- Volume 62, Issue Pt_8, 2012
Volume 62, Issue Pt_8, 2012
- Notification List
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Notification that new names and new combinations have appeared in volume 62, part 5, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Archaea
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Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces
More LessDuring attempts to obtain novel, human-associated species of the domain Archaea , a coccoid micro-organism, designated strain B10T, was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and mcrA gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1 % (w/v) SDS. With hydrogen as the electron donor, strain B10T produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO2, strain B10T could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10T grew optimally with 0.5–1.0 % (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0–98.7 %) were seen between strain B10T and several uncultured, methanogenic Archaea that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic ‘Candidatus Aciduliprofundum boonei’ DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10T (83.0 % 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10T belongs to a novel order that is distinct from the Thermoplasmatales . The novel strain also appeared to be distinct from Methanosphaera stadtmanae DSM 3091T (72.9 % 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10T represents a novel species of a new genus for which the name Methanomassiliicoccus luminyensis gen. nov., sp. nov. is proposed. The type strain of the type species is B10T ( = DSM 24529T = CSUR P135T).
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Halopenitus persicus gen. nov., sp. nov., an archaeon from an inland salt lake
A novel pale pink-pigmented halophilic archaeon, strain DC30T, was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. Cells of strain DC30T were non-motile and pleomorphic, from rods to triangular or disc-shaped. Strain DC30T required at least 1.7 M NaCl and 0.05 M MgCl2 for growth (optimum, 3 M NaCl and 0.1 M MgCl2). The optimum pH and temperature for growth of strain DC30T were pH 7.5 and 40 °C, respectively, although it was capable of growth over pH and temperature ranges of 6.5–8.5 and 25–50 °C, respectively. Analysis of the 16S rRNA gene sequence showed that strain DC30T was a member of the family Halobacteriaceae . However, it had low 16S rRNA gene sequence similarities of 92.4 %, 89.4 % and 89.1 % to the most closely related haloarchaeal taxa, the type species of the genera Halorubrum , Halogranum and Haloplanus , respectively. The DNA G+C content was 66.0 mol%. Phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, common phospholipids found in haloarchaea, were present. Three minor phospholipids and one unidentified glycolipid were also observed. The only quinone present was MK-8(II-H2). The physiological, biochemical and phylogenetic differences between strain DC30T and other previously described genera of extremely halophilic archaea suggest that strain DC30T represents a novel species in a new genus within the family Halobacteriaceae , for which the name Halopenitus persicus gen. nov., sp. nov. is proposed. The type strain of Halopenitus persicus is DC30T ( = IBRC 10041T = KCTC 4046T).
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- Actinobacteria
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Streptomyces shaanxiensis sp. nov., a blue pigment-producing streptomycete from sewage irrigation soil
More LessA novel isolate belonging to the genus Streptomyces , strain CCNWHQ 0031T, was isolated from soil in a sewage irrigation area in Shaanxi province, China. The isolate produced light greyish-blue aerial mycelium and dark blue diffusible pigment on Gause’s synthetic agar. Strain CCNWHQ 0031T formed Spirales-type chains with spiny spores. Chemotaxonomic data confirmed that strain CCNWHQ 0031T belonged to the genus Streptomyces . Analysis of the almost complete 16S rRNA gene sequence placed strain CCNWHQ 0031T in the genus Streptomyces where it formed a distinct phyletic line with recognized Streptomyces species. Strain CCNWHQ 0031T exhibited highest sequence similarities to Streptomyces caeruleatus GIMN4.002T (99.3 %), Streptomyces coeruleorubidus NBRC 12855T (98.9 %), Streptomyces curacoi NBRC 12761T (98.8 %) and Streptomyces lincolnensis NBRC 13054T (98.0 %). DNA–DNA hybridization studies of strain CCNWHQ 0031T with these four closest relatives showed relatedness values of 56.6±0.4, 50.3±0.6, 49.8±0.7 and 36.9±0.9 %, respectively. On the basis of its molecular and physiological properties, it is evident that strain CCNWHQ 0031T represents a novel species of the genus Streptomyces , for which the name Streptomyces shaanxiensis sp. nov. is proposed. The type strain is CCNWHQ 0031T ( = CCNWTJ 0031T = JCM 16925T = ACCC 41873T).
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Lysinimicrobium mangrovi gen. nov., sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove
More LessA novel strain of Gram-staining-positive bacterium, designated HI08-69T, was isolated from the rhizosphere of a mangrove on Iriomote Island, Japan, and its taxonomic position was investigated by a polyphasic approach. The strain had peptidoglycan of the A4α type, with lysine as the diagnostic diamino acid. The predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified polar lipid but minor amounts of other polar lipids were also detected. The genomic DNA G+C content of strain HI08-69T was 71.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the novel strain and members of the genus Demequina formed a monophyletic cluster, with pairwise sequence similarities of 95.6–96.8 %. However, strain HI08-69T was clearly distinguishable from all established members of the genus Demequina in terms of several chemotaxonomic characteristics. On the basis of the phenotypic and genotypic characteristics, strain HI08-69T represents a novel species in a new genus for which the name Lysinimicrobium mangrovi gen. nov., sp. nov. is proposed. The type strain of the type species is HI08-69T ( = NBRC 105856T = DSM 24868T).
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Actinomyces weissii sp. nov., isolated from dogs
Two Gram-positive, rod-shaped, non-spore-forming bacteria were isolated from the oral cavities of two dogs. On the basis of 16S rRNA gene sequence similarities both strains were shown to belong to the genus Actinomyces and were most closely related to Actinomyces bovis (97.3 % and 97.5 %, respectively). The polyamine profile of the two isolates and Actinomyces bovis DSM 43014T was composed of spermidine and spermine as the major components. Menaquinone MK-9 was the major compound in the quinone system of the two strains and Actinomyces bovis . The polar lipid profiles of strains 2298T and 4321 were almost identical, containing diphosphatidylglycerol as the major compound, and moderate to trace amounts of phosphatidylcholine, phosphatidylinositol, phosphatidylinositol-mannoside, phosphatidylglycerol and several unidentified lipids. A highly similar polar lipid profile was detected in Actinomyces bovis DSM 43014T supporting the affiliation of strains 2298T and 4321 to the genus Actinomyces . The typical major fatty acids were C16 : 0, C18 : 0 and C18 : 1ω9c. Fatty acids C14 : 0 and C18 : 2ω6,9c were found in minor amounts. The results of physiological and biochemical analyses revealed clear differences between both strains and the most closely related species of the genus Actinomyces . Thus, strains 2298T and 4321 represent a novel species, for which the name Actinomyces weissii sp. nov., is proposed, with strain 2298T ( = CIP 110333T = LMG 26472T = CCM 7951T = CCUG 61299T) as the type strain.
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Labedaea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere soil
More LessA novel actinomycete, designated strain RS-49T, was isolated from the rhizosphere soil of a cliff-associated plant (Peucedanum japonicum Thunb.) in the Republic of Korea and subjected to a polyphasic taxonomic study. The results of comparative 16S rRNA gene sequence analyses showed that the organism belonged to the family Pseudonocardiaceae , suborder Pseudonocardineae and that it was most closely related to members of the genera Kibdelosporangium (96.6–97.0 % sequence similarity), Actinokineospora (96.3–96.7 %), Streptoalloteichus (96.2 %) and Actinophytocola (96.2 %). Substrate mycelia were well-developed and whitish or pale yellow to strong yellow. Aerial mycelia were branched and fragmented into rod-shaped elements. Single spherical spores were produced directly on the substrate mycelium. Sporangium-like structures and fragmentation of the substrate mycelium were absent. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The acyl type of the muramic acid residues in the peptidoglycan was N-acetylated. Whole-cell sugars were glucose, rhamnose, galactose, ribose, mannose, arabinose and xylose. The major menaquinone was MK-9(H4). Small amounts of MK-8 and MK-9(H2) were also detected. The polar lipids contained diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and an unknown lipid. The predominant fatty acids were iso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 64.2 mol%. The phenotypic and phylogenetic characteristics show that strain RS-49T can be differentiated from members of all genera in the suborder Pseudonocardineae and thus represents a novel species in a new genus for which the name Labedaea rhizosphaerae gen. nov., sp. nov. is proposed; the type strain of the type species is RS-49T ( = KCTC 19662T = DSM 45361T).
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Actinokineospora soli sp. nov., a thermotolerant actinomycete isolated from soil, and emended description of the genus Actinokineospora
More LessA strain of thermotolerant actinomycete, designated YIM 75948T, was isolated from a soil sample in Yunnan province, China. The strain grew at 25–55 °C (optimum 37 °C). The substrate mycelium and aerial mycelium produced on Czapek’s agar were both pale yellow to white. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid, and the whole-cell sugars were mannose, ribose, glucose, galactose and arabinose. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and C16 : 0 and the predominant respiratory quinone was MK-9(H4). The polar lipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The genomic DNA G+C content was 73.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 75948T belonged in the genus Actinokineospora and that its closest relative among recognized species was Actinokineospora fastidiosa DSM 43855T (97.6 % sequence similarity). The mean level of DNA–DNA relatedness between the novel strain and A. fastidiosa DSM 43855T was, however, only 47.8 %. Based on the phenotypic, chemotaxonomic and phylogenetic data and the results of the DNA–DNA hybridizations, strain YIM 75948T represents a novel species of the genus Actinokineospora for which the name Actinokineospora soli sp. nov. is proposed. The type strain is YIM 75948T ( = JCM 17695T = DSM 45613T). The description of the genus Actinokineospora is emended to reflect the fact that the genomic DNA G+C contents of A. fastidiosa DSM 43855T and the type strain of Actinokineospora soli sp. nov. recorded in the present study fell above the range given in previous descriptions of this genus.
