- Volume 67, Issue 5, 2017
Volume 67, Issue 5, 2017
- New Taxa
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- Other Bacteria
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Chloroflexus islandicus sp. nov., a thermophilic filamentous anoxygenic phototrophic bacterium from a geyser
A novel, thermophilic filamentous anoxygenic phototrophic bacterium, strain isl-2T, was isolated from the Strokkur Geyser, Iceland. Strain isl-2T formed unbranched multicellular filaments with gliding motility. The cells formed no spores and stained Gram-negative. The existence of pili was described in a species of the genus Chloroflexus for the first time, to our knowledge. Optimal growth occurred at a pH range of 7.5–7.7 and at a temperature of 55 °C. Strain isl-2T grew photoheterotrophically under anaerobic conditions in the light and chemoheterotrophically under aerobic conditions in the dark. The major cellular fatty acids were C18 : 1ω9, C16 : 0, C18 : 0 and C18 : 0-OH. The major quinone was menaquinone-10. The photosynthetic pigments were bacteriochlorophylls c and a as well as β- and γ-carotenes. The results of phylogenetic analysis of the 16S rRNA gene sequences placed strain isl-2T into the genus Chloroflexus of the phylum Chloroflexi with Chloroflexus aggregans DSM 9485T as the closest relative (97.0 % identity). The whole-genome sequence of isl-2T was determined. Average nucleotide identity values obtained for isl-2T in comparison to available genomic sequences of other strains of members of the genus Chloroflexus were 81.4 % or less and digital DNA–DNA hybridisation values 22.8 % or less. The results of additional phylogenetic analysis of the PufLM and BchG amino acid sequences supported the separate position of the isl-2T phylotype from the phylotypes of other members of the genus Chloroflexus . On the basis of physiological and phylogenetic data as well as genomic data, it was suggested that isl-2T represents a novel species within the genus Chloroflexus , with the proposed name Chloroflexus islandicus sp. nov. The type strain of the species is isl-2T (=VKM B-2978T,=DSM 29225T,=JCM 30533T).
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Luteitalea pratensis gen. nov., sp. nov. a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil
More LessAlbeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date, only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_−6_39T, a novel representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_−6_39T are Gram-stain-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies. This slow growing bacterium is psychrotolerant and grows between 0 and 36 °C. It displays a narrower pH tolerance (5.3–8.3) than most acidobacteria. The strain is an aerobe that grows chemo-organotrophically utilizing mostly sugars and proteinaceous substrates such as peptone, yeast extract, casein hydrolysate and casamino acids as substrates. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and two unknown phospholipids are identified as polar lipids. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C18 : 1ω9c and iso-C17 : 1ω9c. The major respiratory quinone is MK-8. The G+C content of the genomic DNA is 64.7 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Vicinamibacter silvestris Ac_5_C6T with 93.6 % sequence similarity. Based on the present taxonomic characterization, strain HEG_-6_39T represents a new species of a novel genus for which the name Luteitalea pratensis gen. nov., sp. nov., is proposed. The type strain of the type species is HEG_−6_39T (=DSM 100886T=KCTC 52215T).
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Sphingobacterium cellulitidis sp. nov., isolated from clinical and environmental sources
The taxonomic position of two isolates belonging to the genus Sphingobacterium was determined. The first isolate, R-53603T, was obtained from purulent discharge from the toe of a cellulitis patient in Kuwait. Comparative 16S rRNA gene sequence analysis revealed 99.87 % similarity of R-53603T with environmental isolate P031 (=R-53745) originating from activated sludge in Singapore. The two isolates were phylogenetically positioned on the same sub-branch. Highest 16S rRNA gene sequence similarity was found with the type strains of Sphingobacterium mizutaii (98.23 %), Sphingobacterium lactis (97.78 %) and Sphingobacterium daejeonense (97.14 %). DNA–DNA hybridizations revealed <70 % relatedness between the two isolates and the type strains of the close phylogenetic neighbours S. mizutaii (18.0–24.5 %), S. lactis (20.3–25.9 %) and S. daejeonense (13.2–20.0 %). The high relative contribution of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) in the cellular fatty acid profiles of R-53603T and R-53745, the presence of sphingophospholipids, MK-7 as the dominant menaquinone and phosphatidylethanolamine as the major polar lipid in strain R-53603T are typical chemotaxonomic characteristics for members of the genus Sphingobacterium . Phenotypic features most useful for differentiation of the two novel strains from the most closely related species S. mizutaii include growth on MacConkey agar, and utilization of stachyose, guanidine HCl and lithium chloride in Biolog GEN III tests. Strains R-53603T and R-53745 thus represent a novel species, for which the name Sphingobacterium cellulitidis sp. nov. is proposed. The type strain is R-53603T (=LMG 28764T=DSM 102028T).
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- Proteobacteria
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Lysobacter solanacearum sp. nov., isolated from rhizosphere of tomato
A bacterial strain, designated T20R-70T, was isolated from tomato rhizosphere soil collected in Yecheon-gun, Gyeongsangbuk-do in South Korea. Growth was observed within the ranges 10–40 °C (optimally at 28–30 °C), pH 7.0–8.0 (optimally at pH 7.0) and 0–1 % NaCl (optimally at 0 %). The 16S rRNA gene sequence showed the highest similarities with those of Lysobacter hankyongensis KTCe-2T (98.7 %), Lysobacter brunescens KCTC 12130T (98.0 %), ‘ Lysobacter daecheongensis ' Dae08 (97.2 %) and Lysobacter oligotrophicus 107-E2T (97.1 %). The phylogenetic tree showed that strain T20R-70T formed a clade with Lysobacter hankyongensis KTCe-2T and Lysobacter brunescens KCTC 12130T. The dominant fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0, iso-C17 : 1ω9c and summed feature 3 (including iso-C15 : 0 2-OH and/or iso-C16 : 1ω7c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was Q-8. DNA–DNA hybridization data revealed that strain T20R-70T had a hybridization value of 42±4 % (mean±sd) to the most closely related species of the genus Lysobacter . The DNA G+C content was 63.0 mol%. The physiological, biochemical and chemotaxonomic data allowed the discrimination of the new isolate from its phylogenetic relatives. Strain T20R-70T is thus considered to be a representative of a novel species of the genus Lysobacter , for which the name Lysobacter solanacearum sp. nov. is proposed. The type strain is T20R-70T (=KACC 18656T=NBRC 111881T).
