- Volume 67, Issue 8, 2017
Volume 67, Issue 8, 2017
- New Taxa
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- Firmicutes and Related Organisms
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Lactobacillus caviae sp. nov., an obligately heterofermentative bacterium isolated from the oral cavity of a guinea pig (Cavia aperea f. porcellus)
A Gram-stain-positive, facultatively anaerobic, and catalase- and oxidase-negative bacterial strain designated MOZM2T, having 98.4 % 16S rRNA gene sequence identity with Lactobacillus reuteri DSM 20016T, was isolated from a swab of the oral cavity of a home-bred guinea pig. Comparative analyses based on the hsp60, pheS and tuf genes confirmed L. reuteri as its closest relative species, with calculated sequence similarities of 92.8, 88.8 and 96.9 %, respectively. DNA–DNA hybridisation revealed a 42 % degree of genetic similarity between the novel strain and L. reuteri DSM 20016T. Strain MOZM2T degrades carbohydrates via the 6-phosphogluconate/phosphoketolase pathway, evidenced by its production of gas from glucose and the end products of hexose catabolism. Comparative analysis of the cellular fatty acid profiles determined significant differences between MOZM2T and L. reuteri DSM 20016T in their proportions of C8 : 0, C14 : 1, C17 : 0, C18 : 2ω6t and C20 : 0 fatty acids. Results of genotypic analyses also demonstrated differences between these two strains. They also differed in DNA G+C content, and some biochemical and physiological characteristics. We therefore believe that the examined bacterial isolate should be considered as a new taxon within the group of obligately heterofermentative lactobacilli. The species name Lactobacillus caviae sp. nov. is proposed, of which the type strain is MOZM2T (=CCM 8609T=DSM 100239T=LMG 28780T).
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- Other Bacteria
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Dictyobacter aurantiacus gen. nov., sp. nov., a member of the family Ktedonobacteraceae, isolated from soil, and emended description of the genus Thermosporothrix
A mesophilic, Gram-stain-positive, spore-forming bacterium that formed branched mycelia was isolated from paddy soil in Gunung Salak (Mount Salak), West Java, Indonesia. This strain, designated S-27T, grew at temperatures between 20 and 37 °C; the optimum growth temperature was 25 to 30 °C, and no growth was observed at 15 or 45 °C. The pH range for growth was pH 3.5 to 8.6; the optimum pH was 6.0, and no growth was observed at pH 3.0 or 9.2. Strain S-27T was able to hydrolyse polysaccharides such as starch, cellulose and xylan. The G+C content of the DNA of strain S-27T was 55.7 mol%. The major fatty acids were iso-C17 : 0 and C16 : 1 2-OH, and the major menaquinone was MK-9 (H2). The cell wall of strain S-27T contained d-glutamic acid, glycine, l-alanine, d-alanine, l-ornithine and β-alanine in a molar ratio of 1.0 : 1.6 : 1.4 : 0.6 : 0.9 : 1.1. The polar lipids consisted of phosphatidylglycerol, phosphatidylinositol and two glycolipids. The major cell-wall sugar was arabinose. Detailed phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S-27T belongs to the order Ktedonobacterales and is most closely related to Ktedonobacter racemifer SOSP1-21T (89.6 % sequence identity). On the basis of its chemotaxonomic and phenotypic features and phylogenetic position, we concluded that strain S-27T represents a novel genus and species, for which we propose the name Dictyobacter aurantiacus gen. nov., sp. nov. The type strain of Dictyobacter aurantiacus is strain S-27T (=NBRC 109595T=InaCC B312T). Emendation of the description of the genus Thermosporothrix is also provided.
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Meiothermus luteus sp. nov., a slightly thermophilic bacterium isolated from a hot spring
A slightly thermophilic, aerobic bacterium, designated YIM 72257T, was isolated from a sediment sample taken from a hot spring in Tengchong county, Yunnan province, south-west China. The isolate was Gram-stain-negative, non-sporulating and forms non-motile rods, appearing in chains. The isolate grew at 50–65 °C, pH 6.0–9.0 and with 0.5–1 % NaCl (w/v). 16S rRNA gene sequence analysis showed that strain YIM 72257T was most closely related to Meiothermus cateniformans LY1T (95.6 %), Meiothermus ruber DSM 1279T (95.1 %) and Meiothermus taiwanensis WR-30T (94.6 %). The genomic DNA G+C content of strain YIM 72257T was 62.6 mol%. The main cellular fatty acids (>5 %) were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, iso-C17 : 0, iso-C15 : 0 and C16 : 0. The polar lipids consisted of an uncharacterized phospholipid and two glycolipids. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain YIM 72257T is proposed to be a representative of a novel species of the genus Meiothermus , for which the name Meiothermus luteus sp. nov. is proposed. The type strain is YIM 72257T (=KCTC 52599T=CCTCC AB 2017100T).