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Streptomyces herbaceus sp. nov., Streptomyces incanus sp. nov. and Streptomyces pratens sp. nov., isolated from the soil of a hay meadow
The taxonomic positions of three streptomycetes isolated from a soil sample from a hay meadow were determined using a polyphasic approach. The isolates had chemical and morphological properties typical of the genus Streptomyces and, in phylogenetic analyses based on 16S rRNA gene sequences, formed a distinct subclade that was most closely related to the Streptomyces prasinus subclade. DNA–DNA relatedness studies showed that the novel strains belonged to three different genomic species. The novel strains could be distinguished from one another and from the type strains of the species classified in the S. prasinus subclade using a combination of genotypic and phenotypic properties. On the basis of these data, it is proposed that the novel strains be assigned to the genus Streptomyces as Streptomyces herbaceus sp. nov., Streptomyces incanus sp. nov. and Streptomyces pratens sp. nov., with BK119T ( = KACC 21001T = CGMCC 4.5797T), BK128T ( = KACC 21002T = CGMCC 4.5799T) and BK138T ( = KACC 20904T = CGMCC 4.5800T) as the respective type strains.
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Cellulomonas carbonis sp. nov., isolated from coal mine soil
More LessA Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain T26T, was isolated from subsurface soil of Tianjin coal mine, China. Colonies were yellow–white, convex, circular, smooth and non-transparent on R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain T26T was closely related to members of the genus Cellulomonas and a member of the genus Actinotalea with 96.8–94.7 % and 96.7 % gene sequence similarities, respectively. The peptidoglycan type of strain T26T was A4β, containing l-ornithine–d-glutamic acid as the interpeptide bridge. The cell-wall sugars were rhamnose, galactose, xylose and inositol. The major fatty acids (>10 %) were anteiso-C15 : 0 (33.6 %), anteiso-C15 : 1 A (22.1 %), C16 : 0 (14.4 %) and C14 : 0 (12.1 %). The predominant respiratory quinone was MK-9(H4) and the genomic DNA G+C content was 74.4 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol-mannosides and phosphatidylinositol. Comparison of phenotypic and phylogenetic characteristics between strain T26T and related organisms revealed that the new isolate represented a novel species of the genus Cellulomonas , for which the name Cellulomonas carbonis sp. nov. is proposed. The type strain is T26T ( = CGMCC 1.10786T = KCTC 19824T = CCTCC AB2010450T).
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Actinomadura geliboluensis sp. nov., isolated from soil
More LessA novel actinobacterium, strain A8036T, isolated from soil, was investigated by using a polyphasic taxonomic approach. The organism formed extensively branched substrate hyphae that generated spiral chains of spores with irregular surfaces. The cell wall contained meso-diaminopimelic acid (type III) and cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H4). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis9, C16 : 0, C15 : 0 and 10-methyl C17 : 0. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain A8036T were Actinomadura meyerae DSM 44715T (99.23 % similarity), Actinomadura bangladeshensis DSM 45347T (98.9 %) and Actinomadura chokoriensis DSM 45346T (98.3 %). However, DNA–DNA relatedness and phenotypic data demonstrated that strain A8036T could be clearly distinguished from the type strains of all closely related Actinomadura species. Strain A8036T is therefore considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura geliboluensis sp. nov. is proposed. The type strain is A8036T ( = DSM 45508T = KCTC 19868T).
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- Firmicutes and Related Organisms
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Gracilibacillus bigeumensis sp. nov., a moderately halophilic bacterium from solar saltern soil
More LessA Gram-staining-positive, moderately halophilic bacterium, designated strain BH097T, was isolated from solar saltern soil of Bigeum Island in south-west Korea. Cells were motile rods, producing spherical endospores at a terminal position in swollen sporangia. Strain BH097T was strictly aerobic, grew at pH 5.5–9.5 (optimum, pH 8.0), at 10–52 °C (optimum, 37 °C) and at salinities of 1–22 % (w/v) NaCl (optimum, 7 % NaCl). On the basis of 16S rRNA gene sequence analysis, strain BH097T was shown to belong to the genus Gracilibacillus within the phylum Firmicutes , and showed closest sequence similarity to Gracilibacillus saliphilus DSM 19802T (95.8 %), Gracilibacillus thailandensis TP2-8T (95.6 %), Gracilibacillus boraciitolerans DSM 17256T (95.5 %), ‘Gracilibacillus quinghaiensis’ DSM 17858 (95.4 %) and Gracilibacillus halophilus DSM 17856T (95.2 %). The DNA G+C content of this novel isolate was 37.9 mol%. The major cellular fatty acids of strain BH097T were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0, and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol two unknown phospholipids and a glycolipid. The isoprenoid quinone was MK-7, and the peptidoglycan type was A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of polyphasic evidence from this study, strain BH097T represents a novel species of the genus Gracilibacillus for which the name Gracilibacillus bigeumensis sp. nov. is proposed. The type strain is BH097T ( = KCTC 13130T = DSM 19028T).
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Chungangia koreensis gen. nov., sp. nov., isolated from marine sediment
A Gram-staining-positive, strictly aerobic, non-spore-forming, rod-shaped bacterial strain, CAU 9163T, was isolated from marine sediment collected in the Republic of Korea and its taxonomic position was investigated using a polyphasic approach. The novel strain grew optimally at 30 °C and pH 8.0. In phylogenetic analysis based on 16S rRNA gene sequences, strain CAU 9163T formed a hitherto unknown lineage within the order Bacillales , which contains the genera Planomicrobium , Planococcus , Sporosarcina , Rummeliibacillus , Viridibacillus , Lysinibacillus and Bacillus . The levels of 16S rRNA gene sequence similarity between the novel strain and any established bacterial species were all <95.7 %. The major isoprenoid quinines of strain CAU 9163T were MK-8 (65.2 %) and MK-7 (22.8 %) and the predominant fatty acid was anteiso-C15 : 0. The peptidoglycan was of the A4α type and based on l-Lys-d-Asp. The major whole-cell sugars were ribose and glucose. The polar lipid profile mainly consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified polar lipid. The genomic DNA G+C content of the novel strain was 44.3 mol%. These data were sufficient to differentiate the novel strain from established genera in the phylum Firmicutes . Based on the phenotypic, chemotaxonomic and genotypic evidence, strain CAU 9163T represents a novel species in a new genus for which the name Chungangia koreensis gen. nov., sp. nov. is proposed. The type strain of Chungangia koreensis is 9163T ( = KCTC 13729T = CCUG 59778T).
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Cohnella cellulosilytica sp. nov., isolated from buffalo faeces
A cellulose-degrading bacterium, strain FCN3-3T, was isolated from buffalo faeces collected in Nakhonnayok province, Thailand. The strain was characterized based on its phenotypic and genotypic characteristics. Strain FCN3-3T was a Gram-positive, aerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in cell-wall peptidoglycan. The major menaquinone was MK-7. Anteiso-C15 : 0 (52.5 %), iso-C16 : 0 (18.9 %) and C16 : 0 (9.1 %) were the predominant cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol were the major phospholipids. The DNA G+C content was 58.0 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain FCN3-3T was affiliated to the genus Cohnella and was closely related to Cohnella phaseoli GSPC1T, Cohnella luojiensis HY-22RT and Cohnella hongkongensis HKU3T, with 97.2, 96.8 and 96.3 % sequence similarity, respectively. Strain FCN3-3T could be clearly distinguished from all known species of the genus Cohnella by its physiological and biochemical characteristics as well as its phylogenetic position and level of DNA–DNA relatedness. Therefore, the strain represents a novel species of the genus Cohnella , for which the name Cohnella cellulosilytica sp. nov. is proposed; the type strain is FCN3-3T ( = KCTC 13645T = TISTR 1996T = PCU 323T).
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Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost
More LessA novel aerobic, Gram-positive, motile, coccoid bacterial strain, designated Or1T, was isolated from permafrost active-layer soil collected from the Canadian high Arctic. Strain Or1T was capable of growth over a broad temperature range, including sub-zero growth (below −10 to 37 °C), and at high salinity (0–19 % NaCl), growing optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % NaCl. Its taxonomic and phylogenetic position was determined by using a polyphasic approach, which indicated that strain Or1T was a member of the genus Planococcus . Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Or1T belonged to the genus Planococcus , differing by 0.4–3.6 % from the type strains of all recognized Planococcus species, and was related most closely to Planococcus antarcticus CMS 26orT (98.8 % similarity) and Planococcus donghaensis JH1T (99.6 %). However, DNA–DNA hybridization experiments showed that strain Or1T had low genomic relatedness to Planococcus antarcticus CMS 26orT (18 %) and Planococcus donghaensis JH1T (46 %). The major menaquinones of strain Or1T were MK-7 (55 %), MK-8 (36 %) and MK-6 (9 %) and the major fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol and anteiso-C17 : 0. The DNA G+C content of strain Or1T was 40.5 mol%. Differential phenotypic, phylogenetic and genomic data suggest that strain Or1T represents a novel species of the genus Planococcus , for which the name Planococcus halocryophilus sp. nov. is proposed. The type strain is Or1T ( = DSM 24743T = JCM 17719T).