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Endothiovibrio diazotrophicus gen. nov., sp. nov., a novel nitrogen-fixing, sulfur-oxidizing gammaproteobacterium isolated from a salt marsh
A novel non-phototrophic, marine, sulfur-oxidizing bacterium, strain S-1T, was isolated from a coastal salt marsh in Massachusetts, USA. Cells are Gram-stain-negative vibrios motile by means of a single polar unsheathed flagellum. S-1T is an obligate microaerophile with limited metabolic capacity. It grows chemolithoautotrophically utilizing sulfide and thiosulfate as electron donors, converting these compounds to sulfate, and the Calvin–Benson–Bassham cycle for carbon fixation. Cells of S-1T did not grow on any of a large number of organic carbon sources and there was no evidence for chemoorganoheterotrophic growth. Cells produced internal sulfur globules during growth on sulfide and thiosulfate. S-1T is strongly diazotrophic, as demonstrated by 15N2 fixation and acetylene reduction activity by cells when a fixed nitrogen source is absent from the growth medium. The marine nature of this organism is evident from its ability to grow in 10 to 100 % artificial seawater but not at lower concentrations and NaCl alone cannot substitute for sea salts. The major cellular fatty acids are C16 : 1ω7c, C16 : 0, and C18 : 1ω7c. Phosphatidylethanolamine and phosphatidylglycerol are the major polar lipids. Q8 is the only respiratory quinone. S-1T genomic DNA has a G+C content of 67.6 mol%. Based on its 16S rRNA gene sequence, S-1T shows the closest phylogenetic relationship to non-phototrophic species within the family Thioalkalispiraceae of the class Gammaproteobacteria . The name Endothiovibrio diazotrophicus is proposed for this organism, with S-1T as the type strain (ATCC BAA-1439T=JCM 17961T).
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Noviherbaspirillum agri sp. nov., isolated from reclaimed grassland soil, and reclassification of Herbaspirillum massiliense (Lagier et al., 2014) as Noviherbaspirillum massiliense comb. nov.
More LessA straw-coloured, Gram-staining-negative, aerobic, motile and rod-shaped bacterium, designated strain K-1-15T, was isolated from reclaimed grassland soil from Biratnagar, Morang, Nepal. This strain was non-spore-forming, catalase-negative and oxidase-positive. It was able to grow at 10–45 °C, pH 6.5–9.5 and 0–1.5 % (w/v) NaCl concentration. This strain was taxonomically characterized by a polyphasic approach. Based on the results of 16S rRNA gene sequence analysis, K-1-15T formed a distinct lineage within the family Oxalobacteraceae and was most closely related to members of the genera Herbaspirillum (96.99–95.34 % sequence similarity), Noviherbaspirillum (96.72–95.45 % sequence similarity) and Paraherbaspirillum (95.85 % sequence similarity). The only respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major fatty acids of K-1-15T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C10 : 0 3-OH, and iso-C16 : 0. The genomic DNA G+C content of this novel strain was 65.2 mol %. The DNA–DNA relatedness between K-1-15T and Herbaspirillum massiliense DSM 25712T and Noviherbaspirillum soli LMG 26149T were 18.3 and 13.7 % repectively. On the basis of the results of morphological, physiological, chemotaxonomic and phylogenetic analyses, K-1-15T represents a novel species of the genus Noviherbaspirillum in the family Oxalobacteraceae , for which the name Noviherbaspirillum agri sp. nov. is proposed. The type strain is K-1-15T (=KEMB 9005-422T=KACC 18909T=JCM 31463T). Based on new data obtained in this study, we also propose the reclassification of Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov. (type strain JC206T=CSUR P159T=DSM 25712T).
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Proposal of Rhodoplanes tepidamans sp. nov. to accommodate the thermotolerant phototrophic bacterium previously referred to as 'Rhodoplanes (Rhodopseudomonas) cryptolactis'
More LessPreviously we proposed the reclassification of a thermotolerant phototrophic bacterium, ‘ Rhodopseudomonas cryptolactis’ Stadtwald-Demchick et al. 1990, as ‘ Rhodoplanes cryptolactis’ nom. rev., comb. nov. with strain DSM 9987T (ATCC 49414T) as the type strain. However, while both the names ‘ Rhodopseudomonas cryptolactis’ and ‘ Rhodoplanes cryptolactis’ have not been validated, strain ATCC 49414T is no longer available from the culture collection. This situation indicates that the taxonomic status of the bacterium with both the names to be validated has been lost. In this study, we re-examined the taxonomic characteristics of strain DSM 9987T (TUT3520T as our own collection number) compared with those of six species of the genus Rhodoplanes with validly published names. The results of 16S rRNA gene sequence comparisons indicated that TUT3520T had a 99.0 % level of similarity to the type strains of Rhodoplanes oryzae and Rhodoplanes elegans as its closest relatives and 98.9–96.2 % similarities to other species of the genus Rhodoplanes . Genomic DNA–DNA similarities between TUT3520T and the type strains of the species of the genus Rhodoplanes were less than 50 %. Results of phenotypic testing indicated that TUT3520T could be differentiated from any species of the genus Rhodoplanes by a combination of in vivo absorption spectra, growth temperature, vitamin requirements, carbon nutrition and some other characteristics. Thus, we propose Rhodoplanes tepidamans sp. nov. to accommodate the bacterium previously referred to as ‘ Rhodoplanes ( Rhodopseudomonas ) cryptolactis’. The type strain is strain TUT3520T (=DSM 9987T=NBRC 104267T).