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Thermus caldifontis sp. nov., a thermophilic bacterium isolated from a hot spring
A thermophilic bacterial strain, designated YIM 73026T was isolated from a sediment sample collected from a hot spring in Tibet, PR China. The taxonomic position of the novel isolate was investigated by a polyphasic approach. The novel isolate was Gram-stain-negative, aerobic and rod-shaped. Colonies were circular, convex, opaque and yellow. The strain grew at 50–70 °C (optimum, 60 °C), pH 6.0–8.0 (optimum, pH 7.0) and in the presence of up to 1.0 % NaCl (w/v). Comparison of the 16S rRNA gene sequences of YIM 73026T and those of other members of the genus Thermus showed sequence similarities ranging from 91.2 to 97.5 %, with YIM 73026T showing closest sequence similarity to Thermus scotoductus SE-1T (97.5 %). DNA–DNA hybridization results, however, revealed that DNA–DNA reassociation values between YIM 73026T and T. scotoductus DSM 8553T (37.6 %), Thermus amyloliquefaciens YIM 77409T (34.5 %), Thermus antranikianii DSM 12462T (30.3 %), Thermus caliditerrae YIM 77925T (28.6 %) and Thermus tengchongensis YIM 77924T (27.3 %) were well below the 70 % limit for species identification. YIM 73026T contained MK-8 as the respiratory quinone, and iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C15 : 0 as the major cellular fatty acids (>10 %). The polar lipids consisted of one aminophospholipid, one phospholipid and two glycolipids. The genomic DNA G+C content of YIM 73026T was 65.4 mol%. On the basis of morphological, chemotaxonomic and genotypic characteristics, it is proposed that the isolate represents a novel species of the genus Thermus , for which the name Thermus caldifontis sp. nov. is proposed. The type strain is YIM 73026T (=NBRC 112415T=CCTCC AB 2016305T).
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- Proteobacteria
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Massilia phosphatilytica sp. nov., a phosphate solubilizing bacteria isolated from a long-term fertilized soil
More LessA Gram-stain-negative and rod-shaped bacterial strain, 12-OD1T, with rock phosphate solubilizing ability was isolated from agricultural soil in Hailun, Heilongjiang, PR China. The isolate was affiliated to the genus Massilia , based on 16S rRNA gene sequence alignments, having the highest similarities with Massilia putida 6 NM-7T (98.67 %), Massilia kyonggiensis TSA1T (98.28 %), and Massilia norwichensis NS9T (98.07 %), respectively. The DNA G+C content was 67.72 mol% and DNA–DNA hybridization showed low relatedness values (less than 47 %) between strain 12-OD1T and other phylogenetically related species of the genus Massilia . The predominant isoprenoid quinone was Q-8 and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C17 : 0 cyclo (25.4 %), C16 : 0 (23.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c) (22.5 %), which differentiates it from close relatives within the genus Massilia . Combined genetic, physiological and biochemical properties indicate that strain 12-OD1T is a novel species of the genus Massilia , for which the name Massilia phosphatilytica sp. nov., is proposed, with the type strain 12-OD1T (=CCTCC AB 2016251T=LMG 29956T=KCTC 52513T).