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Halanaerobacter jeridensis sp. nov., isolated from a hypersaline lake
An obligatory anaerobic, moderately halophilic bacterium, designated strain CEJFG43T, was isolated from a sample of sediment collected below the salt crust on the hypersaline El Jerid lake, in southern Tunisia. The cells of this novel strain were Gram-staining-negative, non-sporulating, motile, short rods. They grew in media with 6–30 % (w/v) NaCl (optimum 15 %), at 20–60 °C (optimum 45 °C) and at pH 5.5–9.5 (optimum pH 8.3). The micro-organism fermented glucose, fructose, ribose, raffinose, galactose, mannose, sucrose, maltose, xylose, mannitol, pyruvate and glycerol. The products of glucose fermentation were lactate, ethanol, acetate, H2 and CO2. The genomic G+C DNA content of strain CEJFG43T was 33.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CEJFG43T belonged in the genus Halanaerobacter and was most closely related to Halanaerobacter lacunarum DSM 6640T (95.3 % gene sequence similarity) and Halanaerobacter chitinivorans DSM 9569T (95.3 %). The predominant cellular fatty acids were non-branched (C16 : 0 and C16 : 1). Based on the phylogenetic and phenotypic evidence, strain CEJFG43T represents a novel species in the genus Halanaerobacter for which the name Halanaerobacter jeridensis sp. nov. is proposed. The type strain is CEJFG43T ( = DSM 23230T = JCM 16696T).
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Enterococcus lactis sp. nov., from Italian raw milk cheeses
More LessTen atypical Enterococcus strains were isolated from Italian raw milk cheeses. The 16S rRNA gene, phenylalanyl-tRNA synthase alpha subunit (pheS), RNA polymerase alpha subunit (rpoA) and the 16S–23S rRNA intergenic transcribed spacer (ITS) sequences, randomly amplified polymorphic DNA (RAPD) PCR and the phenotypic properties revealed that the isolates represent a novel enterococcal species. On the basis of 16S rRNA gene sequence analysis, the isolates were closely related to Enterococcus hirae ATCC 8043T, Enterococcus durans CECT 411T and Enterococcus faecium ATCC 19434T, with 98.8, 98.9 and 99.4 % sequence similarity, respectively. On the basis of sequence analysis of the housekeeping gene pheS, the reference strain, BT159T, occupied a position separate from E. faecium LMG 16198. The group of isolates could be easily differentiated from recognized species of the genus Enterococcus by 16S–23S rRNA ITS analysis, RAPD-PCR and phenotypic characteristics. The name Enterococcus lactis sp. nov. is proposed, with BT159T ( = DSM 23655T = LMG 25958T) as the type strain.
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- Proteobacteria
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Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea
A Gram-negative, oxidase-positive, catalase-negative, facultatively anaerobic, motile, curved rod-shaped bacterium, strain N384T, was isolated from a marine sponge (Scleritoderma cyanea; phylum Porifera) collected from a depth of 795 feet (242 m) off the west coast of Curaçao. On the basis of 16S rRNA gene sequencing, strain N384T was shown to belong to the genus Vibrio , most closely related to Vibrio brasiliensis LMG 20546T (98.8 % similarity), Vibrio nigripulchritudo ATCC 27043T (98.5 %), Vibrio tubiashii ATCC 19109T (98.6 %) and V. sinaloensis DSM 21326T (98.2 %). The DNA G+C content of strain N384T was 41.6 mol%. An analysis of concatenated sequences of five genes (gyrB, rpoA, pyrH, mreB and ftsZ; 4068 bp) demonstrated a clear separation between strain N384T and its closest neighbours and clustered strain N384T into the ‘Orientalis’ clade of vibrios. Phenotypically, the novel species belonged to the arginine dihydrolase-positive, lysine decarboxylase- and ornithine decarboxylase-negative (A+/L−/O−) cluster. The novel species was also differentiated on the basis of fatty acid composition, specifically that the proportions of iso-C13 : 0, iso-C15 : 0, C15 : 0, iso-C16 : 0, C16 : 0, iso-C17 : 0, C17 : 1ω8c and C17 : 0 were significantly different from those found in V. brasiliensis and V. sinaloensis . The results of DNA–DNA hybridization, average nucleotide identity and physiological and biochemical tests further allowed differentiation of this strain from other described species of the genus Vibrio . Collectively, these findings confirm that strain N384T represents a novel Vibrio species, for which the name Vibrio caribbeanicus sp. nov. is proposed, with the type strain N384T ( = ATCC BAA-2122T = DSM 23640T).
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Arenimonas metalli sp. nov., isolated from an iron mine
More LessA Gram-staining-negative, aerobic, rod-shaped bacterium (CF5-1T) was isolated from Hongshan Iron Mine, Daye City, Hubei province, China. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c alcohol and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major respiratory quinone was Q-8. The genomic DNA G+C content was 70.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CF5-1T was most closely related to Arenimonas malthae (95.3 % gene sequence similarity), Arenimonas oryziterrae (94.7 %), Arenimonas donghaensis (94.6 %) and Arenimonas composti (94.5 %). A taxonomic study using a polyphasic approach showed that strain CF5-1T represents a novel species of the genus Arenimonas , for which the name Arenimonas metalli sp. nov. is proposed. The type strain is CF5-1T ( = CGMCC 1.10787T = KCTC 23460T = CCTCC AB 2010449T).
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Elstera litoralis gen. nov., sp. nov., isolated from stone biofilms of Lake Constance, Germany
More LessAn alphaproteobacterium, strain Dia-1T, was isolated from algae-dominated biofilms on stones from the littoral zone of Lake Constance, Germany. This bacterium was isolated after initial enrichment in spent medium obtained after growth of a diatom culture. Numerous sugars and some organic acids and alcohols served as growth substrates. The bacterium grew slowly, was strictly aerobic but microaerophilic, and did not grow in cultures shaken under air. 16S rRNA gene sequence analysis indicated that strain Dia-1T was distantly related to representatives of the genera Azospirillum (90–91 % sequence similarity), Skermanella (88–89 %), Rhodocista (87–88 %) and Dongia (88–89 % sequence similarity). Based on this sequence comparison, on phenotypic characterization including substrate utilization patterns, and comparison of cellular fatty acids, quinones, polar lipids and polyamines, this isolate was found to be substantially different from the genera mentioned above. On the basis of these results, a novel genus and species is proposed for this strain. The name Elstera litoralis gen. nov., sp. nov. is suggested, with strain Dia-1T ( = DSM 19532T = LMG 24234T) as the type strain of the type species.
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Description of Xenorhabdus magdalenensis sp. nov., the symbiotic bacterium associated with Steinernema australe
More LessA symbiotic bacterium, strain IMI 397775T, was isolated from the insect-pathogenic nematode Steinernema australe. On the basis of 16S rRNA gene sequence similarity, this bacterial isolate was shown to belong to the genus Xenorhabdus , in agreement with the genus of its nematode host. The accurate phylogenetic position of this new isolate was defined using a multigene approach and showed that isolate IMI 397775T shares a common ancestor with Xenorhabdus doucetiae FRM16T and Xenorhabdus romanii PR06-AT, the symbiotic bacteria associated with Steinernema diaprepesi and Steinernema puertoricense, respectively. The nucleotide identity (less than 97 %) between isolate IMI 397775T, X. doucetiae FRM16T and X. romanii PR06-AT calculated for the concatenated sequences of five gene fragments encompassing 4275 nt, several phenotypic traits and the difference between the upper temperatures that limit growth of these three bacteria allowed genetic and phenotypic differentiation of isolate IMI 397775T from the two closely related species. Strain IMI 397775T therefore represents a novel species, for which the name Xenorhabdus magdalenensis sp. nov. is proposed, with the type strain IMI 397775T ( = DSM 24915T).
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Legionella steelei sp. nov., isolated from human respiratory specimens in California, USA, and South Australia
More LessLegionella -like bacteria were isolated from the respiratory tract of two patients in California, USA, and South Australia, but were not thought to cause disease. These bacteria, strains F2632 and IMVS-3376T, were found to have identical Legionella macrophage infectivity potentiator (mip) gene sequences and were therefore further characterized to determine their genetic and phenotypic relatedness and properties. Both of these Gram-negative-staining bacterial strains grew on buffered charcoal yeast extract medium, were cysteine auxotrophs and made a characteristic diffusible bright yellow fluorescent pigment, with one strain making a late appearing colony-bound blue–white fluorescent pigment. The optimal in vitro growth temperature was 35 °C, with very poor growth at 37 °C in broth or on solid media. There was no growth in human A549 cells at either 35 or 37 °C, but excellent growth in Acanthamoeba castellani at 30 °C and poorer growth at 35 °C. Phylogenetic analysis of these bacteria was performed by sequence analysis of 16S rRNA, mip, ribonuclease P, ribosomal polymerase B and zinc metalloprotease genes. These studies confirmed that the new strains represented a single novel species of the genus Legionella for which the name Legionella steelei sp. nov. is proposed. The type strain is IMVS-3376T ( = IMVS 3113T = ATCC BAA-2169T).