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Halomonas alkalicola sp. nov., isolated from a household product plant
A Gram-stain-negative, alkaliphilic and moderately halophilic bacterium, designated 56-L4-10aEnT, was isolated from a household product plant in China. Cells of the novel isolate were rod-shaped, non-spore-forming and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 56-L4-10aEnT belongs to the genus Halomonas , with the six closest neighbours being Halomonas mongoliensis Z-7009T (97.59 % 16S rRNA gene sequence similarity), Halomonas ventosae Al12T (97.35 %), Halomonas campaniensis 5AGT (97.22 %), Halomonas alimentaria YKJ-16T (97.22 %), Halomonas shengliensis SL014B-85T (97.12 %) and Halomonas fontilapidosi 5CRT (97.09 %). The main polar lipids of strain 56-L4-10aEnT contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-9, with Q-8 as a minor component. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0. Strain 56-L4-10aEnT was clearly distinguished from the type strains mentioned above through phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics comparisons. It is evident from the genotypic and phenotypic data that strain 56-L4-10aEnTcould be classified as a representative of a novel species of the genus Halomonas , for which the name Halomonas alkalicola sp. nov. is proposed. The type strain is 56-L4-10aEnT (=CICC 11012sT=DSM 103354T).
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Pseudaminobacter manganicus sp. nov., isolated from sludge of a manganese mine
More LessA Gram-staining-negative, aerobic, non-motile, capsule-forming and rod-shaped bacterium, designated JH-7T, was isolated from sludge of a manganese mine. The 16S rRNA gene sequence of JH-7T showed highest similarities to those of Pseudaminobacter salicylatoxidans BN12T (97.4 %), Mesorhizobiumthiogangeticum SJTT (97.0 %) and Pseudaminobacter defluvii THI 051T (96.5 %). Phylogenetic trees clustered JH-7T together with P. salicylatoxidans BN12T and P. defluvii THI 051T. The DNA–DNA hybridization values between JH-7T and P. salicylatoxidans DSM 6986T and between JH-7T and M . thiogangeticum DSM 17097T were 34.8 and 20.1 %, respectively. The major fatty acids of JH-7T (>10 %) were C18 : 1ω7c, C19 : 0cyclo ω8c and C16 : 0. The genomic DNA G+C content was 61.6 mol%. The polyamines of JH-7T were sym-homospermidine (83 %) and putrescine (17 %), and the respiratory quinone was ubiquinone-10. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and two unidentified lipids. Compared with the members of the genera Pseudaminobacter and Mesorhizobium , JH-7T showed some unique physiological and biochemical characters, such as being negative for H2S production, hydrolysis of Tween 40 and Tween 60, esterase lipase (C8) activity and assimilation of d-ribose and positive for acid production from d-galactose and assimilation of d-fructose. On the basis of the results of the polyphasic taxonomic analysis, JH-7T was considered to represent a novel species of the genus Pseudaminobacter , for which the name Pseudaminobacter manganicus sp. nov. is proposed. The type strain is JH-7T (=KCTC 52258T=CCTCC AB 2016107T).
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Xenorhabdus thuongxuanensis sp. nov. and Xenorhabdus eapokensis sp. nov., isolated from Steinernema species
More LessTwo slightly yellowish-pigmented, oxidase-negative, rod-shaped and Gram-stain-negative bacterial strains (30TX1T and DL20T), isolated from Steinernema sangi and Steinernema eapokense, respectively, during soil sampling in Vietnam were studied using a polyphasic taxonomic approach. Strain 30TX1T showed highest 16S rRNA gene sequence similarity to the type strain of Xenorhabdus ehlersii (98.9 %) and strain DL20T to that of Xenorhabdus ishibashii (98.7 %). Sequence similarities to all other Xenorhabdus species were lower (<98.4 %). The two strains shared 98 % 16S rRNA gene sequence similarity. Multilocus sequence analysis (MLSA) based on concatenated partial recA, dnaN, gltX, gyrB and infB gene sequences showed a clear distinction of strains 30TX1T and DL20T among each other and to the closest related type strains. DNA–DNA hybridizations between strain DL20T and the type strain of X. ishibashii resulted in a relatedness value of 53 %. Genome-to-genome-based comparisons gave average nucleotide identities of 93.6 % (reciprocal 93.5 %) for strain 30TX1T and X. ehlersii DSM 16337T, of 92.8 % (reciprocal 93 %) for strain DL20T and X. ishibashii DSM 22670Tand of 93.0 % (reciprocal 93.2 %) for the two novel strains. The fatty acid profile of the strains consisted of the major fatty acids C14 : 0, C16 : 0, C17 : 0 cyclo, C16 : 1ω7c and/or iso-C15 : 0 2-OH, and C18 : 1 ω7c. Genome-to-genome comparison and MLSA results together with the differential biochemical and chemotaxonomic properties showed that strains 30TX1T and DL20T represent novel Xenorhabdus species, for which the names Xenorhabdus thuongxuanensis sp. nov. (type strain 30TX1T=CCM 8727T=LMG 29916T) and Xenorhabdus eapokensis sp. nov. (type strain DL20T=CCM 8728T=LMG 29917T) are proposed, respectively.