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Notoacmeibacter marinus gen. nov., sp. nov., isolated from the gut of a limpet and proposal of Notoacmeibacteraceae fam. nov. in the order Rhizobiales of the class Alphaproteobacteria
More LessA Gram-stain-negative, short rod-shaped and non-flagellated bacterium, named strain XMTR2A4T, was isolated from the gut of a marine limpet, Notoacmea schrenckii on intertidal rocks. Colonies were small, light grey and circular. Catalase- and oxidase-positive. Growth was observed at 15 to 37 °C (optimum 28–30 °C), with salinity range from 0.5 to 9 % (optimum 1–2 %), and at pH 6 to 9 (optimum pH 7). The almost full-length 16S rRNA gene of strain XMTR2A4T had the highest sequence similarity of 93.7 % with Mycoplana ramosa DSM 7292T, and of 93.5 , 93.5 and 93.4 % with Chelativorans intermedius CC-MHSW-5T, Ensifer fredii ATCC 35423T and Phyllobacterium myrsinacearum IAM 13584T, respectively. Phylogenetic analysis showed that strain XMTR2A4T formed a tight cluster with a cultured but uncharacterized strain, YP382-1-A, which was deeply separated from the species within the order Rhizobiales in the class Alphaproteobacteria . The predominant fatty acid of strain XMTR2A4T was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 83.4 %). Ubiquinone-10 (Q-10) was detected as the sole respiratory quinone. The polar lipids were identified as phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified phospholipid and three unknown lipids. The genome size was about 3.6 Mbp and the G+C content was 61.5 mol%. Combining the results above, it was ascertained that strain XMTR2A4Trepresents a novel species of a new genus in the order Rhizobiales , for which the name Notoacmeibacter marinus gen. nov., sp. nov. is proposed. The type strain of the type species is XMTR2A4T (=MCCC 1A01882T=KCTC 52427T). A novel family in the order Rhizobiales , named Notoacmeibacteraceae fam. nov., is also proposed to accommodate the new genus.
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Paracoccus aerius sp. nov., isolated from air
More LessStrain 011410T, isolated from air at the foot of Xiangshan Mountain, Beijing, China, was Gram-reaction-negative, facultatively anaerobic, oval-shaped, motile with two flagella and catalase- and oxidase-positive. Growth of strain 011410T was observed at 4–41 °C (optimum, 30 °C), at pH 4.5–10.0 (optimum, pH 8.0) and at salinities of 0–10 % (w/v) NaCl (optimum, 0–2 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 011410T was a member of the genus Paracoccus and was related most closely to Paracoccus aestuarii B7T (96.62 % similarity) and Paracoccus sediminis CMB17T (96.48 % similarity). The major fatty acid was identified as C18 : 1ω7c, with smaller amounts of C18 : 0, C10 : 0 3-OH and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I). The predominant respiratory quinone was ubiquinone-10 (Q-10), with Q-9 as a minor component. Polar lipid analysis indicated the presence of diphosphatidylglycerol, phosphatidylglycerol, one unknown phosphoglycolipid, five unknown phospholipids, one unknown aminolipid, one unknown glycolipid and two unknown polar lipids. The DNA G+C content of the strain was 63.5 mol%. On the basis of the data from this polyphasic characterization, strain 011410T represents a novel species, for which the name Paracoccus aerius sp. nov. is proposed. The type strain is 011410T (=CFCC 14285T=KCTC 42845T).
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Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales
The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald), Germany, by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of the current classes of the phylum Proteobacteria . Whole-genome sequencing resulted in a genome size of 3.5 Mbp and revealed a quite low DNA G+C content of 32.6 mol%. In-depth phylogenetic analyses based on alignments of 74 protein sequences of a phylogenetically broad range of taxa suggested assignment of the strain to a new order of the class Oligoflexia . These analyses also suggested that the order Bdellovibrionales should be transferred from the class Deltaproteobacteria to the class Oligoflexia , that this order should be split into two orders, and that the family Pseudobacteriovoracaceae should be transferred from the order Bdellovibrionales to the order Oligoflexales . We propose to establish for strain MWH-Nonnen-W8redT (=DSM 23856T=CCUG 58639T) the novel species and genus Silvanigrella aquatica gen. nov., sp. nov. to be placed in the new family Silvanigrellaceae fam. nov. of the new order Silvanigrellales ord. nov.
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Cellvibrio fontiphilus sp. nov., isolated from a spring
More LessA bacterial strain, designated MVW-40T, was isolated from Maolin Spring in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain MVW-40T were Gram-negative, strictly aerobic, motile by a single polar flagellum and bright yellow-pigmented rods with pointed ends. Growth occurred at 15–40 °C (optimum, 20–30 °C), at pH 6–9 (optimum, pH 6) and with 0–2 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MVW-40T belonged to the genus Cellvibrio and showed the highest levels of sequence similarity with respect to Cellvibrio mixtus subsp. mixtus ACM 2601T (98.1 %) and Cellvibrio fibrivorans R-4079T (97.2 %). Strain MVW-40T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two uncharacterized aminophospholipids, two uncharacterized phospholipids and an uncharacterized lipid. The DNA G+C content of the genomic DNA was 52.8 mol%. The DNA–DNA hybridization value for strain MVW-40T with C. mixtus subsp. mixtus ACM 2601T and C. fibrivorans R-4079T was less than 45 %. On the basis of the phylogenetic inference and phenotypic data, strain MVW-40T should be classified as a novel species, for which the name Cellvibrio fontiphilus sp. nov. is proposed. The type strain is MVW-40T (=BCRC 80977T=LMG 29557T=KCTC 52237T).