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Variovorax defluvii sp. nov., isolated from sewage
More LessA polyphasic taxonomic study was carried out on 2C1-bT and 2C-21, two strains isolated from sewage flowing into River Geumho in Korea. Cells of the two strains were Gram-negative, non-spore-forming, motile and oval or rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of these two isolates with members of the Betaproteobacteria ; they were most closely related to Variovorax boronicumulans KCTC 22010T, Variovorax dokdonensis KCTC 12544T, Variovorax ginsengisoli KCTC 12583T, Variovorax paradoxus ATCC 17713T and Variovorax soli KACC 11579T showing 16S rRNA gene sequence similarities of 97.4–98.8 % with these strains and shared 100 % similarity with each other. The genomic DNA G+C contents of strains 2C1-bT and 2C1-21 were 65.5 and 65.2 mol%, respectively. Phenotypic and chemotaxonomic data [Q-8 as the major ubiquinone; C16 : 0, summed feature 4 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C17 : 0 cyclo and summed feature 7 (C18 : 1ω7c and/or ω9t and/or ω12t) as major fatty acids] supported the affiliation of strains 2C1-bT and 2C-21 to the genus Variovorax . Based on evidence derived from this polyphasic analysis, it is proposed that strains 2C1-bT and 2C1-21 represent a novel species for which the name Variovorax defluvii sp. nov. is proposed; the type strain is 2C1-bT ( = KCTC 12768T = JCM 17804T).
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Halioglobus japonicus gen. nov., sp. nov. and Halioglobus pacificus sp. nov., members of the class Gammaproteobacteria isolated from seawater
More LessTwo coccoid, non-motile bacteria were isolated from seawater in the north-western Pacific Ocean near Japan. The two strains, designated S1-36T and S1-72T, were Gram-negative, obligately aerobic, heterotrophic and catalase-negative. They were able to reduce nitrate to nitrogen. Both strains required NaCl for growth, with optimum growth in 2 % NaCl, and grew at 15–30 °C, with optimum growth at 20–25 °C. Genomic DNA G+C contents of strains S1-36T and S1-72T were 59.6 and 59.4 mol%, respectively. The predominant isoprenoid quinone was Q-8 and major cellular fatty acids were C16 : 1ω7c, C18 : 1ω7c and C17 : 1ω8c. Analyses of 16S rRNA gene sequences revealed that strains S1-36T and S1-72T were related to each other (96.1 % sequence similarity) and both strains showed 92.3–94.7 % sequence similarity with members of the genus Haliea . On the basis of phenotypic and phylogenetic features, strains S1-36T and S1-72T should be classified as representatives of two novel species in a new genus, Halioglobus gen. nov., within the class Gammaproteobacteria . The names proposed are Halioglobus japonicus sp. nov., the type species of the genus, with S1-36T ( = NBRC 107739T = KCTC 23429T) as type strain, and Halioglobus pacificus sp. nov., with S1-72T ( = NBRC 107742T = KCTC 23430T) as type strain.
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Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris
Four strains (JA310T, JA531T, JA447 and JA490) of red to reddish brown pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from soil and freshwater sediment samples from different geographical regions of India. All strains contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The major cellular fatty acid of strains JA310T and JA531T was C18 : 1ω7c, the quinone was Q-10 and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminohopanoid and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that all strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria . Strains JA531T, JA447 and JA490 were genotypically (>80 % related based on DNA–DNA hybridization) and phenotypically closely related to each other and the three strains were distinct from strain JA310T (33 % related). Furthermore, all four strains had less than 48 % relatedness (DNA–DNA hybridization) with type strains of members of the genus Rhodopseudomonas , i.e. Rhodopseudomonas palustris ATCC 17001T, Rhodopseudomonas faecalis JCM 11668T and Rhodopseudomonas rhenobacensis DSM 12706T. The genomic DNA G+C contents of strains JA310T and JA531T were 63.8 and 62.4 mol%, respectively. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, it is proposed that strains JA310T ( = NBRC 106083T = KCTC 5839T) and JA531T ( = NBRC 107575T = KCTC 5841T) be classified as the type strains of two novel species of the genus Rhodopseudomonas , Rhodopseudomonas parapalustris sp. nov. and Rhodopseudomonas harwoodiae sp. nov., respectively. In addition, we propose that strain DSM 123T ( = NBRC 100419T) represents a novel species, Rhodopseudomonas pseudopalustris sp. nov., since this strain differs genotypically and phenotypically from R. palustris ATCC 17001T and other members of the genus Rhodopseudomonas . An emended description of R. palustris is also provided.
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Erwinia uzenensis sp. nov., a novel pathogen that affects European pear trees (Pyrus communis L.)
Bacteria were isolated from black lesions on shoots of European pear trees (Pyrus communis L.) in an orchard in Japan. Previous characterization of this novel pathogen by phenotypic and genotypic methods suggested that it should belong to the genus Erwinia but might not correspond to either Erwinia amylovora or Erwinia pyrifoliae . Here, phylogenetic analyses of the 16S rRNA gene, gyrB, and rpoD gene sequences indicated that it could not be assigned to any recognized species of the genus Erwinia . DNA–DNA hybridization confirmed that the bacterial strains represented a novel species. The DNA G+C contents, the fatty acid profile and phenotypic characteristics resembled those previously reported for members of the genus Erwinia . On the basis of these and previous results, the pathogen represents a novel species of the genus Erwinia , for which the name Erwinia uzenensis sp. nov. (type strain: YPPS 951T = LMG 25843T = NCPPB 4475T) is proposed.
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Description of Litoreibacter meonggei sp. nov., isolated from the sea squirt Halocynthia roretzi, reclassification of Thalassobacter arenae as Litoreibacter arenae comb. nov. and emended description of the genus Litoreibacter Romanenko et al. 2011
A Gram-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MA1-1T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain MA1-1T is phylogenetically closely related to Litoreibacter species and to Thalassobacter arenae . It exhibited 16S rRNA gene sequence similarities of 97.3, 97.1 and 97.3 % to the type strains of Litoreibacter albidus , Litoreibacter janthinus and T. arenae , respectively. Strain MA1-1T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain MA1-1T was similar to those of the type strains of L. albidus and L. janthinus . T. arenae was found to be phylogenetically and chemotaxonomically more closely related to Litoreibacter species and strain MA1-1T than to Thalassobacter stenotrophicus , the type species of the genus Thalassobacter . The DNA G+C content of strain MA1-1T was 57.9 mol%, and DNA–DNA relatedness to the type strains of the two Litoreibacter species and T. arenae was 9–14 %. Differential phenotypic properties, together with the observed phylogenetic and genetic distinctiveness, distinguished strain MA1-1T from the two Litoreibacter species and T. arenae . On the basis of the data presented, strain MA1-1T is considered to represent a novel species of the genus Litoreibacter , for which the name Litoreibacter meonggei sp. nov. is proposed. The type strain is MA1-1T ( = KCTC 23699T = CCUG 61486T). In this study, it is also proposed that Thalassobacter arenae is reclassified as a member of the genus Litoreibacter , Litoreibacter arenae comb. nov. (type strain GA2-M15T = DSM 19593T = KACC 12675T). An emended description of the genus Litoreibacter is also presented.
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Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field
A novel methane-oxidizing bacterium, strain Fw12E-YT, was isolated from floodwater of a rice paddy field in Japan. Cells of strain Fw12E-YT were Gram-negative, motile rods with a single polar flagellum and type I intracytoplasmic membrane arrangement. The strain grew only on methane or methanol as sole carbon and energy source. It was able to grow at 10–40 °C (optimum 30 °C), at pH 5.5–7.0 (optimum 6.5) and with 0–0.1 % (w/w) NaCl (no growth above 0.5 % NaCl). 16S rRNA gene sequence analysis showed that strain Fw12E-YT is related most closely to members of the genus Methylomonas , but at low levels of similarity (95.0–95.4 %). Phylogenetic analysis of pmoA and mxaF genes indicated that the strain belongs to the genus Methylomonas (97 and 92 % deduced amino acid sequence identities to Methylomonas methanica S1T, respectively). The DNA G+C content of strain Fw12E-YT was 57.1 mol%. Chemotaxonomic data regarding the major quinone (MQ-8) and major fatty acids (C16 : 1 and C14 : 0) also supported its affiliation to the genus Methylomonas . Based on phenotypic, genomic and phylogenetic data, strain Fw12E-YT is considered to represent a novel species of the genus Methylomonas , for which the name Methylomonas koyamae sp. nov. is proposed. The type strain is Fw12E-YT ( = JCM 16701T = NBRC 105905T = NCIMB 14606T).