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Neisseria arctica sp. nov., isolated from nonviable eggs of greater white-fronted geese (Anser albifrons) in Arctic Alaska
During the summers of 2013 and 2014, isolates of a novel Gram-stain-negative coccus in the genus Neisseria were obtained from the contents of nonviable greater white-fronted goose (Anseralbifrons) eggs on the Arctic Coastal Plain of Alaska. We used a polyphasic approach to determine whether these isolates represent a novel species. 16S rRNA gene sequences, 23S rRNA gene sequences, and chaperonin 60 gene sequences suggested that these Alaskan isolates are members of a distinct species that is most closely related to Neisseria canis , N eisseria animaloris and N eisseria shayeganii . Analysis of the rplF gene additionally showed that the isolates are unique and most closely related to N eisseria weaveri . Average nucleotide identity of the whole genome sequence of the type strain was between 71.5 and 74.6 % compared to close relatives, further supporting designation as a novel species. Fatty acid methyl ester analysis showed a predominance of C14 : 0, C16 : 0 and C16 : 1ω7c fatty acids. Finally, biochemical characteristics distinguished the isolates from other species of the genus Neisseria . On the basis of these combined data, the isolates are proposed to represent a novel species of the genus Neisseria , with the name Neisseria arctica sp. nov. The type strain is KH1503T (=ATCC TSD-57T=DSM 103136T).
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Tibeticola sediminis gen. nov., sp. nov., a thermophilic bacterium isolated from a hot spring
Two closely related thermophilic bacterial strains, designated YIM 73013T and YIM 73008, were isolated from a sediment sample collected from a hot spring in Tibet, western Tibet province, China. The taxonomic positions of the two isolates were investigated using a polyphasic approach. The novel isolates were Gram-stain-negative, aerobic, short-rod-shaped and motile by means of a polar flagellum. They were oxidase- and catalase-positive and were able to grow at 30–55 °C (optimum, 37–45 °C), at pH 6.0–8.0 (optimum, pH 7.0) and with NaCl tolerance up to 1 % (w/v). Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 73013T and YIM 73008 formed a distinct lineage with respect to closely related genera in the family Comamonadaceae and shared highest 16S rRNA gene sequences similarities with Acidovorax caeni R-24608T (96.3 and 96.4 %, respectively). The respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids observed were C17 : 1ω6c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The genomic DNA G+C contents of strains YIM 73013T and YIM 73008 were 68.7 and 68.3 mol%, respectively. Based on the morphological, phylogenetic and chemotaxonomic results, the two isolates represent a novel species in a new genus, for which the name Tibeticola sediminis gen. nov., sp. nov. is proposed. The type strain of Tibeticola sediminis is YIM 73013T (=DSM 101684T=KCTC 42873T).
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Hyphobacterium vulgare gen. nov., sp. nov., a novel alphaproteobacterium isolated from seawater
A Gram-stain-negative, aerobic, non-spore-forming, non-motile, oval to rod-shaped, prosthecate bacterium, designated strain WM6T, was isolated from a seawater sample collected from the South China Sea at a depth of 150 m and subjected to a polyphasic taxonomic investigation. Cells of strain WM6T were approximately 0.5–0.6 µm in width and 0.8–1.2 µm in length, and colonies were smooth, circular, convex and whitish yellow. Strain WM6T was found to grow at 10–45 °C (optimum, 30 °C), at pH 6.5–9.0 (optimum, pH 7.5–8.5) and with 1–6 % (w/v) NaCl (optimum, 1–2 %). Chemotaxonomic analysis showed the predominant respiratory quinone and the major fatty acid of strains WM6T were ubiquinone-10 and C18 : 1ω7c, respectively. The polar lipids of strain WM6T were phosphatidylglycerol, glucuronopyranosyldiglyceride, monoglycosyldiglyceride, sulfo-quinovosyl diacylglycerol, seven unknown glycolipids and two unknown lipids. The DNA G+C content of strain WM6T was determined to be 59.8 mol% by HPLC. 16S rRNA gene sequence similarities showed that strain WM6T was related most closely to the genus Maricaulis with a similarity range from 92.3 to 93.8 %. Phylogenetic trees reconstructed with the neighbour-joining and maximum-likelihood methods using mega and maximum-likelihood methods using arb showed that strain WM6T constituted a separated branch in the family Hyphomonadaceae . Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain WM6T is clearly distinct from any validly published genus. On the basis of these features, strain WM6T represents a novel species of a new genus with the name Hyphobacterium vulgare gen. nov., sp. nov. The type strain of Hyphobacterium vulgare is WM6T (=MCCC 1K03222T=KCTC 52487T).
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Rhodanobacter humi sp. nov., an acid-tolerant and alkalitolerant gammaproteobacterium isolated from forest soil
More LessA novel acid-tolerant and alkalitolerant gammaproteobacterium designated strain RS22T was isolated from Kyonggi University forest soil. Cells were aerobic, Gram-stain-negative, catalase- and oxidase-positive, non-motile, non-spore-forming, rod-shaped and yellow-pigmented. Flexirubin-type pigments were absent. Strain RS22T was able to assimilate lactic acid, l-proline and 3-hydroxybenzoic acid; it tolerated 4 % (w/v) NaCl, fermented glucose and was able to grow at pH 11.0. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RS22T formed a lineage within the class Gammaproteobacteria of the phylum Proteobacteria that was distinct from various species of the genus Rhodanobacter , including Rhodanobacter denitrificans 2APBS1T (97.7 % sequence similarity), Rhodanobacter thiooxydans LCS2T (97.5 %), Rhodanobacter terrae GP18-1T (97.5 %) and Rhodanobacter soli DCY45T (97.2 %). The predominant respiratory quinone was Q-8. The major polar lipids of strain RS22T were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0, iso-C17 : 0, iso-C16 : 0, anteiso-C15 : 0 and C16 : 0. The DNA G+C content of strain RS22T was 63.2 mol%. DNA–DNA hybridization between strain RS22T and other closest members of the genus Rhodanobacter revealed relatedness values from 28 to 51 %. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strain RS22T represents a novel species of the genus Rhodanobacter , for which the name Rhodanobacter humi sp. nov. is proposed. The type strain is RS22T (=KEMB 9005-480T=KACC 19048T=NBRC 112473T).