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Marinomonas epiphytica sp. nov., isolated from a marine intertidal macroalga
A novel Gram-stain-negative, aerobic marine bacterial strain, SAB-3T, was isolated from brown macroalgae (Dictyota sp.) growing in the Arabian sea, Goa, India. The strain grew optimally at 30 °C, with 2.0–4.0 % (w/v) NaCl and at pH 7.0 on marine agar medium. Strain SAB-3T was unable to hydrolyse aesculin and did not grow in the presence of rifamycin but showed resistance to antibiotics such as cefadroxil and co-trimoxazole. The major fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω 6c) and C16 : 0, and Q-8 was the major ubiquinone. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.0 mol%. 16S rRNA gene sequencing and phylogenetic analysis indicated that the strain was a member of the genus Marinomonas with Marinomonas aquiplantarum IVIA-Po-159T (97.6 % similarity), Marinomonas posidonica IVIA-Po-181T (97.5 %) and Marinomonas dokdonensis DSM 17202T (97.4 %) as the closest relatives. Whole genome relatedness determined through DNA–DNA hybridization revealed values of 40–50 % (below the 70 % threshold recommended for species delineation) with the above three species, thus confirming it as representing a distinct and novel species of the genus Marinomonas for which the name Marinomonas epiphytica sp. nov. is proposed. The type strain is SAB-3T (=JCM 31365T=KCTC 52293T=MTCC 12569T).
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Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil
More LessA yellow-coloured, Gram-stain-negative, non-motile, rod-shaped bacterium, designated K-1-16T, that is capable of degrading aliphatic hydrocarbons was isolated from oil-contaminated soil at Biratnagar, Morang, Nepal. It was able to grow at 15–45 °C, at pH 5.5–9.5 and with 0–5 % (w/v) NaCl. This strain was taxonomically characterized by a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain K-1-16T belongs to the genus Sphingomonas and is closely related to Sphingomonas mucosissima CP173-2T (98.6 % similarity), Sphingomonas dokdonensis DS-4T (97.9 %), Sphingomonas faeni MA-olkiT (97.9 %), Sphingomonas aurantiaca MA101bT (97.8 %) and Sphingomonas xinjiangensis 10-1-84T (96.6 %). The predominant respiratory quinone was ubiquinone Q-10 and the major polyamine was homospermidine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine and sphingoglycolipid. The predominant fatty acids of strain K-1-16T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c 11-methyl and C14 : 0 2-OH. The genomic DNA G+C content was 64.8 mol%. Levels of DNA–DNA relatedness between strain K-1-16T and S. mucosissima DSM 17494T, S. dokdonensis KACC 17420T, S. faeni KCCM 41909T and S. aurantiaca KCCM 41908T were 49.7, 41.3, 43.7 and 36.7 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-1-16T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas olei sp. nov. is proposed. The type strain is K-1-16T (=KEMB 9005-450T=KACC 19002T=JCM 31674T).
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Pseudoalteromonas piratica sp. nov., a budding, prosthecate bacterium from diseased Montipora capitata, and emended description of the genus Pseudoalteromonas
A Gram-stain-negative, motile, rod-shaped bacterium designated OCN003T was cultivated from mucus taken from a diseased colony of the coral Montipora capitata in Kāne‘ohe Bay, O‘ahu, Hawai‘i. Colonies of OCN003T were pale yellow, 1–3 mm in diameter, convex, smooth and entire. The strain was heterotrophic, strictly aerobic and strictly halophilic. Cells of OCN003T produced buds on peritrichous prosthecae. Growth occurred within the pH range of 5.5 to 10, and the temperature range of 14 to 39 °C. Major fatty acids were 16 : 1ω7c, 16 : 0, 18 : 1ω7c, 17 : 1ω8c, 12 : 0 3-OH and 17 : 0. Phylogenetic analysis of 1399 nucleotides of the 16S rRNA gene nucleotide sequence and a multi-locus sequence analysis of three genes placed OCN003T in the genus Pseudoalteromonas and indicated that the nearest relatives described are Pseudoalteromonas spongiae , P. luteoviolacea , P. ruthenica and P. phenolica (97–99 % sequence identity). The DNA G+C content of the strain’s genome was 40.0 mol%. Based on in silico DNA–DNA hybridization and phenotypic differences from related type strains, we propose that OCN003T represents the type strain of a novel species in the genus Pseudoalteromonas , proposed as Pseudoalteromonas piratica sp. nov. OCN003T (=CCOS1042T=CIP 111189T). An emended description of the genus Pseudoalteromonas is presented.
