similarity to Oleiagrimonas soli 3.5XT (96.7 %). Growth was observed at 18–38 °C (optimum 30 °C), at pH 4.0–8.5 (optimum pH 7.5) and with 0–6 % (w/v) (optimum 2.5 %) NaCl. The predominant cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and summed feature 9 (comprising 10-methyl C16 : 0 and/or iso-C17 : 1ω9c). The DNA G+C content was 66.1 mol%. The major respiratory quinone was Q-8. Biochemical characteristics such as production of acetoin and enzyme activities of trypsin, α-chymotrypsin and N-acetyl-β-glucosaminidase differentiated strain MEBiC09124T from O. soli 3.5XT. On the basis of data from this polyphasic taxonomic study, strain MEBiC09124T (=KCCM 43131T=JCM 30904T) is classified as the type strain of a novel species in the genus Oleiagrimonas , for which the name Oleiagrimonas citrea sp. nov. is proposed. Emended descriptions of the genus Oleiagrimonas and Oleiagrimonas soli are also given.
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Acinetobacter defluvii sp. nov., recovered from hospital sewage
More LessA Gram-stain-negative, non-motile Acinetobacter strain, WCHA30T, was isolated from hospital sewage in West China Hospital of Sichuan University in Chengdu, south-western China. Strain WCHA30T was a non-spore-forming, catalase-positive, oxidase-negative, strictly aerobic coccobacillus. The DNA G+C content was 38 mol%. Phylogenetic analysis based on 16S rRNA, rpoB and gyrB gene sequences revealed that the strain was distinct from any previously described species of the genus Acinetobacter . Strain WCHA30T could be distinguished from all known Acinetobacter species by its ability to assimilate β-alanine but not l-glutamate. Genotypic and phenotypic characteristics from this study indicate that strain WCHA30T should be considered to represent a novel species of the genus Acinetobacter , for which the name Acinetobacter defluvii sp. nov. is proposed. The type strain is WCHA30T (=CCTCC AB 2016203T=GDMCC 1.1101T=KCTC 52503T).
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Thioclava arenosa sp. nov., isolated from sea sand
More LessA Gram-staining-negative, non-spore-forming, non-motile, rod-shaped, facultatively anaerobe bacterial strain, designated CAU 1312T, was isolated from sea sand of Eurwangri beach, South Korea. The strain’s taxonomic position was investigated using a polyphasic approach. CAU 1312T grew at temperatures from 20 to 40 °C, in the range of pH 6.0–9.0 and at salinities from 1–4 % (w/v). The results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that CAU 1312T represented a member of the genus Thioclava and was most closely related to Thioclava atlantica 13D2W-2T (similarity 96.53 %). The strain contained Q-10 as the predominant menaquinone and summed feature 8 (C18 : 1ω7c/ω6c) as the major fatty acid. The polar lipids of CAU 1312T consisted of phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, a phosphoglycolipid, and two unidentified phospholipids. The DNA G+C content was 64.7 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic inference, CAU 1312T is considered to represent a novel species of the genus Thioclava , for which the name Thioclava arenosa sp. nov. is proposed. The type strain is CAU 1312T(=KCTC 52190T=NBRC 111989T).
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Paracandidimonas soli gen. nov., sp. nov., isolated from soil
More LessA 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 C16:1 ω7c/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).
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C aulobacter rhizosphaerae sp. nov., a stalked bacterium isolated from rhizosphere soil
More LessThe Gram-reaction-negative, aerobic, white- to pale-yellow-coloured and rod-shaped bacterium with a single polar flagellum or a stalk, designated strain 7F14T, was isolated from rhizosphere soil of cultivated watermelon (Citrullus lanatus) collected from Hefei, China. Growth of strain 7F14T was observed at pH 6.0–9.0, 10–30 °C and in the presence of 0–1 % (w/v) NaCl. Cells were catalase-negative and oxidase-positive. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain 7F14T formed a phyletic lineage within the genus Caulobacter of the family Caulobacteraceae and showed the highest 16S rRNA gene sequence similarities to Caulobacter henricii ATCC 15253T (98.66 %), Caulobacter segnis ATCC 21756T (98.27 %), Caulobacter vibrioides CB51T (97.92 %) and C aulobacter flavus RHGG3T (97.44 %). The G+C content of the genomic DNA was 68.6 mol%. Strain 7F14T contained Q-10 as the sole ubiquinone and 11-methyl C18 : 1ω7c, C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The polar lipids profile consisted of phosphatidylglycerol, an unknown phosphoglycolipid, five unknown glycolipids, an unknown phospholipid and three unknown lipids. DNA–DNA relatedness values to the most closely related type strains Caulobacter henricii DSM 4730T and Caulobacter segnis DSM 7131T were 26.0 and 19.7 %, respectively. Based on unique phenotypic traits, and phylogenetic, chemotaxonomic and DNA–DNA hybridization results, strain 7F14T should be classified as a representative of a novel species of the genus Caulobacter , for which the name C aulobacter rhizosphaerae sp. nov. is proposed. The type strain is 7F14T (=CGMCC 1.15915T=KCTC 52515T).