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Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka
A facultatively anaerobic, Gram-stain-negative, rod-shaped, nitrogen-fixing, endophytic bacterial strain designated MP23T was isolated from the roots of Phragmites karka growing in Chilika Lagoon, Odisha, India. Strain MP23T was slightly halophilic, and the optimal NaCl concentration and temperature for growth were 1 % and 30 °C, respectively. On the basis of 16S rRNA gene sequence similarities, strain MP23T was affiliated to the family Enterobacteriaceae and most closely related to Mangrovibacter yixingensis KCTC 42181T and Mangrovibacter plantisponsor DSM 19579T with 99.71 % similarity, followed by Salmonella enterica subsp. salamae DSM 9220T (97.22 %), Cronobacter condimenti LMG 26250T (97.14 %) and Salmonella enterica subsp. diarizonae DSM 14847T (97 %). Sequence analysis of 16S rRNA, hsp60, gyrB and rpoB genes showed that strain MP23T formed a phylogenetic cluster with M. yixingensis KCTC 42181T and M. plantisponsor DSM 19579T indicating that it belongs to the genus Mangrovibacter . The major cellular fatty acids were C16 : 0, C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C14 : 0, C14 : 0 3-OH and/or iso-C16 : 1 I and C17 : 0 cyclo. Polar lipids of strain MP23T consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 50.3 mol%. Based on experimental DNA–DNA hybridization values and average nucleotide identity derived from in silico comparison of whole-genome sequences, strain MP23T could be distinguished from its closest neighbours. We therefore conclude that strain MP23T represents a novel species of the genus Mangrovibacter for which the name Mangrovibacter phragmitis sp. nov. is proposed. The type strain is MP23T (=DSM 100250T=KCTC 42580T).
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Rouxiella badensis sp. nov. and Rouxiella silvae sp. nov. isolated from peat bog soil and emendation description of the genus Rouxiella
Four bacterial strains isolated from peat bog soil or swampy meadow in Baden-Württemberg (Germany) and found to have rrs sequences close to that of Rouxiella chamberiensis were compared to this species by using multi-locus sequence analysis and phenotypic tests. The four strains constituted two discrete groups (referred to as the Baden and the Silva groups) belonging to the genus Rouxiella . These groups differed in their ability to grow at 37 °C, reduce nitrate into nitrite, and to produce acid from several carbohydrates. Two novel species are, therefore, proposed: Rouxiella badensis sp. nov. for the Baden group (type strain, 323T=CIP 111153T=DSM 100043T) and Rouxiella silvae for the Silva group (type strain, 213T=CIP 111154T=DSM 103735T). The definition of the genus Rouxiella has also been emended in order to take these two novel species into account.
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Nioella sediminis sp. nov., isolated from surface sediment and emended description of the genus Nioella
More LessA bacterial strain, designated JS7-11T, was isolated from the surface sediment of the Jiulong River and characterized using a polyphasic taxonomic approach. Cells of JS7-11T were Gram-staining-negative, non-motile and short-rod-shaped. Growth was observed at 10–40 °C (optimum 25–30 °C), at pH 6–8 (optimum 7) and in 1–12 % NaCl (optimum 3–4 %, w/v). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that JS7-11T and Nioella nitratireducens SSW136T formed an independent cluster, sharing 97.9 % similarity between the two strains, and less than 96.0 % similarities with other type strains of members of the family Rhodobacteraceae . The major fatty acids were summed feature 8 and C16 : 0. The quinone was identified as Q-10. The polar lipids comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids. The DNA G+C content was 63.4 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between JS7-11T and N. nitratireducens SSW136T were 22.1 and 79.4 %, respectively. The results of phenotypic, phylogenetic and chemotaxonomic analyses clearly indicated that JS7-11T represents a novel species within the genus Nioella , for which the name Nioellasediminis sp. nov. is proposed. The type strain of the novel species is JS7-11T (=MCCC 1A00710T=KCTC 42144T).
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Psychromonas aquatilis sp. nov., isolated from seawater samples obtained in the Chilean Antarctica
A slightly beige-white pigmented, Gram-staining-negative, rod-shaped bacterium, strain M1A1T, was isolated from seawater samples obtained in Fildes Bay, Antarctica (62°12′ S 58° 57′ W). Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the isolate shared 98.4 % 16S rRNA gene sequence identity to the type strain of Psychromonas arctica , but less than 97 % 16S rRNA gene sequence similarities to all other species of the genus Psychromonas . DNA–DNA hybridization with Psychromonas arctica DSM 14288T showed low values (21 %, reciprocal 27 %). The main cellular fatty acid of strain M1A1T was summed feature 3 fatty acids (C16 : 1ω7c/C16 : 1ω8c), followed by C16 : 0. Based on phylogenetic, chemotaxonomic, genomic and phenotypic analyses, we propose a novel species of the genus Psychromonas with the name Psychromonas aquatilis sp. nov. and the strain M1A1T (=CIP 111183T=CCM 8710T=LMG 29766T) as type strain.