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Marinobacter antarcticus sp. nov., a halotolerant bacterium isolated from Antarctic intertidal sandy sediment
A Gram-staining-negative, aerobic, motile, oxidase- and catalase-positive, rod-shaped strain, designated ZS2-30T, was isolated from Antarctic intertidal sandy sediment. The strain grew at 4–35 °C (optimum, 25 °C) and in 0–25 % (w/v) NaCl (optimum, 3.0–4.0 %). It could reduce nitrate to nitrite and hydrolyse Tween 80. The predominant cellular fatty acids of strain ZS2-30T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C18 : 1ω9c, C16 : 1ω9c, C12 : 0 3-OH and C12 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified aminophospholipid. The genomic DNA G+C content of strain ZS2-30T was 55.8 mol%. Analyses of 16S rRNA gene sequences revealed that strain ZS2-30T was affiliated with the genus Marinobacter . It showed highest 16S rRNA gene sequence similarities to the type strains of three species of the genus Marinobacter , namely Marinobacter maritimus (98.3 %), Marinobacter psychrophilus (98.1 %) and Marinobacter goseongensis (97.1 %), but the DNA–DNA relatedness values between strain ZS2-30T and the above three species were all lower than 45 %. Moreover, strain ZS2-30T could be distinguished from closely related species of the genus Marinobacter by various phenotypic properties. Based on this taxonomic study using a polyphasic approach, strain ZS2-30T is considered to represent a novel species in the genus Marinobacter , for which the name Marinobacter antarcticus sp. nov. is proposed. The type strain of Marinobacter antarcticus is ZS2-30T ( = CGMCC 1.10835T = KCTC 23684T).
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Vibrio jasicida sp. nov., a member of the Harveyi clade, isolated from marine animals (packhorse lobster, abalone and Atlantic salmon)
Six isolates of a facultatively anaerobic bacterium were recovered in culture from marine invertebrates and vertebrates, including packhorse lobster (Jasus verreauxi), abalone (Haliotis sp.) and Atlantic salmon (Salmo salar), between 1994 and 2002. The bacteria were Gram-negative, rod-shaped and motile by means of more than one polar flagellum, oxidase-positive, catalase-positive and able to grow in the presence of 0.5–8.0 % NaCl (optimum 3.0–6.0 %) and at 10–37 °C (optimum 25–30 °C). On the basis of 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA) using five loci (2443 bp; gyrB, pyrH, ftsZ, mreB and gapA), the closest phylogenetic neighbours of strain TCFB 0772T were the type strains of Vibrio communis (99.8 and 94.6 % similarity, respectively), Vibrio owensii (99.8 and 94.1 %), Vibrio natriegens (99.4 and 88.8 %), Vibrio parahaemolyticus (99.4 and 90.3 %), Vibrio rotiferianus (99.2 and 94.4 %), Vibrio alginolyticus (99.1 and 89.3 %) and Vibrio campbellii (99.1 and 92.3 %). DNA–DNA hybridization confirmed that the six isolates constitute a unique taxon that is distinct from other known species of Vibrio . In addition, this taxon can be readily differentiated phenotypically from other Vibrio species. The six isolates therefore represent a novel species, for which the name Vibrio jasicida sp. nov. is proposed; the novel species is represented by the type strain TCFB 0772T ( = JCM 16453T = LMG 25398T) (DNA G+C content 45.9 mol%) and reference strains TCFB 1977 ( = JCM 16454) and TCFB 1000 ( = JCM 16455).
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Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil
More LessTwo Gram-negative, aerobic, rod-shaped bacteria, designated strains SL-1T and F11, which had the ability to decompose polycyclic aromatic hydrocarbons (PAHs), were isolated from soil samples contaminated by oil. The cells were motile by polar or lateral flagella. According to comparison of 16S rRNA gene sequences, strains SL-1T and F11 were identical and showed the greatest degree of similarity (96.8 %) to both Rhizobium oryzae Alt505T and Rhizobium mesosinicum CCBAU 25010T; however, only Rhizobium oryzae with SL-1T and F11 formed a separate clade. There were low similarities (<90 %) between the atpD and recA sequences of the two strains and those of the genus of Rhizobium . The bacteria grew at temperatures of 10–40 °C with an optimum of 30 °C. The pH range for growth was 6.0–10.0 and optimum pH was 7.0–8.0. Growth occurred at NaCl concentrations up to 3.0 % (w/v). They were catalase- and oxidase-positive. The main cellular fatty acids were summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c) and 16 : 0. The DNA G+C content was 62.2 mol%. Strain SL-1T showed 29 and 0 % DNA–DNA relatedness, respectively, with the most related strains R. oryzae Alt505T and R. mesosinicum CCBAU 25010T according to phylogenic analysis of the 16S rRNA gene. According to physiological and biochemical characteristics and genotypic data obtained in this work, the bacteria represent a novel species of the genus Rhizobium , and the name Rhizobium petrolearium is proposed. The type strain is SL-1T ( = ACCC 11238T = KCTC 23288T) and it could nodulate Medicago sativa in nodulation tests.
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Salinisphaera orenii sp. nov., isolated from a solar saltern
A taxonomic study was performed on two isolates, designated strains MK-B5T and MK-B7, isolated from sediment of a solar saltern pond in Gomso Bay, Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that strains MK-B5T and MK-B7 belong to the Gammaproteobacteria and are related most closely to Salinisphaera shabanensis JCM 11575T ( = E1L3AT) (96.3 and 96.5 % similarity, respectively), Salinisphaera dokdonensis KCCM 90064T ( = CL-ES53T) (95.6 and 95.6 %) and Salinisphaera hydrothermalis JCM 115514T ( = EPR70T) (95.1 and 95.3 %). The level of 16S rRNA gene sequence similarity between strains MK-B5T and MK-B7 was 99.8 %. The G+C contents of their genomic DNAs were 63.4 and 63.6 mol%, respectively, and the major respiratory quinone was ubiquinone-8. DNA–DNA relatedness between strains MK-B5T and MK-B7 was 98 %, indicating that the two isolates represent a single species. However, the level of DNA–DNA relatedness between the two isolates and S. shabanensis E1L3AT (26.4–30.8 %) indicates that they represent a novel species. Strains MK-B5T and MK-B7 possessed C14 : 0, C16 : 0 and C19 : 0ω8c cyclo as major fatty acids. The two isolates were Gram-stain-negative, strictly aerobic, short rod-shaped and motile. They grew at 10–40 °C (optimum, 35–37 °C), at pH 5.0–8.5 (optimum, 7.0–7.5) and with 5–25 % (w/v) NaCl (optimum, 15 % NaCl). On the basis of phenotypic and phylogenetic analyses, strains MK-B5T and MK-B7 are thus considered to represent a novel species of the genus Salinisphaera , for which the name Salinisphaera orenii sp. nov. is proposed. The type strain is MK-B5T ( = KCTC 23198T = JCM 17073T).
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Thioalkalivibrio sulfidiphilus sp. nov., a haloalkaliphilic, sulfur-oxidizing gammaproteobacterium from alkaline habitats
More LessA moderately salt-tolerant and obligately alkaliphilic, chemolithoautotrophic sulfur-oxidizing bacterium, strain HL-EbGr7T, was isolated from a full-scale bioreactor removing H2S from biogas under oxygen-limited conditions. Another strain, ALJ17, closely related to HL-EbGr7T, was isolated from a Kenyan soda lake. Cells of the isolates were relatively long, slender rods, motile by a polar flagellum. Although both strains were obligately aerobic, micro-oxic conditions were preferred, especially at the beginning of growth. Chemolithoautotrophic growth was observed with sulfide and thiosulfate in a pH range of 8.0–10.5 (optimum at pH 10.0) and a salinity range of 0.2–1.5 M total Na+ (optimum at 0.4 M). The genome sequence of strain HL-EbGr7T demonstrated the presence of genes encoding the reverse Dsr pathway and a truncated Sox pathway for sulfur oxidation and enzymes of the Calvin–Benson cycle of autotrophic CO2 assimilation with ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) type I. The dominant cellular fatty acids were C18 : 1ω7, C16 : 0 and C19 : 0 cyclo. Based on 16S rRNA gene sequencing, the two strains belonged to a single phylotype within the genus Thioalkalivibrio in the Gammaproteobacteria . Despite being related most closely to Thioalkalivibrio denitrificans , the isolates were unable to grow by denitrification. On the basis of phenotypic and phylogenetic analysis, the novel isolates are proposed to represent a novel species, Thioalkalivibrio sulfidiphilus sp. nov., with the type strain HL-EbGr7T ( = NCCB 100376T = UNIQEM U246T).
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Roseivivax sediminis sp. nov., a moderately halophilic bacterium isolated from salt mine sediment
A Gram-negative, facultatively anaerobic, short rod-shaped, heterotrophic bacterium, designated strain YIM D21T, was isolated from a salt mine in Yunnan province, south-west China. Strain YIM D21T formed cream–yellow colonies, was non-motile and moderately halophilic, and tolerated NaCl concentrations of 1–15 % (w/v), with optimum growth at 5–10 % (w/v). Growth occurred at 15–42 °C (optimum 28 °C) and at pH 6.5–8.5 (optimum 7.5–8.0). The respiratory quinone was ubiquinone-10 (Q-10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, three unidentified phospholipids, one unidentified aminolipid and two unidentified lipids. The major fatty acids were C18 : 1ω7c and cyclo C19 : 0ω8c and the DNA G+C content was 67.7 mol%. Phylogenetic analyses revealed that strain YIM D21T belongs to the genus Roseivivax . 16S rRNA gene sequence similarities of YIM D21T were 95.7, 95.0 and 94.8 % with the type strains of Roseivivax halodurans , Roseivivax lentus and Roseivivax halotolerans , respectively. Physiological and biochemical tests allowed phenotypic differentiation of strain YIM D21T from closely related species with validly published names. We therefore propose that this isolate represents a novel species, Roseivivax sediminis sp. nov.; the type strain is YIM D21T ( = KCTC 23444T = ACCC 10710T).