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Reclassification of Arthrobacter viscosus as Rhizobium viscosum comb. nov
The species Arthrobacter viscosus was isolated from soil from Guatemala and it was classified into the genus Arthrobacter on the basis of phenotypic traits. Nevertheless, the results of16S rRNA gene analysis indicated that this species is a member of the genus Rhizobium , with Rhizobium alamii GBV016T and Rhizobium mesosinicum CCBAU 25010T as the most closely related species with 99.64 and 99.48 % similarity, respectively. The similarity values for the recA gene are 92.2 and 94.4 % with respect to R. alamii GBV016T and R. mesosinicum CCBAU 25010T, respectively, and those for the atpD gene are 92.9 and 98.7 %, respectively. Results of DNA–DNA hybridization analysis yield averages of 46 and 41 % relatedness with respect to the type strains of R. alamii and R. mesosinicum , respectively. Phenotypic characteristics also differed from those of the most closely related species of the genus Rhizobium . Therefore, based on the data obtained in this study, we propose to classify strain LMG 16473T as representing a novel species named Rhizobium viscosum comb. nov. (type strain LMG 16473T=CECT 908T).
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Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies
Rodentibacter gen. nov. is proposed based on isolation and phenotypic characterization of strains, predominantly from rodents. The strains showed 86 % or higher rpoB gene sequence similarity and indicated a genus-level relationship within Pasteurellaceae . The strains compared at 16S rRNA gene sequence level showed 93.8 % or higher similarity, and their genus-level relationship within Pasteurellaceae was confirmed by phenotypic analysis. The type species Rodentibacter pneumotropicus comb. nov. is reclassified from [ Pasteurella ] pneumotropica with type strain NCTC 8141T (=CCUG 12398T). Whole genomic comparison allowed the estimation of DNA–DNA renaturation. Rodentibacter heylii sp. nov. was proposed for a group that included the biovar Heyl of [ Pasteurella ] pneumotropica with the type strain ATCC 12555T (=CCUG 998T). A group was proposed as Rodentibacter ratti sp. nov., which included the taxon 22 of Bisgaard; the type strain is F75T (=CCUG 69665T=DSM 103977T). Taxon 41 of Bisgaard was proposed as Rodentibacter myodis sp. nov. with type strain Ac151T (=CCUG 69666T=DSM 103994T). Rodentibacter heidelbergensis sp. nov. included the type strain 1996025094T (=Ac69T) (=CCUG 69667T=DSM 103978T). A group strains of was proposed as Rodentibacter trehalosifermentans sp. nov. with type strain H1987082031T (=CCUG 69668T=DSM 104075T). Two strains including the reference strain of taxon 17 of Bisgaard that showed 16S rRNA gene similarity of 97.3 % were proposed as Rodentibacter rarus sp. nov. 2325/79T (=CCUG 17206T=DSM 103980T). Rodentibacter mrazii sp. nov. was proposed with type strain Ppn418T (Bisgaard taxon 21) (=CCUG 69669T=DSM 103979T). The eight species could be separated based on phenotypic characteristics such as NAD requirement, ornithine decarboxylase and indole formation, α-glucosidase, β-galactosidase and in acid formation from (+)-l-arabinose, (−)-d-ribose, (+)-d-xylose, myo-inositol, (−)-d-mannitol, lactose, melibiose and trehalose. Forty-six strains including taxon 48 of Bisgaard formed a monophyletic group by rpoB and 16S rRNA gene sequence analysis, but could not be separated phenotypically from R. pneumotropicus and R. heylii, and it was left as an unnamed genomospecies 1 of Rodentibacter with reference strain Ppn416. Another taxon that included 13 strains, mainly isolated from Apodemus sylvaticus, could not be separated phenotypically from R. pneumotropicus or R. heylii and was designated as genomospecies 2. Strain Ppn85 with 95 % or less rpoB gene sequence similarity and with 16S rRNA gene sequence similarity of 97 % or less to the other members of Rodentibacter was left as an unnamed singleton.
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Pseudoxanthomonas putridarboris sp. nov. isolated from rotten tree
More LessA 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 Pseudoxanthomonas ranged 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 Pseudoxanthomonas showing 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).