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Aquaspirillum soli sp. nov., isolated from a soil sample
A Gram-stain-negative, smooth, opaque, white-pigmented, helical-shaped, catalase- and oxidase-positive bacterium that was motile by means of bipolar tufts of flagella and grew under microaerophilic conditions, was isolated from a soil sample of a reed pond in Shangqiu, Henan province, PR China. The strain, designated THG-SQE6T, grows well at 25–42 °C, pH 6.5–7.5 and in the presence of 0–1 % (w/v) NaCl. hylogenetic analysis based on 16S rRNA gene sequences showed that strain THG-SQE6T was most closely related to Aquaspirillum serpens IAM 13944T (97.23 % 16S rRNA gene sequence similarity). The DNA G+C content of strain THG-SQE6T was 53.10 mol%. In DNA–DNA hybridization experiments, the DNA–DNA relatedness between strain THG-SQE6T and its closest phylogenetic neighbour was below 62.6 %. The predominant isoprenoid quinone detected in strain THG-SQE6T was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. The major fatty acids were identified as C12 : 0 3-OH, C16 : 0, C18 : 0, summed feature 3 and summed feature 8. These data support the affiliation of strain THG-SQE6T to the genus Aquaspirillum . Based on findings from the phenotypic, genotypic and phylogenetic characterization of strain THG-SQE6T, a novel species of the genus Aquaspirillum named Aquaspirillum soli sp. nov. is proposed. The type strain is THG-SQE6T (=KACC 18846T=CCTCC AB 2016081T).
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Arcobacter lekithochrous sp. nov., isolated from a molluscan hatchery
More LessFour bacterial strains, LFT 1.7T, LT2C 2.5, LT4C 2.8 and TM 4.6, were isolated from great scallop (Pecten maximus) larvae and tank seawater in a Norwegian hatchery and characterized by a polyphasic approach including determination of phenotypic, chemotaxonomic and genomic traits. All were Gram-stain-negative, motile rods, oxidase- and catalase-positive and required sea salts for growth. Major fatty acids present were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), summed feature 8 (C18 : 1ω7c or C18 : 1ω6c), C16 : 0, C14 : 0, summed feature 2 (C14 : 0 3-OH/iso-C16 : 1 I), C12 : 0 3-OH and C12 : 0. Strain LFT 1.7T contained menaquinone MK-6 as the sole respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that all strains formed a distinct lineage within the genus Arcobacter with a low similarity to known species (94.77–95.32 %). The DNA G+C content was 28.7 mol%. Results of in silico DNA–DNA hybridization and average nucleotide identity confirmed that the isolates constitute a novel species of Arcobacter , for which the name Arcobacter lekithochrous sp. nov. is proposed. The type strain is LFT 1.7T (=CECT 8942T=DSM 100870T).
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Sulfuritortus calidifontis gen. nov., sp. nov., a sulfur oxidizer isolated from a hot spring microbial mat
More LessA novel sulfur-oxidizing autotrophic bacterium, strain J1AT was isolated from a hot spring microbial mat. The cells were Gram-stain-negative, catalase-negative and oxidase-positive. As sole electron donor for chemolithoautotrophic growth, strain J1AT utilized sulfide, thiosulfate, elemental sulfur, and tetrathionate. The G+C content of the genomic DNA was 66 mol%. Major cellular fatty acids (>40 % of total) were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The predominant quinone was Q-8. Phylogenetic analysis of the 16S rRNA gene indicated that strain J1AT is a relative of species of the genus Thiobacillus , but shares only 93 % or lower sequence similarities with them. On the basis of its properties, strain J1AT represents a novel species of a new genus, for which the name Sulfuritortus calidifontis gen. nov., sp. nov. is proposed. The type strain of the type species is J1AT (=DSM 103923T=NBRC 112474T).
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Rhodanobacter rhizosphaerae sp. nov., isolated from soil of ginseng rhizosphere
More LessA Gram-stain-negative, aerobic, non-motile, non-spore-forming, yellow and rod-shaped bacterium, designated strain CR164T, was isolated from the rhizosphere soil of a ginseng field at Geumsan in Korea. CR164T grew at between 15 and 37 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.0) and at salinities of 0–1.0 % (w/v) NaCl, growing optimally in the absence of NaCl. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that CR164T represents a member of the genus Rhodanobacter , showing the highest sequence similarity to Rhodanobacter caeni MJ01T (98.5 %), Rhodanobacter ginsenosidimutans Gsoil 3054T (98.4 %), Rhodanobacter thiooxydans LCS2T (98.3 %), Rhodanobacter lindaniclasticus RP5557T (98.1 %), Rhodanobacter denitrificans 2APBS1T (98.0 %), Rhodanobacter fulvus Jip2T (97.6 %), Rhodanobacter soli DCY45T (97.3 %) and ‘ Rhodanobacter xiangquanii’ BJQ-6 (97.0 %). The major fatty acids were iso-C17 : 1ω9c (21.8 %), iso-C15 : 0 (12.1 %), iso-C11 : 0 (11.9 %) and iso-C16 : 0 (11.1 %). The predominant ubiquinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The G+C content of the genomic DNA was 62.3 mol%. DNA–DNA relatedness between CR164T and the type strains of eight other species of the genus ranged from 51 to 9 %. On the basis of the polyphasic analysis, CR164T represents a novel species of the genus Rhodanobacter , for which the name Rhodanobacter rhizosphaerae sp. nov. is proposed. The type strain is CR164T (=KACC 18699T=NBRC 111845T).