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Natronospira proteinivora gen. nov., sp. nov, an extremely salt-tolerant, alkaliphilic gammaproteobacterium from hypersaline soda lakes
More LessBrine samples from Kulunda Steppe soda lakes (Altai, Russia) were inoculated into a hypersaline alkaline mineral medium with β-keratin (chicken feather) as a substrate. The micro-organisms dominating the enrichment culture were isolated by limiting serial dilution on the same medium with casein as a substrate. The cells of strain BSker1T were motile, curved rods. The strain was an obligately aerobic heterotroph utilizing proteins and peptides as growth substrates. The isolate was an obligate alkaliphile with a pH range for growth from pH 8.5 to 10.25 (optimum at pH 9.5), and it was extremely salt tolerant, growing with between 1 and 4.5 M total Na+ (optimally at 2–2.5 M). BSker1T had a unique composition of polar lipid fatty acids, dominated by two C17 species. The membrane polar lipids included multiple unidentified phospholipids and two aminolipids. According to phylogenetic analysis of the 16S rRNA gene sequence, the isolate forms a novel branch within the family Ectothiorhodospiraceae (class Gammaproteobacteria ) with the highest sequence similarity to the members of this family being 91 %. On the basis of distinct phenotypic and genotypic properties, strain BSker1T (=JCM 31341T=UNIQEM U1008T) is proposed to be classified as a representative of a novel genus and species, Natronospira proteinivora gen. nov., sp. nov.
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Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern
More LessA moderately halophilic bacterium designated strain M6-53T was isolated from water of a pond from a marine saltern located in Huelva, south-west Spain. Cells of the strain were Gram-stain-negative, strictly aerobic, motile, slightly curved rods, able to grow in media containing 5–25 % (w/v) NaCl (optimal growth at 10 %, w/v), at temperatures from 20 to 40 °C (optimally at 37 °C) and at pH 6.5–9 (optimally at pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequences placed the new isolate within the genus Marinobacter , with the type strains of the most closely related species being Marinobacter persicus IBRC-M 10445T (98.5 % similarity), Marinobacter oulmenensis Set74T (97.2 %) and Marinobacter hydrocarbonoclasticus ATCC 49840T (97.1 %). The major fatty acids present in strain M6-53T were C18 : 1ω9c (29.5 %), C16 : 0 (26.7 %), C12 : 0 3-OH (15.1 %), C18 : 0 (10.2 %) and C16 : ω9c (9.6 %). The G+C content of the genomic DNA for this strain was determined to be 56.4 mol%. The DNA–DNA hybridization values between strain M6-53T and M. persicus CECT 7991T, M. oulmenensis CECT 7499T and M. hydrocarbonoclasticus DSM 50418 were 8, 41 and 38 %, respectively. These values are lower than the accepted 70 % threshold and showed that the new isolate represented a different species within the genus Marinobacter . Phylogenetic analysis based on the 16S rRNA gene sequence and the phenotypic, genotypic and chemotaxonomic features of this new isolate support the placement of strain M6-53T as a representative of a novel species of the genus Marinobacter , for which we propose the name Marinobacter aquaticus sp. nov., with strain M6-53T (=CECT 9228T=LMG 30006T) as the type strain.