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Salinicola tamaricis sp. nov., a heavy-metal-tolerant, endophytic bacterium isolated from the halophyte Tamarix chinensis Lour
A Gram-stain-negative, rod-shaped bacterium, strain F01T, was isolated from leaves of Tamarix chinensis Lour. The isolate grew optimally at 30 °C, at pH 7.0 and with 5.0 % (w/v) NaCl, and showed a high tolerance to manganese, lead, nickel, ferrous ions and copper ions. The major fatty acids were C18 : 1ω7c and C16 : 0, and the predominant respiratory quinone was Q-9. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminoglycolipids and phospholipids. The DNA G+C content was 65.8 %. Based on multilocus phylogenetic analysis, strain F01T belonged to the genus Salinicola , with highest 16S rRNA gene sequence similarity to Salinicola peritrichatus CGMCC 1.12381T (97.7 %). The level of DNA–DNA hybridization between strain F01T and closely related Salinicola strains was well below 70 %. According to the phenotypic, genetic and chemotaxonomic data, strain F01T is considered to represent a novel species in the genus Salinicola , for which the name Salinicola tamaricis sp. nov. is proposed. The type strain is F01T (=CCTCC AB 2015304T=KCTC 42855T).
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Sphingopyxis solisilvae sp. nov., isolated from forest soil
More LessA yellow-coloured, Gram-staining-negative, motile and rod shaped bacterium, designated strain R366T, was isolated from forest soil of Kyonggi University, South Korea. It was able to grow at 15–42 °C, pH 6.0–10.0 and with 0–4 % (w/v) NaCl concentration. Based on the 16S rRNA gene sequence analysis, strain R366T belongs to the genus Sphingopyxis and is closely related to Sphingopyxis italica SC13E-S71T (98.72 % sequence similarity), Sphingopyxis chilensis S37T (98.51 %), Sphingopyxis fribergensis Kp5.2T (98.29 %), Sphingopyxis alaskensis RB2256T (98.15 %), Sphingopyxis ginsengisoli Gsoli 250T (98.15 %) and Sphingopyxis taejonensis JSS54T (98.01 %). The predominant respiratory quinone was ubiquinone-10, and the major polyamine was spermidine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and sphingoglycolipid. The predominant fatty acids of strain R366T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω6c, C16 : 0, C18 : 1ω7c 11-methyl and C14 : 0 2-OH. The genomic DNA G+C content of this novel strain was 65.1 mol%. The DNA–DNA relatedness between strain R366T and Sphingopyxis italica DSM 25229T, Sphingopyxis chilensis KCCM 41918T, Sphingopyxis alaskensis KCCM 41983T, Sphingopyxis ginsengisoli KACC 13918T and Sphingopyxis taejonensis KACC 12341T was 51.7, 45.3, 39.0, 41.3 and 44.7 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain R366T represents a novel species of the genus Sphingopyxis , for which the name Sphingopyxis solisilvae sp. nov. is proposed. The type strain is R366T (=KEMB 9005-451T=KACC 19003T=JCM 31675T).
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Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus)
Some bacteria collectively known as rhizobia can establish symbiotic relationships and the N2-fixation process with several legumes used as green manure, in pastures and for wood production. Symbionts belonging to the genus Bradyrhizobium are predominant in the tropics, and an increasing number of studies report high genetic diversity within the genus. We performed a polyphasic study with two strains belonging to the genus Bradyrhizobium – SEMIA 6399T and SEMIA 6404–isolated from root nodules of Deguelia costata (syn. Lonchocarpus costatus), an important legume native to eastern Brazil. In general, sequences of the 16S rRNA gene were highly conserved in members of the genus Bradyrhizobium , and the two strains were positioned in the Bradyrhizobium elkanii superclade, sharing 100 % nucleotide identity with Bradyrhizobium embrapense , Bradyrhizobium erythrophlei and Bradyrhizobium viridifuturi . However, multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed that the two strains belong to a distinct clade, sharing from 87.7 to 96.1 % nucleotide identity with related species of the genus Bradyrhizobium , being most closely related to B. viridifuturi . Average nucleotide identity of genome sequences between SEMIA 6399T and related species was lower than 92 %, below the threshold of species circumscription. nifH phylogeny clustered the SEMIA strains in a clade separated from other species of the genus Bradyrhizobium , and the nodD phylogeny revealed that SEMIA 6399T presents a more divergent sequence. Other phenotypic and genotypic traits were determined for the new group, and our data support the description of the SEMIA strains as representatives of Bradyrhizobium mercantei sp. nov.; SEMIA 6399T (=CNPSo 1165T=BR 6010T=U675T=LMG 30031T) was chosen as the type strain.