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Vitiosangium cumulatum gen. nov., sp. nov. and Vitiosangium subalbum sp. nov., soil myxobacteria, and emended descriptions of the genera Archangium and Angiococcus, and of the family Cystobacteraceae
Bacterial strains MCy10943T and MCy10944T were isolated in 2014 from dried Nepalese soil samples collected in 2013 from Phukot, Kalikot, Western Nepal, and Godawari, Lalitpur, Central Nepal. The novel organisms showed typical myxobacterial growth characteristics, which include swarming colony and fruiting body formation on solid surfaces, and a predatory ability to lyse micro-organisms. The strains were aerobic, mesophilic, chemoheterotrophic and showed resistance to various antibiotics. The major cellular fatty acids common to both organisms were C17 : 0 2-OH, iso-C15 : 0, C16 : 1 and iso-C17 : 0. The G+C content of the genomic DNA was 72–75 mol%. Phylogenetic analysis showed that the strains belong to the family Cystobacteraceae , suborder Cystobacterineae, order Myxococcales . The 16S rRNA gene sequences of both strains showed 97–98 % similarity to Archangium gephyra DSM 2261T and Cystobacter violaceus DSM 14727T, and 96.7–97 % to Cystobacter fuscus DSM 2262T and Angiococcus disciformis DSM 52716T. Polyphasic taxonomic characterization suggested that strains MCy10943T and MCy10944T represent two distinct species of a new genus, for which the names Vitiosangium cumulatum gen. nov., sp. nov. and Vitiosangium subalbum sp. nov. are proposed. The type strain of Vitiosangium cumulatum is MCy10943T (=DSM 102952T=NCCB 100600T) while that for Vitiosangium subalbum is MCy10944T (=DSM 102953T=NCCB 100601T). In addition, emended descriptions of the genera Archangium and Angiococcus , and of the family Cystobacteraceae are provided.
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Parahaliea aestuarii sp. nov., isolated from the Asan Bay estuary
More LessA Gram-stain-negative, strictly aerobic and moderate halotolerant bacterial strain, designated S2-26T, was isolated from sediment of the Asan Bay estuary in South Korea. Cells were motile rods with two polar flagella showing oxidase and catalase activities. Growth of S2-26T was observed at 15–45 °C (optimum, 25 °C) and pH 5.5–10.0 (optimum, pH 7.0–8.5) and in the presence of 0–8.0 % (w/v) NaCl (optimum, 2.0 %). S2-26T contained C17 : 1ω8c, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (comprising C16:1 ω7c/C16:1 ω6c) and C17 : 0 as the major fatty acids and ubiquinone-8 as the sole isoprenoid quinone. The polar lipids of S2-26T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid, an unknown aminolipid, an unknown glycolipid and an unknown lipid. The G+C content of the genomic DNA was 62.2 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that S2-26T formed a tight phylogenetic lineage with Parahaliea mediterranea 7SM29T with a 100 % bootstrap value. S2-26T was most closely related to the type strain of Parahaliea mediterranea , with a 97.8 % 16S rRNA gene sequence similarity, and its DNA–DNA relatedness level was 45.2±2.2 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that S2-26T represents a novel species of the genus Parahaliea, for which the name Parahaliea aestuarii sp. nov. is proposed. The type strain is S2-26T (=KACC 18801T=JCM 31547T).
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Microbulbifer aestuariivivens sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-motile, aerobic and coccoid or rod-shaped bacterium, designated GHTF-23T, was isolated from a tidal flat of the South Sea, South Korea. GHTF-23T grew optimally at 37 °C, at pH 6.5–7.5 and in the presence of 2.0 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, GHTF-23T fell within the clade comprising the type strains of species of the genus Microbulbifer . GHTF-23T exhibited 16S rRNA gene sequence similarities of 97.1–97.9 % to the type strains of Microbulbifer salipaludis , Microbulbifer hydrolyticus , Microbulbifer elongatus , Microbulbifer mangrovi and Microbulbifer yueqingensis and 94.5–96.8 % to the type strains of the other species of the genus Microbulbifer . GHTF-23T contained Q-8 as the predominant ubiquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids detected in GHTF-23T and M. hydrolyticus DSM 11525T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified glycolipid. The DNA G+C content of GHTF-23T was 60.1 mol% and its mean DNA–DNA relatedness values with the type strains of M. salipaludis , M. hydrolyticus , M. elongatus , M. mangrovi and M. yueqingensis were 11–31 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that GHTF-23T is separated from species of the genus Microbulbifer with validly published names. On the basis of the data presented, GHTF-23T is considered to represent a novel species of the genus Microbulbifer , for which the name Microbulbifer aestuariivivenssp. nov. is proposed. The type strain is GHTF-23T (=KCTC 52569T=NBRC 112533T).
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An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomicrospira
Thiomicrospira (Tms) species are small sulfur-oxidizing chemolithoautotrophic members of the Gammaproteobacteria . Whilst the type species Tms. pelophila and closely related Tms. thyasirae exhibit canonical spiral morphology under sub-optimal growth conditions, most species are vibrios or rods. The 16S rRNA gene diversity is vast, with identities as low as 91.6 % for Tms. pelophila versus Tms. frisia, for example. Thiomicrospira was examined with closely related genera Hydrogenovibrio and Thioalkalimicrobium and, to rationalize organisms on the basis of the 16S rRNA gene phylogeny, physiology and morphology, we reclassify Tms. kuenenii, Tms. crunogena, Tms. thermophila and Tms. halophila to Hydrogenovibrio kuenenii comb. nov., H. crunogenus corrig. comb. nov., H. thermophilus corrig. comb. nov. and H. halophilus corrig. comb. nov. We reclassify Tms. frisia, Tms. arctica, Tms. psychrophila and Tms. chilensis to Thiomicrorhabdus (Tmr) gen. nov., as Tmr. frisia comb. nov., Tmr. arctica comb. nov., Tmr. psychrophila comb. nov. and Tmr. chilensis comb. nov. – the type species of Thiomicrorhabdus is Tmr. frisia. We demonstrate that Thioalkalimicrobium species fall within the genus Thiomicrospira sensu stricto, thus reclassifying them as Tms. aerophila corrig. comb. nov., Tms. microaerophila corrig. comb. nov., Tms. cyclica corrig. comb. nov. and Tms. sibirica corrig. comb. nov. We provide emended descriptions of the genera Thiomicrospira and Hydrogenovibrio and of Tms. thyasirae.