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Oceanisphaera arctica sp. nov., isolated from Arctic marine sediment, and emended description of the genus Oceanisphaera
More LessA novel Gram-staining-negative, coccoid, non-motile bacterium, designated strain V1-41T, was isolated from a sample of marine sediment collected, at a depth of 200 m, from Kongsfjorden (an inlet on the west coast of Spitsbergen, an island that forms part of the Svalbard archipelago in the Arctic Ocean). The strain formed cream–brown colonies on marine agar. Cells of the novel strain were positive in tests for catalase, oxidase, lysine decarboxylase and ornithine decarboxylase activities but negative for gelatinase and lipase activities. They hydrolysed aesculin, starch and urea, but not casein or DNA. Most of the cellular fatty acids were medium-chain and saturated (37.1 %) or long-chain and unsaturated (27.8 %), with C12 : 0 (37.1 %), C18:1ω7c, and summed features 2 (19.3%) and 3 (24.1%) predominating. The major respiratory quinone was Q-8. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, four unidentified phospholipids and one other unidentified lipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain’s closest known relatives were Oceanisphaera litoralis DSM 15406T (98.5 % sequence similarity) and Oceanisphaera donghaensis BL1T (98.3 %). In DNA–DNA hybridizations, however, the levels of relatedness between strain V1-41T and O. litoralis DSM 15406T and between the novel strain and O. donghaensis DSM 17589T were found to be only 19 % and 29 %, respectively. Based on these low levels of similarity at the DNA–DNA level and the phenotypic and chemotaxonomic differences from O. litoralis DSM 15406T and O. donghaensis DSM 17589T, strain V1-41T represents a novel species of the genus Oceanisphaera for which the name Oceanisphaera arctica sp. nov. is proposed. The type strain is V1-41T ( = CCUG 58690T = KCTC 23013T = NBRC 106171T).
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Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake
More LessA Gram-stain-negative, non-spore-forming, non-motile, irregularly circular, aerobic/microaerobic appendaged bacterium (strain 120-1T) was isolated from Naga-ike, one of the freshwater lakes in the Skarvsnes ice-free area of Antarctica. Strain 120-1T grew between 5 and 35 °C, with optimum growth at 30 °C. The pH range for growth was between 6.0 and 9.0 (optimum of approximately pH 7.0). The range of NaCl concentration allowing growth of strain 120-1T was between 0 and 5.0 %, with an optimum of 0.5–1.0 %. Strain 120-1T was able to utilize organic compounds such as glucose, arabinose, gluconate, adipate and malate. Red colonies were formed on plate medium and the carotenoids were present in the cells. Ubiquinones Q-9 and Q-10 were the major respiratory quinones. The major cellular fatty acids were C16 : 0, C18 : 1ω9c and C18 : 1ω7c. The G+C content of the genomic DNA was 61.1 mol%. Comparative analyses of 16S rRNA gene sequences and physiological characteristics of strain 120-1T indicate that strain 120-1T is a phylogenetically novel bacterium, and that it represents a novel species in a new genus, Rhodoligotrophos gen. nov., in the order Rhizobiales , family Rhodobiaceae . The name Rhodoligotrophos appendicifer gen. nov. sp. nov. is proposed as the type species of this new genus, with 120-1T ( = JCM 16873T = ATCC BAA-2115T) as the type strain.
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Bradyrhizobium huanghuaihaiense sp. nov., an effective symbiotic bacterium isolated from soybean (Glycine max L.) nodules
In a survey of the biodiversity and biogeography of rhizobia associated with soybean (Glycine max L.) in different sites of the Northern (Huang-Huai-Hai) Plain of China, ten strains were defined as representing a novel genomic species in the genus of Bradyrhizobium . They were distinguished from defined species in restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and the 16S–23S rRNA gene intergenic spacer (IGS). In BOX-PCR, these strains presented two patterns that shared 94 % similarity, demonstrating that they were a homogenous group with limited diversity. In phylogenetic analyses of the 16S rRNA gene, IGS and housekeeping gene sequences, four representative strains formed a distant lineage within the genus Bradyrhizobium , which was consistent with the results of DNA–DNA hybridization. The strains of this novel group formed effective nodules with G. max, Glycine soja and Vigna unguiculata in cross-nodulation tests and harboured symbiotic genes (nodC and nifH) identical to those of reference strains of Bradyrhizobium japonicum , Bradyrhizobium liaoningense and ‘Bradyrhizobium daqingense’ originating from soybean, implying that the novel group may have obtained these symbiotic genes by lateral gene transfer. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related Bradyrhizobium species, demonstrating that the novel group is distinct phenotypically from other Bradyrhizobium species. Based upon the data obtained, these strains are proposed to represent a novel species, Bradyrhizobium huanghuaihaiense sp. nov., with CCBAU 23303T ( = LMG 26136T = CGMCC 1.10948T = HAMBI 3180T) as the type strain. The DNA G+C content of strain CCBAU 23303T is 61.5 mol% (T m).
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Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil
More LessA taxonomic study was carried out on a cellulase-producing bacterium, strain G21T, isolated from mangrove soil in Xiamen, Fujian province, China. Cells were Gram-negative, slightly curved rods, motile with a single polar flagellum. The strain grew at 15–40 °C and in 0.5–10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G21T belonged to the genus Vibrio and formed a clade with Vibrio furnissii ATCC 350116T (97.4 % sequence similarity), V. fluvialis LMG 7894T (97.1 %) and V. ponticus CECT 5869T (96.1 %). However, multilocus sequence analysis (using rpoA, recA, mreB, gapA, gyrB and pyrH sequences) and DNA–DNA hybridization experiments indicated that the strain was distinct from the closest related Vibrio species. Additionally, strain G21T could be differentiated from them phenotypically by the ability to grow in 10 % NaCl but not on TCBS plates, its enzyme activity spectrum, citrate utilization, oxidization of various carbon sources, hydrolysis of several substrates and its cellular fatty acid profile. The G+C content of the genomic DNA was 46.0 mol%. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, with trace amounts of diphosphatidylglycerol. The predominant quinones were Q-8 and Q-7. Based on phylogenetic, phenotypic and chemotaxonomic characteristics and DNA–DNA hybridization analysis, it is concluded that strain G21T represents a novel species of the genus Vibrio , for which the name Vibrio xiamenensis sp. nov. is proposed. The type strain is G21T ( = DSM 22851T = CGMCC 1.10228T).
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Marinobacter xestospongiae sp. nov., isolated from the marine sponge Xestospongia testudinaria collected from the Red Sea
More LessA Gram-negative, catalase- and oxidase-positive, non-sporulating, rod-shaped and slightly halophilic bacterial strain, designated UST090418-1611T, was isolated from the marine sponge Xestospongia testudinaria collected from the Red Sea coast of Saudi Arabia. Phylogenetic trees based on the 16S rRNA gene sequence placed strain UST090418-1611T in the family Alteromonadaceae with the closest relationship to the genus Marinobacter . The 16S rRNA gene sequence similarity between the strain and the type strains of recognized Marinobacter species ranged from 92.9 to 98.3 %. Although strain UST090418-1611T shared high 16S rRNA gene sequence similarity with Marinobacter mobilis CN46T, M. zhejiangensis CN74T and M. sediminum R65T (98.3, 97.4 and 97.3 %, respectively), the relatedness of the strain to these three strains in DNA–DNA hybridization was only 58, 56 and 33 %, respectively, supporting the novelty of the strain. In contrast to most strains in the genus Marinobacter , strain UST090418-1611T tolerated only 6 % (w/v) NaCl, and optimal growth occurred at 2.0 % (w/v) NaCl, pH 7.0–8.0 and 28–36 °C. The predominant cellular fatty acids were C12 : 0 3-OH, C16 : 0, C12 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The genomic DNA G+C content was 57.1 mol%. Based on the physiological, phylogenetic and chemotaxonomic characteristics presented in this study, we suggest that the strain represents a novel species in the genus Marinobacter , for which the name Marinobacter xestospongiae sp. nov. is proposed, with UST090418-1611T ( = JCM 17469T = NRRL B-59512T) as the type strain.