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Photobacterium proteolyticum sp. nov., a protease-producing bacterium isolated from ocean sediments of Laizhou Bay
A protease-producing bacterial strain, 13-12T, was isolated from the ocean sediment of Laizhou Bay, PR China and systematically studied. The bacterium was Gram-stain negative, non spore-forming rods, which were motile with two flagella. It was positive for oxidase, the hydrolysis of starch, agar and gelatin, and for nitrate reduction. It was negative for catalase, esterase and the degradation of CM-cellulose. Optimum growth was observed at 28 °C, pH 6.5–7.0 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene, and whole genome data, affiliated it to the genus Photobacterium . It was most closely related to Photobacterium jeanii R-40508T (96.7 % 16S rRNA gene similarity). Strain 13-12T was found to have less than 86.1 % similarities with the type strains of its most closely related species in multi-locus sequence analysis, less than 75.2 % using genome average nucleotide identities (ANI), and less than 18.5 % in DNA–DNA relatedness studies. Q8 was the predominant respiratory menaquinone. Phosphatidylethanolamine, phosphoaminolipid and phospholipid were the major polar phospholipids and summed feature 3 (48.2 %), C16 : 0 (18.4 %) and C18 : 1ω5c (14.1 %) the major fatty acids. The combined phenotypic, phylogenetic, genomic and chemotaxonomic data support this strain representing a novel species of the genus Photobacterium , for which the name Photobacterium proteolyticum sp. nov. is proposed, with 13-12T (=KCTC 42764T=CGMCC 1.14970) as the type strain. The genome size of 13-12T is 6.2 Mbp, comprising 5806 predicted genes and the DNA G+C content is 47.9 mol%.
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Paracoccus hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L. (Mugunghwa flower)
A Gram-stain-negative, aerobic, short-rod-shaped bacterium, motile by means of one flagellum (THG-T2.8T), was isolated from the rhizosphere of Mugunghwa flower. Growth occurred at 10–37 °C (optimum 28 °C), at pH 6–8 (optimum 7) and with 0–5 % NaCl (optimum 1 %). The major quinone was ubiquinone-10 (Q-10). The major fatty acids were C10 : 0 3-OH, C16 : 0, C18 : 0 and C18 : 1 ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid, two unknown phospholipids, one unknown glycolipid and one unidentified lipid. The DNA G+C content of strain THG-T2.8T was 65.5 mol%. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-T2.8T were identified as Paracoccus tibetensis Tibet-S9a3T (98.6 %), Paracoccus aestuarii B7T (98.4 %), Paracoccus rhizosphaerae CC-CCM15-8T (98.3 %) and Paracoccus beibuensis JLT1284T (98.2 %). Levels of sequence similarity among strain THG-T2.8T and other species of the genus Paracoccus were lower than 98.0 %. DNA–DNA hybridization values between strain THG-T2.8T and P. tibetensis Tibet-S9A3TT, P. aestuarii B7T, P. rhizosphaerae CC-CCM15-8T and P. beibuensis JLT1284 T were 36.5 % (38.8 %, reciprocal analysis), 32.8 % (34.8 %), 31.6 % (33.8 %) and 15.3 % (24.8 %), respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA–DNA hybridization data, strain THG-T2.8T represents a novel species of the genus Paracoccus , for which the name Paracoccus hibisci sp. nov. is proposed. The type strain is THG-T2.8T (=KACC 18932T=CCTCC AB 2016181T).
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Pseudorhodobacter ponti sp. nov., isolated from seawater
More LessA Gram-stain-negative, short-rod-shaped, non-motile bacterial strain, designated HWR-46T, was isolated from seawater of the Yellow Sea, South Korea, and was subjected to a polyphasic taxonomic study. Strain HWR-46T grew optimally at pH 7.0–8.0, at 20–25 °C and in the presence of 2–3 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain HWR-46T fell within the clade comprising Pseudorhodobacter species, clustering with the type strain of Pseudorhodobacter aquimaris , with which it exhibited 98.4 % sequence similarity. 16S rRNA gene sequence similarity between strain HWR-46T and the type strains of other Pseudorhodobacter species was 95.1–96.3 %. The DNA G+C content of strain HWR-46T was 63.1 mol% and its mean DNA–DNA relatedness value with P. aquimaris HDW-19T was 24.6±1.5 %. Strain HWR-46T contained only Q-10 as the ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified aminophospholipid. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain HWR-46T is distinguishable from other Pseudorhodobacter species. On the basis of the data presented, strain HWR-46T is considered to represent a novel species of the genus Pseudorhodobacter , for which the name Pseudorhodobacter ponti sp. nov. is proposed. The type strain is HWR-46T (=KCTC 52470T=NBRC 112426T).
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Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.
Thirty-nine denitrifying bacterial strains closely related to one another, represented by strains TSA40T and TSA66T, were isolated from rice paddy soils. Strains TSA40T and TSA66T were Gram-stain-negative, slightly curved rod-shaped, and motile by means of polar flagella. They were able to reduce nitrate, nitrite and nitrous oxide, but unable to fix atmospheric N2. While strain TSA66T was able to grow autotrophically by H2-dependent denitrification, strain TSA40T could not. Phylogenetic analysis suggested that they belong to the family Oxalobacteraceae , the order Burkholderiale s in the class Betaproteobacteria . Major components in the fatty acids (C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and summed feature 3) and quinone (Q-8) also supported the affiliation of strains TSA40T and TSA66T to the family Oxalobacteraceae . Based on 16S rRNA gene sequence comparisons, strains TSA40T and TSA66T showed the greatest degree of similarity to Herbaspirillum massiliense JC206T, Noviherbaspirillum malthae CC-AFH3T, Noviherbaspirillum humi U15T, Herbaspirillum seropedicae Z67T and Paucimonas lemoignei LMG 2207T, and lower similarities to the members of other genera. Average nucleotide identity values between the genomes of strain TSA40T, TSA66T and H. massiliense JC206T were 75–77 %, which was lower than the threshold value for species discrimination (95–96 %). Based on the 16S rRNA gene sequence analysis in combination with physiological, chemotaxonomic and genomic properties, strains TSA40T (=JCM 17722T=ATCC TSD-69T) and TSA66T (=JCM 17723T=DSM 25787T) are the type strains of two novel species within the genus Noviherbaspirillum , for which the names Noviherbaspirillum denitrificans sp. nov. and Noviherbaspirillum autotrophicum sp. nov. are proposed, respectively. We also propose the reclassification of Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.