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Arcobacter haliotis sp. nov., isolated from abalone species Haliotis gigantea
More LessA Gram-negative, aerobic, polar-flagellated and rod-shaped, sometimes slightly curved bacterium, designated MA5T, was isolated from the gut of an abalone of the species Haliotis gigantea collected in Japan. Phylogenetic analyses based on 16S rRNA, gyrB, hsp60 and rpoB gene sequences placed strain MA5T in the genus Arcobacter in an independent phylogenetic line. Comparison of the 16S rRNA gene sequence of this strain with those of the type strains of the established Arcobacter species revealed A. nitrofigilis (95.1 %) as nearest neighbour. Strain MA5T grew optimally at 25 °C, pH 6.0 to 9.0 and in the presence of 2 to 5 % (w/v) NaCl under both aerobic and microaerobic conditions. The predominant fatty acids found were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C12 : 0 3-OH and C18 : 1 ω7c. Menaquinone-6 (MK-6) and menaquinone-7 (MK-7) were found as the major respiratory quinones. The major polar lipids detected were phosphatidylethanolamine and phosphatidylglycerol. Strain MA5T could be differentiated phenotypically from the phylogenetic closest Arcobacter species by its ability to grow on 0.05 % safranin and 0.01 % 2,3,5-triphenyl tetrazolium chloride (TTC), but not on 0.5 % NaCl. The obtained DNA G+C content of strain MA5T was 27.9 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic distinctiveness of MA5T, this strain is considered to represent a novel species of the genus Arcobacter , for which the name Arcobacter haliotis sp. nov. is proposed. The type strain is MA5T (=LMG 28652T=JCM 31147T).
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Serratia oryzae sp. nov., isolated from rice stems
More LessA novel endophytic bacterium, strain J11-6T, was isolated from rice stems. Its taxonomic position was investigated using a polyphasic approach. The novel strain was Gram-staining-negative, facultatively anaerobic, motile and rod-shaped. Although the results of phylogenetic analysis based on 16S rRNA gene sequences indicated that J11-6T represented a member of the genus Rahnella , multilocus sequence analysis (MLSA) on the basis of concatenated partial atpD, gyrB, rpoB and infB gene sequences showed a clear distinction of J11-6T from the type strains of species of the genus Rahnella but indicated that it lay within the clade of the genus Serratia . The phylogenetically closest species were Serratia fonticola and Serratia aquatilis on the basis of the results of the MLSA phylogenetic analysis. The predominant cellular fatty acids were C16 : 1ω7c (38.7 %) and C16 : 0 (25.0 %). The DNA G+C content was 53.2 mol%. The DNA–DNA relatedness was 17.4 % between J11-6T and Rahnella aquatilis CIP 78.65T, and 29.2 % between J11-6T and S. fonticola LMG 7882T which indicates that this strain represents a novel species of the genus Serratia . Characterization by genotypic and phenotypic analysis indicated that J11-6T (=ACCC 19934T=KCTC 52529T) represents a novel species of the genus Serratia , for which the name Serratia oryzae sp. nov. is proposed.
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Mongoliimonas terrestris gen. nov., sp. nov., isolated from desert soil
More LessA Gram-stain-negative, non-motile, aerobic, non-spore-forming, spherical bacterium (strain MIMtkB18T) was isolated from desert soil collected from part of a Mongolian Plateau, territory of Inner Mongolia, PR China. Cell growth could be observed at 20–45 °C (optimum at 40 °C), at a pH of 6–9 (optimum at pH 8.6) and in the presence of 0–1 % (w/v) NaCl (optimum 0 %). The genomic DNA G+C content was 69.6 mol%. 16S rRNA gene sequence analysis showed that strain MIMtkB18T was most closely related to Methylobrevis pamukkalensis PK2T (94.1 %), species of the genus Pleomorphomonas (93.4–94.0 %), and Hartmannibacter diazotrophicus E19T (93.9 %). The sole respiratory quinone was Q-10. The major fatty acids (>5 %) were C18 : 0 (5.7 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (81.6 %). Polar lipids were mainly composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and unidentified phospholipids. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is concluded that strain MIMtkB18T represents a novel genus and species, for which the name Mongoliimonas terrestris sp. nov. is proposed. The type strain is MIMtkB18T (=KCTC 42635T=MCCC 1K00571T).
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Blastomonas marina sp. nov., a bacteriochlorophyll-containing bacterium isolated from seawater
More LessA Gram-stain-negative, facultatively anaerobic, dark-yellow-pigmented bacterium, named SSR2A-4-2T, was isolated from coastal water in the East China Sea. Cells were ovoid or short rods with peritrichous flagella and contained carotenoid in addition to bacteriochlorophyll a pigment. A phylogenetic dendrogram based on 16S rRNA gene sequences showed that strain SSR2A-4-2T formed a distinct clade with members of the genus Blastomonas , with Blastomonas natatoria EY 4220T (=DSM 3183T) (similarity 95.6 %), Blastomonas ursincola KR-99T (=DSM 9006T) (95.5 %) and Blastomonas aquatica PE4-5T (=JCM 30179T) (94.8 %) as its closest phylogenetic relatives. Q-10 was the predominant respiratory quinone. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C17 : 1ω6c and C18 : 1ω7c 11-methyl. The polar lipids contained diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, sphingoglycolipid, four unknown glycolipids and one unknown lipid. The DNA G+C content was 65.1 mol%. On the basis of the evidence presented in this study, strain SSR2A-4-2T represents a novel species of the genus Blastomonas , for which the name Blastomonas marina sp. nov. is proposed, with strain SSR2A-4-2T (=CGMCC 1.15297T=DSM 103453T) as the type strain.