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Alishewanella tabrizica sp. nov., isolated from Qurugöl Lake
A novel Gram-negative, aerobic, motile and rod-shaped bacterium was isolated from Qurugöl Lake located in a mountainous region near Tabriz city in the north-west of Iran. Growth occurred at pH 6–10 (optimum, pH 7±0.5) and at 10–40 °C (optimum, 30 °C). Strain RCRI4T was able to grow in the absence and presence of NaCl to 3 % (w/v). The major fatty acids were C17 : 0, C16 : 1ω7c/C15 iso3-OH, C17 : 1ω8c and C16 : 0. The G+C content of genomic DNA was 45.3 mol%. Based on the 16S rRNA and gyrB gene sequences, phylogenetic analyses indicated that strain RCRI4T associated with the genus Alishewanella , and closely related type strains include Alishewanella agri BLO6T (97.8 %), Alishewanella aestuarii B11T (97.7 %), Rheinheimera perlucida BA131T (97.5 %), Alishewanella fetalis CCUG 30811T (97.3 %) and Alishewanella jeotgali MS1T (97.1 %). The level of DNA–DNA relatedness between strain RCRI4T and phylogenetically the closest related strains, A. agri BLO6T and R. perlucida BA131T, was 9 and 14 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic results, it is suggested that strain RCRI4T represents a novel species of the genus Alishewanella , for which the name Alishewanella tabrizica sp. nov. is proposed. The type strain is RCRI4T ( = LMG 26473T = JCM 17275T = KCTC 23723T).
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Rhizobium halophytocola sp. nov., isolated from the root of a coastal dune plant
More LessDuring a study of endophytic bacteria from coastal dune plants, a bacterial strain, designated YC6881T, was isolated from the root of Rosa rugosa collected from the coastal dune areas of Namhae Island, Korea. The bacterium was found to be Gram-staining-negative, motile, halophilic and heterotrophic with a single polar flagellum. Strain YC6881T grew at temperatures of 4–37 °C (optimum, 28–32 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0), and at NaCl concentrations in the range of 0–7.5 % (w/v) (optimum, 4–5 % NaCl). Strain YC6881T was catalase- and oxidase-positive and negative for nitrate reduction. According to phylogenetic analysis using 16S rRNA gene sequences, strain YC6881T belonged to the genus Rhizobium and showed the highest 16S rRNA gene sequence similarity of 96.9 % to Rhizobium rosettiformans , followed by Rhizobium borbori (96.3 %), Rhizobium radiobacter (96.1 %), Rhizobium daejeonense (95.9 %), Rhizobium larrymoorei (95.6 %) and Rhizobium giardinii (95.4 %). Phylogenetic analysis of strain YC6881T by recA, atpD, glnII and 16S–23S intergenic spacer (IGS) sequences all confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Cross-nodulation tests showed that strain YC6881T was a symbiotic bacterium that nodulated Vigna unguiculata and Pisum sativum. The major components of the cellular fatty acids were C18 : 1ω7c (53.7 %), C19 : 0 cyclo ω8c (12.6 %) and C12 : 0 (8.1 %). The DNA G+C content was 52.8 mol%. Phenotypic and physiological tests with respect to carbon source utilization, antibiotic resistance, growth conditions, phylogenetic analyses of housekeeping genes recA, atpD and glnII, and fatty acid composition could be used to discriminate strain YC6881T from other species of the genus Rhizobium in the same sublineage. Based on the results obtained in this study, strain YC6881T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium halophytocola sp. nov. is proposed. The type strain is YC6881T ( = KACC 13775T = DSM 21600T).
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Lutibaculum baratangense gen. nov., sp. nov., a proteobacterium isolated from a mud volcano
More LessA novel Gram-negative, oval to rod-shaped, motile bacterium, strain AMV1T, was isolated from a soil sample collected from a mud volcano of Baratang Island, Andamans, India. The predominant fatty acids were C16 : 0 (5.7 %), C18 : 1ω7c (78.6 %) and C19 : 0 cyclo ω8c (6.3 %). Strain AMV1T contained ubiquinone 10 (Q-10) as the major respiratory quinone and minor quantities of ubiquinone 9 (Q-9). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified lipids, one unidentified phospholipid and one unidentified aminolipid. 16S rRNA gene sequence analysis indicated that strain AMV1T was related most closely to the type strains of Tepidamorphus gemmatus , Bauldia consociata , Afifella pfennigii and Amorphus coralli , four members of the order Rhizobiales (class Alphaproteobacteria ), with pairwise sequence similarities of 95.0, 94.5, 94.4 and 94.0 %, respectively; it shared <94 % 16S rRNA gene sequence similarity with all the other members of the order Rhizobiales . Phylogenetic analyses indicated that strain AMV1T clustered with Tepidamorphus gemmatus and with species of the genera Amorphus , Rhodobium and Afifella . Phenotypic and phylogenetic characteristics thus suggest that strain AMV1T is a representative of a novel species of a new genus, for which the name Lutibaculum baratangense gen. nov., sp. nov. is proposed. The type strain of Lutibaculum baratangense is AMV1T ( = KCTC 22669T = NBRC 105799T = CCUG 58046T).
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Gluconacetobacter tumulicola sp. nov. and Gluconacetobacter asukensis sp. nov., isolated from the stone chamber interior of the Kitora Tumulus
More LessSix Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from small holes on plaster walls of the stone chamber interior of the Kitora Tumulus in Asuka village, Nara Prefecture, Japan. These were investigated by means of a polyphasic approach. All the isolates were strictly aerobic and motile by peritrichous flagella. Phylogenetic trees generated based on 16S rRNA gene sequences identified two novel lineages (comprising five isolates and one isolate, respectively) within the genus Gluconacetobacter . The isolates were characterized by having Q-10 as the major ubiquinone system and C18 : 1ω7c (58.7–63.1 % of the total) as the predominant fatty acid. DNA–DNA hybridization experiments endorsed the species rank for the two lineages, for which the names Gluconacetobacter tumulicola sp. nov. (type strain K5929-2-1bT = JCM 17774T = NCIMB 14760T) and Gluconacetobacter asukensis sp. nov. (type strain K8617-1-1bT = JCM 17772T = NCIMB 14759T) are proposed.
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- Bacteroidetes
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Mesonia ostreae sp. nov., isolated from seawater of an oyster farm, and emended description of the genus Mesonia
More LessA Gram-negative, aerobic, non-flagellated, non-gliding rod, designated T-y2T, was isolated from seawater of an oyster farm in the South Sea, Korea. Strain T-y2T grew optimally at 25 °C, at pH 7.0–7.5 and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain T-y2T belonged to the genus Mesonia and exhibited 94.3–96.4 % 16S rRNA gene sequence similarity with the type strains of species of the genus Mesonia . The DNA G+C content of strain T-y2T was 42.1 mol%. Strain T-y2T contained MK-6 as the predominant menaquinone and anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids. The only major phospholipid identified was phosphatidylethanolamine. The differential phenotypic properties and phylogenetic distinctiveness of strain T-y2T revealed that it is distinguishable from recognized members of the genus Mesonia . On the basis of the data presented here, strain T-y2T is considered to represent a novel species of the genus Mesonia , for which the name Mesonia ostreae sp. nov. is proposed. The type strain is T-y2T ( = KCTC 23500T = CCUG 60802T).
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Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco
A novel Gram-negative strain, designated M-SX103T, was isolated from a fresh leaf of Nicotiana tabacum Linn. collected at Yuxi City, Yunnan province, China, and subjected to a polyphasic taxonomic study. Growth occurred at 10–40 °C, at pH 6.0–9.0 and with 0–3 % (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids of strain M-SX103T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The G+C content of the genomic DNA was 40.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Sphingobacterium , sharing 95.4–89.7 % sequence similarity with type strains of members of the genus Sphingobacterium ; it was most closely related to Sphingobacterium composti T5-12T. On the basis of the taxonomic evidence, a novel species, Sphingobacterium nematocida sp. nov., is proposed. The type strain is M-SX103T ( = JCM 17339T = CCTCC AB 2010390T).
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Winogradskyella aquimaris sp. nov., isolated from seawater
More LessA Gram-negative, non-flagellated, motile by gliding, aerobic rod, designated DPG-24T, was isolated from seawater of Geoje Island in the South Sea, Korea. Strain DPG-24T grew optimally at 30–37 °C, at pH 7.0–7.5 and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DPG-24T belonged to the genus Winogradskyella and clustered with Winogradskyella poriferorum UST030701-295T and Winogradskyella exilis 022-2-26T. Strain DPG-24T exhibited 97.6 and 95.8 % 16S rRNA gene sequence similarities with W. poriferorum UST030701-295T and W. exilis 022-2-26T, respectively, and 92.4–95.7 % with other members of the genus Winogradskyella . Strain DPG-24T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. The DNA G+C content was 36.7 mol%. DNA–DNA relatedness between the isolate and W. poriferorum JCM 12885T was 10.8 %. The differential phenotypic properties and phylogenetic and genetic distinctiveness enabled strain DPG-24T to be differentiated from recognized members of the genus Winogradskyella . On the basis of the data presented, strain DPG-24T is considered to represent a novel species of the genus Winogradskyella , for which the name Winogradskyella aquimaris sp. nov. is proposed; the type strain is DPG-24T ( = KCTC 23502T = CCUG 60798T).