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Transfer of Pseudomonas pictorum Gray and Thornton 1928 to genus Stenotrophomonas as Stenotrophomonas pictorum comb. nov., and emended description of the genus Stenotrophomonas
More LessA polyphasic taxonomic approach including analysis of phenotypic, physiological and genotypic characteristics, 16S rRNA gene sequence and DNA–DNA hybridization analysis was used to determine the most consistent affiliation of Pseudomonas pictorum . Pseudomonas pictorum ATCC 23328T exhibited phenotypic traits of members of the genus Stenotrophomonas including cellular fatty acid composition, quinone and limited range of substrates that could be used. Antibiotic susceptibility and physiological characteristics were determined. The DNA G+C content was 65.7 mol%. Phylogenetic analysis revealed that the type strains of Stenotrophomonas terrae , Stenotrophomonas humi , Stenotrophomonas nitritireducens and Stenotrophomonas acidaminiphila were the nearest relatives (16S rRNA gene sequence similarity of 98.0 to 98.8 %). All the other type strains of species of the genus Stenotrophomonas showed high 16S rRNA gene sequence similarities (96.8 to 97.2 %). DNA–DNA hybridizations revealed 31.0, 32.0, 43.3 and 43.6 % reassociation between Pseudomonas pictorum ATCC 23328T and the type strains of S. terrae , S. humi , S. nitritireducens and S. acidaminiphila , respectively. Our overall results indicate that Pseudomonas pictorum should be transferred to the genus Stenotrophomonas as a novel species of this genus, Stenotrophomonas pictorum comb. nov. Since the original description of the genus Stenotrophomonas was made with only one species ( Stenotrophomonas maltophilia ), an emendation of the genus description is proposed in order to match better with the characteristics of the eleven novel species assigned to this genus since then.
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Shewanella intestini sp. nov., isolated from the intestine of abalone, Haliotis diversicolor
More LessA Gram-stain-negative, rod-shaped bacterium with a singular polar flagellum, designated as strain XMDDZSB0408T, was isolated from the intestine of adult abalone, Haliotis diversicolor. Activity of oxidase was positive and catalase activity was negative. It could grow at salinities from 3 to 6 % NaCl (w/v), and pH 7–9. It had the highest sequence similarity of <96.0 % with all previously established species for the complete 16S rRNA gene (1531 bp). The results of phylogenetic analysis indicated that the strain was affiliated to the genus Shewanella and closely related to Shewanella gaetbuli TF-27T and Shewanella japonica KMM 3299T (95.8 % sequence similarity), Shewanella electrodiphila MAR441T (95.6 %), Shewanella pacifica KMM 3597T (95.4 %), Shewanella donghaensis LT17T (95.3 %) and Shewanella olleyana ACEM 9T (94.7 %). The respiratory quinones were MK-7, Q-8, Q-7, MK-8, Q-7 (H4) and Q-6. The predominant fatty acids consisted of C16:0, summed feature 3 (comprised of C16 : 1ω7c/C16 : 1ω6c), C18 : 0, summed feature 8 (comprised of C18 : 1ω7c/C18 : 1ω6c), C12 : 0 and C14 : 0. The polar lipids were identified as phosphatidylethanolamine (PE), a glycolipid (GL), a phospholipid (PL) and one unidentified lipid (L). The DNA G+C content was 41.4 mol% calculated from the draft genome sequence. On the basis of its polyphasic taxonomic properties, strain XMDDZSB0408T represented a novel species, for which the name Shewanella intestini sp. nov. was proposed, with the type strain XMDDZSB0408T (=KCTC 52125T=MCCC 1A01895T).