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Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations
A Gram-stain negative, rod-shaped, aerobic bacterial strain, BII-R7T, was isolated during a study targeting the culture-dependent microbial diversity occurring in bentonite formations from southern Spain. Comparative 16S rRNA gene sequence analysis showed that BII-R7T represented a member of the genus Stenotrophomonas (class Gammaproteobacteria ), and was related most closely to Stenotrophomonas rhizophila e-p10T (99.2 % sequence similarity), followed by Stenotrophomonas pavanii ICB 89T (98.5 %), Stenotrophomonas maltophilia IAM 12423T, Stenotrophomonas chelatiphaga LPM-5T and Stenotrophomonas tumulicola T5916-2-1bT (all 98.3 %). Pairwise sequence similarities to all other type strains of species of the genus Stenotrophomonas were below 98 %. Genome-based calculations (orthologous average nucleotide identity, original average nucleotide identity, genome-to-genome distance and DNA G+C percentage) indicated clearly that the isolate represents a novel species within this genus. Different phenotypic analyses, such as the detection of a quinone system composed of the major compound ubiquinone Q-8 and a fatty acid profile with iso-C15 : 0 and anteiso-C15 : 0 as major components, supported this finding at the same time as contributing to a comprehensive characterization of BII-R7T. Based on this polyphasic approach comprising phenotypic and genotypic/molecular characterization, BII-R7T can be differentiated clearly from its phylogenetic neighbours, establishing a novel species for which the name Stenotrophomonas bentonitica sp. nov. is proposed with BII-R7T as the type strain (=LMG 29893T=CECT 9180T=DSM 103927T).
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Arenimonas soli sp. nov., isolated from saline–alkaline soil
More LessA Gram-staining-negative, non-motile, aerobic bacterial strain, designated Y3L17T, was isolated from the saline–alkaline soil of a farmland, Hangjin Banner, Inner Mongolia, northern China. Y3L17T could grow at 15–45 °C (optimum 35 °C), pH 6.0–10.0 (optimum pH 8.0) and with 0–4 % (w/v) NaCl (optimum 0 %). The results of phylogenetic analysis based on the 16S rRNA gene and gyrB gene sequences revealed that Y3L17T tightly clustered with strains of members of the genus Arenimonas , sharing the highest 16S rRNA gene similarities with Arenimonas aestuarii S2-21T (99.5 %) and Arenimonas donghaensis HO3-R19T (98.2 %), and lower similarities (<97 %) with all the other type strains of species of this genus. However, Y3L17T shared only 92.62 % gyrB gene similarities with A. aestuarii S2-21T. The DNA–DNA hybridization values of Y3L17T with A. aestuarii S2-21T and A. donghaensis HO3-R19T were 20.1±2.5 and 18.2±3.2 %, respectively. Y3L17T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, five unknown phospholipids and one unknown lipid as the major polar lipids. Ubiquinone-8 (Q-8) was the predominant respiratory quinone, while iso-C15 : 0, iso-C17 : 0ω9c and iso-C11 : 0 3-OH were the major cellular fatty acids. Its genomic DNA G+C content was 65.4 mol%. On the basis of its phenotypic, phylogenetic and genotypic characteristics, Y3L17T represents a novel species within the genus Arenimonas , for which the name Arenimonas soli sp. nov. is proposed, the type strain is Y3L17T (=CGMCC 1.15905T =KCTC 52420T).