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Mangroviflexus xiamenensis gen. nov., sp. nov., a member of the family Marinilabiliaceae isolated from mangrove sediment
More LessA Gram-negative, obligately anaerobic, non-spore-forming, long rod-shaped bacterium strain P2T was isolated from the offshore mangrove sediment of the South China Sea. Growth was observed at between 22 and 39 °C, with an optimum at 35 °C. The pH range for growth was 5.0–8.5, with an optimum around pH 7.0–7.5. Salt tolerance was determined between 0.2 and 3.5 % (w/v), optimum at 0.5–1.0 %. Catalase and oxidase activities were negative. Strain P2T utilized cysteine, lactate, pyruvate, yeast extract or H2/CO2+acetate as electron donors, and sulfate or sulfite as electron acceptors. Metabolism was strictly fermentative. The main organic fermentation products were propionate, acetate and succinate. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P2T formed a distinct evolutionary lineage within the family Marinilabiliaceae . Strain P2T was most closely related to members of the genera Alkaliflexus (92.0 % 16S rRNA gene sequence similarity), Marinilabilia (91.7 %) and Anaerophaga (89.9 %) of the family Marinilabiliaceae . The DNA G+C content of the novel strain was 44.2±1.0 mol%. The dominant fatty acids of strain P2T were iso-C15 : 0 (33.5 %), anteiso-C15 : 0 (18.9 %), C16 : 0 (5.4 %), C16 : 0 3-OH (7.7 %) and iso-C17 : 0 3-OH (13.3 %). The respiratory quinone was menaquinone 7 (100 % of total quinone) and the major polar lipid was phosphatidylethanolamine. Strain P2T was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of phylogenetic, phenotypic and physiological evidence, a novel genus, Mangroviflexus, is proposed to harbour strain P2T ( = CGMCC 1.5167T = DSM 24214T) which is described as the type strain of a novel species, Mangroviflexus xiamenensis gen. nov., sp. nov.
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Psychroflexus halocasei sp. nov., isolated from a microbial consortium on a cheese
More LessA novel halophilic, Gram-reaction-negative, strictly aerobic, non-motile, rod-shaped and oxidase- and catalase-positive bacterial strain, designated WCC 4520T, was isolated from a semi-hard, Raclette-type cheese. The colonies were yellow–orange; flexirubin-type pigments were not found. The strain hydrolysed gelatin, hippurate, tyrosine and Tweens 20 and 80. Optimal growth was observed with 6–8 % (w/v) NaCl, at pH 7–8 and at 27–30 °C. The genomic DNA G+C content was 33.6 mol%. In phylogenetic analysis based on 16S rRNA gene sequences, strain WCC 4520T appeared to be a member of the family Flavobacteriaceae and the closest phylogenetic neighbours were identified as Psychroflexus gondwanensis DSM 5423T (94.0 % 16S rRNA gene sequence similarity) and Psychroflexus salinarum CCUG 56752T (94.0 %). The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The only detected quinone was MK-6 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified polar lipid. Minor polar lipids and traces of polyamines were also detected. On the basis of the data presented, strain WCC 4520T represents a novel species of the genus Psychroflexus , for which the name Psychroflexus halocasei sp. nov. is proposed. The type strain is WCC 4520T ( = LMG 25857T = CCUG 59705T).
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Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005
More LessThe genera Dokdonia and Krokinobacter , members of the family Flavobacteriaceae in the phylum Bacteroidetes , were found to be phylogenetically closely related from the result of 16S rRNA gene sequence analysis. Dokdonia donghaensis DSW-1T exhibited 16S rRNA gene sequence similarity values of 99.3, 98.1 and 98.1 % to Krokinobacter genikus Cos-13T, Krokinobacter diaphorus MSKK-32T and Krokinobacter eikastus PMA-26T, respectively. A taxonomic study of D. donghaensis DSW-1T, K. genikus CIP 108744T, K. diaphorus CIP 108745T and K. eikastus CIP 108743T was conducted using a polyphasic approach. The major fatty acids (>10 % of the total fatty acids) in the four strains were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH, and their overall fatty acid profiles were essentially similar. The predominant menaquinone found in the type strains of the three species of the genus Krokinobacter was MK-6, in line with the genus Dokdonia . The polar lipid profiles of the type strains of the three species of the genus Krokinobacter were similar to that of D. donghaensis DSW-1T in that phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid were the major polar lipids. In addition, one unidentified aminophospholipid was also present as a major polar lipid in K. diaphorus CIP 108745T and K. eikastus CIP 108743T. D. donghaensis DSW-1T was distinguishable from K. genikus CIP 108744T, K. diaphorus CIP 108745T and K. eikastus CIP 108743T by genetic relatedness and differential phenotypic properties. On the basis of these data, it is proposed that K. genikus , K. diaphorus and K. eikastus be reclassified into the genus Dokdonia as Dokdonia genika comb. nov. (type strain is Cos-13T = NBRC 100811T = CIP 108744T), Dokdonia diaphoros comb. nov. (type strain is MSKK-32T = NBRC 100817T = CIP 108745T), and Dokdonia eikasta comb. nov. (type strain is PMA-26T = NBRC 100814T = CIP 108743T), respectively. An emended description of the genus Dokdonia is also presented.
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Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter , Pedobacter heparinus , Pedobacter daechungensis , Pedobacter terricola , Pedobacter glucosidilyticus and Pedobacter lentus
More LessA Gram-stain-negative, short rod-shaped, motile (by gliding) bacterial strain, designated A12T, was isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. The temperature, NaCl and pH ranges for growth were 4–25 °C (optimum, 18 °C), 0–2 % (optimum, 0 %) and pH 6–9 (optimum, pH 7). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Arctic isolate belonged to the genus Pedobacter and showed highest sequence similarity (94.4 %) to Pedobacter daechungensis KCTC 12637T. The DNA G+C content (38.3 mol%), polar lipid profile, presence of sphingolipid, MK-7 as the only respiratory quinone, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids supported the allocation of strain A12T to the genus Pedobacter as a representative of a novel species, for which the name Pedobacter arcticus sp. nov. is proposed. The type strain is A12T ( = CCTCC AB 2010223T = NRRL B-59457T). Emended descriptions of the genus Pedobacter and of Pedobacter heparinus , Pedobacter daechungensis , Pedobacter terricola , Pedobacter glucosidilyticus and Pedobacter lentus are also given.
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Aquimarina mytili sp. nov., isolated from the gut microflora of a mussel, Mytilus coruscus, and emended description of Aquimarina macrocephali
More LessAn orange, rod-shaped, gliding bacterium, designated strain PSC33T, was isolated from the gut microflora of a mussel collected from Gwangyang Bay, South Sea (Republic of Korea). Cells were Gram-reaction-negative, strictly aerobic, and catalase- and oxidase-positive. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, C15 : 0 3-OH and iso-C17 : 1ω9c. The only isoprenoid quinone was menaquinone-6 (MK-6). The DNA G+C content of strain PSC33T was 37.9 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain PSC33T formed an evolutionary lineage within the radiation encompassing members of the genus Aquimarina with Aquimarina macrocephali JAMB N27T as its nearest neighbour (96.3 % sequence similarity). A number of phenotypic characteristics distinguished strain PSC33T from recognized members of the genus Aquimarina . On the basis of the data presented in this study, strain PSC33T is considered to represent a novel species of the genus Aquimarina , for which the name Aquimarina mytili sp. nov. is proposed. The type strain is PSC33T ( = KCTC 23302T = JCM 17454T). An emended description of A. macrocephali is also provided.
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Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium , Flavobacterium resistens and Flavobacterium johnsoniae
A strictly aerobic, Gram-negative, yellow-pigmented, non-spore-forming rod, designated 15C3T, was isolated from aerobic leaf-and-branch compost at EXPO Park in Osaka, Japan. Growth was observed at 9–33 °C (optimum 25 °C) and pH 5.6–7.9 (optimum pH 6.1–7.0). No growth occurred with >2 % (w/v) NaCl. Strain 15C3T reduced nitrate to nitrogen and showed catalase activity but not oxidase activity. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The isolate contained phosphatidylethanolamine as the major polar lipid and menaquinone-6 as the major respiratory quinone. The G+C content of the genomic DNA of strain 15C3T was 33.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 15C3T belonged to the genus Flavobacterium and was most closely related to Flavobacterium hercynium WB 4.2-33T (96.9 % sequence similarity). On the basis of phenotypic and phylogenetic distinctiveness, strain 15C3T is considered to represent a novel species in the genus Flavobacterium , for which the name Flavobacterium compostarboris sp. nov. is proposed. The type strain is 15C3T ( = KACC 14224T = JCM 16527T). Emended descriptions of F. hercynium , Flavobacterium resistens and Flavobacterium johnsoniae are also given.
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- Eukaryotic Micro-organisms
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Bensingtonia rectispora sp. nov. and Bensingtonia bomiensis sp. nov., ballistoconidium-forming yeast species from Tibetan plant leaves
More LessFive yeast strains isolated from plant leaves collected in south-east Tibet formed cream to brownish colonies and produced asymmetrical ballistoconidia and CoQ-9 as the major ubiquinone. Sequence analysis of the 26S rRNA D1/D2 domain and the internal transcribed spacer region indicated that these strains represented two novel species of the genus Bensingtonia. The names Bensingtonia rectispora sp. nov. (type strain XZ 4C5T = CGMCC 2.02635T = CBS 10710T) and Bensingtonia bomiensis sp. nov. (type strain XZ 33D1T = CGMCC 2.02670T = CBS 10713T) are proposed for the two novel species, which are phylogenetically closely related to Bensingtonia naganoensis, Bensingtonia pseudonaganoensis and the type species of the genus, Bensingtonia ciliata.
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Volumes and issues
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