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Agrobacterium salinitolerans sp. nov., a saline–alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina
More LessTwo Gram-staining-negative, aerobic bacteria (YIC 5082T and YIC4104) isolated from root nodules of Sesbania cannabina grown in a high-salt and alkaline environment were identified as a group in the genus Agrobacterium because they shared 100 and 99.7 % sequence similarities of 16S rRNA and recA+atpD genes, respectively. These two strains showed 99.2/100 % and 93.9/95.4 % 16S rRNA and recA+atpD gene sequence similarities to Agrobacterium radiobacter LMG140T and Agrobacterium . pusense NRCPB10T, respectively. The average nucleotide identities (ANI) of genome sequences were 89.95 % or lower between YIC 5082T and the species of the genus Agrobacterium examined. Moreover, these two test strains formed a unique nifH lineage deeply separated from other rhizobia. Although the nodC gene was not detected in YIC 5082T and YIC4104, they could form effective root nodules on S. cannabina plants. The main cellular fatty acids in YIC 5082T were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C19 : 0cyclo ω8c, summed feature 2 (C12 : 0 aldehyde/unknown equivalent chain length 10.9525) and C16 : 0. The DNA G+C content of YIC 5082T was 59.3 mol%. The failure to utilize d-sorbitol as a carbon source distinguished YIC 5082T from the type strains of related species. YIC 5082T could grow in presence of 5.0 % (w/v) NaCl and at a pH of up to 10.0. Based on results regarding the genetic and phenotypic properties of YIC 5082T and YIC4104 the name Agrobacterium salinitolerans sp. nov. is proposed and YIC 5082T (=HAMBI 3646T=LMG 29287T) is designed as the type strain.
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Photobacterium alginatilyticum sp. nov., a marine bacterium isolated from bottom seawater
More LessA 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).
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Imhoffiella gen. nov., a marine phototrophic member of the family Chromatiaceae including the description of Imhoffiella purpurea sp. nov. and the reclassification of Thiorhodococcus bheemlicus Anil Kumar et al. 2007 as Imhoffiella bheemlica comb. nov.
A coccoid-shaped phototrophic purple sulfur bacterium, strain AK35T, was isolated from a coastal surface water sample collected from Visakhapatnam, India. Cells were Gram-stain-negative, motile and purple, containing bacteriochlorophyll a and the carotenoid rhodopinal as major photosynthetic pigments. Strain AK35T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically. Strain AK35T was able to utilize sulfide and thiosulfate as electron donors. The main fatty acids present were identified as C16 : 0, C18 : 1ω7c, and C16 : 1ω7c and/or iso-C15 : 0 2OH (summed feature 3). Strain AK35T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and six unidentified lipids as polar lipids. The G+C content of the DNA of strain AK35T was 63.1 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae . 16S rRNA gene sequence analysis indicated that strain AK35T is phylogenetically distinctly positioned outside the groups of most members of the genus Thiorhodococcus , clustered with members of the genera Marichromatium and Phaeochromatium , but was most closely related to Thiorhodococcus bheemlicus with a pairwise sequence similarity of 98.75 %. Based on DNA–DNA hybridization between strain AK35T and Thiorhodococcus bheemlicus MTCC 8120T a relatedness of 39.46 % was established. Distinct morphological, physiological and genotypic differences from these previously described taxa supported the classification of the new isolate as a representative of a novel species in a new genus, for which the name Imhoffiella purpurea gen. nov., sp. nov. is proposed. The type strain of Imhoffiella purpurea is AK35T (=JCM 18851T=KCTC 15575T=MTCC 12304T). In addition, Thiorhodococcus bheemlicus is recognized as another species of this genus and transferred to Imhoffiella bheemlica comb. nov.
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Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer
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).
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Campylobacter pinnipediorum sp. nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov.
During independent diagnostic screenings of otariid seals in California (USA) and phocid seals in Scotland (UK), Campylobacter -like isolates, which differed from the established taxa of the genus Campylobacter , were cultured from abscesses and internal organs of different seal species. A polyphasic study was undertaken to determine the taxonomic position of these six isolates. The isolates were characterized by 16S rRNA gene and AtpA sequence analysis and by conventional phenotypic testing. The whole-genome sequences were determined for all isolates, and the average nucleotide identity (ANI) was determined. The isolates formed a separate phylogenetic clade, divergent from all other taxa of the genus Campylobacter and most closely related to Campylobacter mucosalis . Although all isolates showed 100 % 16S rRNA gene sequence homology, AtpA and ANI analyses indicated divergence between the otariid isolates from California and the phocid isolates from Scotland, which warrants subspecies status for each clade. The two subspecies could also be distinguished phenotypically on the basis of catalase activity. This study shows clearly that the isolates obtained from pinnipeds represent a novel species within the genus Campylobacter, for which the name Campylobacter pinnipediorum sp. nov. is proposed. Within this novel species, the Californian isolates represent a separate subspecies, for which the name C. pinnipediorum subsp. pinnipediorum subsp. nov. is proposed. The type strain for both this novel species and subspecies is RM17260T (=LMG 29472T=CCUG 69570T). The Scottish isolates represent another subspecies, for which the name C. pinnipediorum subsp. caledonicus subsp. nov. is proposed. The type strain of this subspecies is M302/10/6T (=LMG 29473T=CCUG 68650T).
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Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater
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).