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Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the ‘Proteobacteria’, and four new families within the orders Nitrosomonadales and Rhodocyclales
More LessThe genus Thiobacillus comprises four species with validly published names, of which Thiobacillus aquaesulis DSM 4255T (=ATCC 43788T) is the only species that can grow heterotrophically or mixotrophically – the rest being obligate autotrophs – and has a significant metabolic difference in not producing tetrathionate during the oxidation of thiosulfate during autotrophic growth. On the basis of this and differential chemotaxonomic properties and a 16S rRNA gene sequence similarity of 93.4 % to the type species Thiobacillus thioparus DSM 505T, we propose that it is moved to a novel genus, Annwoodia gen. nov., for which the type species is Annwoodia aquaesulis gen. nov., comb. nov. We confirm that the position of the genus Thiobacillus in the Betaproteobacteria falls within the Nitrosomonadales rather than the Hydrogenophilales as previously proposed. Within the Nitrosomonadales we propose the circumscription of genera to form the Thiobacilliaceae fam. nov. and the Sterolibacteriaceae fam. nov. We propose the merging of the family Methylophilaceae into the Nitrosomonadales , and that the Sulfuricellaceae be merged into the Gallionellaceae , leaving the orders Methylophilales and Sulfuricellales defunct. In the Rhodocyclales we propose the Azonexaceae fam. nov. and the Zoogloeaceae fam. nov. We also reject the Hydrogenophilales from the Betaproteobacteria on the basis of a very low 16S rRNA gene sequence similarity with the class-proper as well as physiological properties, forming the Hydrogenophilalia class. nov. in the ‘ Proteobacteria ’. We provide emended descriptions of Thiobacillus , Hydrogenophilales , Hydrogenophilaceae , Nitrosomonadales , Gallionellaceae , Rhodocyclaceae and the Betaproteobacteria .
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Dyella lipolytica sp. nov., a lipolytic bacterium isolated from lower subtropical forest soil
More LessA Gram-stain-negative, aerobic, yellow-pigmented, non-spore-forming, non-motile, rod-shaped bacterium, designated strain DHOB07T, was isolated from a soil sample collected from the lower subtropical forest of the Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10′ N 112° 31′ E). Strain DHOB07T grew at 10–37 °C, pH 4–7 and 0–0.5 % (w/v) NaCl, with an optimum at 28 °C, pH 5–5.5 and 0% (w/v) NaCl on R2A medium. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a clade with Dyella jejuensis JP1T, Dyella nitratireducens DHG59T, Dyella koreensis BB4T, Dyella marensis CS5-B2Tand Dyellasoli JS12-10T, with sequence similarities of 98.9, 98.0, 97.9, 97.9 and 97.8 %, respectively. Multilocus sequence analysis based on the concatenated sequences of partial housekeeping genes gyrB, lepA and recA confirmed that strain DHOB07T belongs to thegenus Dyella but is distinct from all currently known species of the genus Dyella . The G+C content of the genomic DNA was 58.2 mol%. The DNA–DNA relatedness value between strain DHOB07T and D. jejuensis JP1T was 41.8 %. Iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1ω9c were the major fatty acids, and ubiquinone-8 was the only respiratory quinone detected, all of which supported the affiliation of strain DHOB07T to the genus Dyella . On the basis of the polyphasic characterization results presented above, strain DHOB07T represents a novel species of the genus Dyella , for which the name Dyella lipolytica sp. nov. is proposed. The type strain is DHOB07T (=NBRC 111473T=KCTC 52132T).
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- Eukaryotic Micro-organisms
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Starmerella anomalae f.a., sp. nov., Starmerella asiatica f.a., sp. nov., Starmerella henanensis f.a., sp. nov. and Starmerella scarabaei f.a., sp. nov., four yeast species isolated from scarab beetles
More LessEleven yeast strains representing four novel species of the genus Starmerella were isolated from scarabs beetles collected in Nanyang, Henan Province, Central China. Phylogenetic analysis using combined sequences of the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions placed all the novel species in a clade distinct from the other known species in the clade representing the members of the genus Starmerella. These novel species differed from each other or their closest known species by more than 4.9 % nucleotide substitutions in the D1/D2 domains and by more than 9.1 % nucleotide substitutions in the ITS regions. The four novel species can also be separated from their closest relatives in terms of physiological characteristics. No asci or signs of conjugation were found in the novel species on the most common sporulation media. The novel species are designated as Starmerella anomalae f.a., sp. nov. (type strain NYNU 157145T=CICC 33094T=CBS 14178T), Starmerella asiatica f.a., sp. nov. (type strain NYNU 15782T=CICC 33089T=CBS 14173T), Starmerella henanensis f.a., sp. nov. (type strain NYNU 15766T=CICC 33088T=CBS 14172T) and Starmerella scarabaei f.a., sp. nov. (type strain NYNU 15821T=CICC 33090T=CBS 14174T).
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- Evolution, Phylogeny and Biodiversity
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Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies
More LessThe recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.
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- ICSP Matters
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‘Localimania’ revisited: guidelines for the formation of specific epithets for names of prokaryotes based on names of institutions or their acronyms. A proposal for emendation of Appendix 9 to the International Code of Nomenclature of Prokaryotes
More LessWe here present a survey of the increasing use of the -ensis (-ense) ending for the formation of specific epithets that do not refer to geographical locations but to names of research institutes or their acronyms. To our opinion the use of the -ensis (-ense) ending must be discouraged for such purposes, the formation of nouns in the genitive case being preferred for the formation of such arbitrary epithets. Emendation of Appendix 9 – Orthography to the International Code of Nomenclature of Prokaryotes is proposed with guidelines for the formation of such names.
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- Corrigendum
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)