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Oceanisphaera marina sp. nov., isolated from a deep-sea seamount
More LessA 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).
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Blastomonas quesadae sp. nov., isolated from a saline soil by dilution-to-extinction cultivation
More LessWe isolated a Gram-stain-negative, aerobic bacterial strain, 912T, from a soil sample taken from Rambla Salada (Murcia), south-eastern Spain, by using the dilution-to-extinction method. Cells of the strain were motile with a polar flagellum, short rod-shaped, catalase- and oxidase-positive and grew at NaCl concentrations within the range 0–5 % (w/v) (optimum 3 %, w/v), at 4–32 °C (optimum 30 °C) and at pH 6–9 (optimum pH 7); bacteriochlorophyll a was produced. Analysis of the 16S rRNA gene sequence indicated that this strain belonged to the genus Blastomonas in the class Alphaproteobacteria . Its closest relatives were Blastomonas natatoria EY 4220T, Blastomonas ursincola KR-99T and Blastomonas aquatica PE 4-5T, to which the strain showed 16S rRNA gene sequence similarity values of 95.9, 95.8 and 95.1 %, respectively. The DNA G+C content was 63 mol%. The major fatty acids of strain 912T were C18 : 1ω7c/C18 : 1ω6c, C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C17 : 1ω6c. The predominant isoprenoid quinone was ubiquinone 10 (Q-10). The polar lipids contained diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphoglycolipid, one unidentified phospholipid and two unidentified polar lipids. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, the strain represents a novel species of the genus Blastomonas , for which the name Blastomonas quesadae sp. nov. is proposed. Strain 912T (=CECT 9186T=LMG 29921T) is the type strain.
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Saccharospirillum correiae sp. nov., an endophytic bacterium isolated from the halophyte Halimione portulacoides
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 aestuarii IMCC 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.
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Reyranella terrae sp. nov., isolated from an agricultural soil, and emended description of the genus Reyranella
More LessA novel strain designated 11G32T was isolated from an agricultural soil cultivated with Chinese cabbage in Korea. The cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. The strain grew at 15–28 °C (optimum, 20 °C), pH 5.0–7.0 (optimum, pH 5.0–6.0) and without NaCl. Phylogenetically, the strain was found to be closely related to members of the genus Reyranella and showed 16S rRNA gene sequence similarities of 97.18, 96.76 and 95.99 % with Reyranella graminifolii Wo-34T, Reyranella massiliensis 521T and Reyranella soli KIS14-15T, respectively. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and 11-methyl C18 : 1ω7c. The predominant ubiquinone was Q-10. The polar lipids profile revealed the presence of phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, unidentified aminolipids, unidentified phospholipids and unidentified lipids. On the basis of data presented, strain 11G32T is considered to represent a novel species of the genus Reyranella , for which the name Reyranella terrae sp. nov. is proposed. The type strain is 11G32T (=KACC 18486T=NBRC 111476T).
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Salipiger nanhaiensis Dai et al. 2015 is a later heterotypic synonym of Thiobacimonas profunda Li et al. 2015
More LessSalipiger nanhaiensis ZH114T was compared with Thiobacimonas profunda JLT2016T to clarify their taxonomic relationship. The results of the 16S rRNA gene sequence comparison indicated that the two strains had 99.7 % sequence similarity. Results of phylogenetic analysis indicated that the two strains formed a tight cluster, distinctly branching from Salipiger mucosus A3T and other representatives in the family Rhodobacteraceae . Whole genomic comparison between the two strains yielded a digital DDH estimate of 97.3 % and ANI value of 99.7 %, strongly supporting the hypothesis that the two strains represented a single species. In addition, the two strains displayed no striking differences in physiological and biochemical properties, fatty acid composition or polar lipids profile. Due to priority, Salipiger nanhaiensis is reclassified as a later heterotypic synonym of Thiobacimonas profunda based on the phylogenetic relationship inferred from the 16S rRNA gene sequence, whole genomic comparison, fatty acid composition and polar lipid profile and other phenotypic and biochemical properties.
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- Eukaryotic Micro-organisms
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Carlosrosaea hohenbergiae sp. nov. and Carlosrosaea aechmeae sp. nov., two tremellaceous yeasts isolated from bromeliads in north-eastern Brazil
Yeast surveys associated with different bromeliads in north-eastern Brazil led to the proposal of two novel yeast species, Carlosrosaea hohenbergiae sp. nov. and Carlosrosaea aechmeae sp. nov., belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and D1/D2 domain of the LSU rRNA gene suggested an affinity with a phylogenetic lineage that includes recently reclassified Carlosrosaea vrieseae. Six isolates of the novel species were obtained from different bromeliad species collected in three Atlantic Forest fragments in Alagoas state, Brazil. Ca. hohenbergiae sp. nov. differs by 69 and 12 nucleotide substitutions in the ITS and D1/D2 domain, respectively, from Ca. vrieseae. The type strain is UFMG-CM-Y405T (=BSB 34T=CBS 14563T), Mycobank 819227. Ca. aechmeae sp. nov. is represented by one strain isolated from Aechmea constantinii leaves. Ca. aechmeae sp. nov. differs from the related species Ca. hohenbergiae and Ca. vrieseae by 36 and 65 nucleotide substitutions, respectively, in the ITS region and by 12 and 15 nucleotide substitutions in the D1/D2 domain, respectively. The type strain of Ca. aechmeae sp. nov. is UFMG-CM-Y6095T (=BM 94T=CBS 14578), Mycobank 819228.
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Hannaella dianchiensis sp. nov., a basidiomycetous yeast species isolated from lake water
More LessThree strains (YIM-HL1107T, YIM-HL1045, YIM-HL1112) representing a novel yeast species were isolated from surface water samples collected from the Caohai region of Dianchi Lake in Yunnan, south-western China. On the basis of morphological, physiological and biochemical characteristics and sequence analysis of the D1/D2 region of the LSU rRNA gene and the internal transcribed spacer (ITS) region, they were assigned to a novel species of the genus Hannaella. The closest relative to the novel species was Hannaella pagnoccae, but it showed 6.3 % nucleotide differences (34 nt substitutions out of 541 nt) in the D1/D2 region of the LSU rRNA gene and 9.3–9.6 % nucleotide differences (40–41 substitutions and 7–8 gaps out of 430 nt) in the ITS region. The name Hannaella dianchiensis sp. nov. is proposed. The type strain is YIM-HL1107T (=CBS 14191T=CCTCC AY 2015009T), and the MycoBank number is MB 816297.
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Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur
Two strains, D5088T and D5095, representing a novel yeast species belonging to the genus Saccharomyces were isolated from oak tree bark and surrounding soil located at an altitude of 1000 m above sea level in Saint Auban, France. Sequence analyses of the internal transcribed spacer (ITS) region and 26S rRNA D1/D2 domains indicated that the two strains were most closely related to Saccharomyces mikatae and Saccharomyces paradoxus. Genetic hybridization analyses showed that both strains are reproductively isolated from all other Saccharomyces species and, therefore, represent a distinct biological species. The species name Saccharomyces jurei sp. nov. is proposed to accommodate these two strains, with D5088T (=CBS 14759T=NCYC 3947T) designated as the type strain.
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- Evolution, Phylogeny and Biodiversity
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ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences
More LessThanks to the recent advancement of DNA sequencing technology, the cost and time of prokaryotic genome sequencing have been dramatically decreased. It has repeatedly been reported that genome sequencing using high-throughput next-generation sequencing is prone to contaminations due to its high depth of sequencing coverage. Although a few bioinformatics tools are available to detect potential contaminations, these have inherited limitations as they only use protein-coding genes. Here we introduce a new algorithm, called ContEst16S, to detect potential contaminations using 16S rRNA genes from genome assemblies. We screened 69 745 prokaryotic genomes from the NCBI Assembly Database using ContEst16S and found that 594 were contaminated by bacteria, human and plants. Of the predicted contaminated genomes, 8 % were not predicted by the existing protein-coding gene-based tool, implying that both methods can be complementary in the detection of contaminations. A web-based service of the algorithm is available at www.ezbiocloud.net/tools/contest16s.
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- Letter to the Editor
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Division of the genus Borrelia into two genera (corresponding to Lyme disease and relapsing fever groups) reflects their genetic and phenotypic distinctiveness and will lead to a better understanding of these two groups of microbes (Margos et al. (2016) There is inadequate evidence to support the division of the genus Borrelia. Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijsem.0.001717)
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- ICSP Minutes
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Proposed revisions of the Statutes of the International Committee of Systematics of Prokaryotes
More LessThe following revisions of the Statutes (Labeda D, Whitman WB. Int J Syst Evol Microbiol 2015;65:1093–1100) are proposed by the Executive Board of the International Committee of Systematics of Prokaryotes (ICSP) to eliminate some internal inconsistencies and address other issues as discussed below. Comments may be sent to the Secretary of the ICSP, Lenie Dijkshoom at [email protected] for distribution to the delegates at the Plenary Meeting in Valencia, Spain, on July 7–9, 2017.
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- Corrigendum
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Corrigendum: There is inadequate evidence to support the division of the genus Borrelia
G. Margos, D. Marosevic, S. Cutler, M. Derdakova, M. Diuk-Wasser, S. Emler, D. Fish, J. Gray, K.-P. Hunfeld, B. Jaulhac, O. Kahl, S. Kovalev, P. Kraiczy, R. S. Lane, R. Lienhard, P. E. Lindgren, N. H. Ogden, K. Ornstein, T. Rupprecht, I. Schwartz, A. Sing, R. K. Straubinger, F. Strle, M. Voordouw, A. Rizzoli, B. Stevenson and V. Fingerle
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Volumes and issues
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