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Aureimonas endophytica sp. nov., a novel endophytic bacterium isolated from Aegiceras corniculatum
More LessA Gram-negative, motile, aerobic and coccoid rod-shaped bacterium, designated strain 2T4P-2-4T, was isolated from a piece of surface-sterilized bark of Aegiceras corniculatum collected from Cotai Ecological Zones in Macao, China, and tested by a polyphasic approach to clarify its taxonomic position. Strain 2T4P-2-4T grew optimally without NaCl at 28–30 °C, pH 7.0–8.0. The 16S rRNA gene sequence of strain 2T4P-2-4T had the highest similarity (96.2 %) to Aureimonas rubiginis CC-CFT034T. Phylogenetic analysis showed that the strain grouped with species of the genus Aureimonas . The predominant quinone system of strain 2T4P-2-4T was ubiquinone 10 (Q-10). The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, sulfoquinovosyldiacylglycerol, phosphatidylmethylethanolamine, two unidentified amino lipids, an unidentified aminophospholipid and five unidentified lipids. The predominant cellular fatty acid was C18 : 1ω7c (61.2 %). The DNA G+C content of strain 2T4P-2-4T was 69.8 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain 2T4P-2-4T is a representative of a novel species of the genus Aureimonas , for which the name Aureimonas endophytica sp. nov. is proposed. The type strain of Aureimonas endophytica sp. nov. is 2T4P-2-4T (=KCTC 52217T=CGMCC 1.15367T).
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Paracoccus mangrovi sp. nov., isolated from a mangrove
More LessA bacterial strain, designated gyp-1T, was isolated from a mangrove in Taiwan and characterized using the polyphasic taxonomic approach. Cells of gyp-1T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate-accumulating, non-motile, coccoid or short-rod-shaped and formed cream-coloured colonies. Growth occurred at 15–37 °C (optimum, 25–30 °C), at pH 5.5–7.0 (optimum, pH 6.0) and with 0–4 % NaCl (optimum, 1–2 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that gyp-1T represented a member of the genus Paracoccus and showed the highest levels of sequence similarity with respect to Paracoccus lutimaris HDM-25T (97.8 %) and Paracoccus aminovorans DM-82T (97.7 %). The major fatty acids (>10 %) of gyp-1T were C18 : 1ω7c and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid and two unidentified phospholipids. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.6 mol%. The DNA–DNA hybridization value for gyp-1T with P. lutimaris HDM-25T and P. aminovorans DM-82T was less than 50 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that gyp-1T should be classified as representing a novel species of the genus Paracoccus , for which the name Paracoccus mangrovi sp. nov. is presented. The type strain is gyp-1T (=BCRC 80920T=LMG 29172T=KCTC 42899T).
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Blastomonas fulva sp. nov., aerobic photosynthetic bacteria isolated from a Microcystis culture
More LessTwo Gram-stain-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacteria, designated strains T2T and T5, were isolated from a culture of Microcystis from Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies placed the new isolates in the class Alphaproteobacteria and, notably, most closely related to Blastomonas aquatica PE 4-5T, Blastomonas natatoria DSM 3183T and Blastomonas ursincola KR-99T showing 99.4 %, 98.2 % and 97.9 % 16S rRNA gene sequence similarities, respectively. The two novel strains shared 100 % similarity with each other. The cells of strains T2T and T5 formed yellow colonies on R2A agar and contained Q-10 as the only ubiquinone, sphingoglycolipid, phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids, and C17 : 1ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C17 : 1ω8c and C17 : 0 as the major fatty acids (>5 %). The DNA G+C content of the genomes was determined to be 64.2 mol% for strain T2T and 64.4 mol% for strain T5. The DNA–DNA hybridization values of strains T2T and T5 with B. aquatica PE 4-5T, B. natatoria DSM 3183T, and B. ursincola KR-99T were 19.7–42.4 %. Based on the combined genotypic and phenotypic data, we propose that strains T2T and T5 represent a novel species of the genus Blastomonas , for which the name Blastomonas fulvasp. nov. is proposed. The type strain is T2T (=KCTC 42354T=JCM 30467T).
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Massilia solisilvae sp. nov., Massilia terrae sp. nov. and Massilia agilis sp. nov., isolated from forest soil in South Korea by using a newly developed culture method
More LessUsing a newly developed culture method for not yet cultured soil bacteria, three Gram-stain-negative, aerobic, non-spore-forming, motile, and rod-shaped bacteria (strain designated J18T, J11T and J9T) were isolated from forest soil at Kyonggi University, South Korea. Isolates were subjected to a taxonomic study by using a polyphasic approach. According to a phylogenetic tree based on 16S rRNA gene sequences, strains J18T, J11T and J9T belonged to the genus Massilia and clustered with Massilia haematophila CCUG 38318T (similarity range: 97.6~98.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, and the genomic DNA G+C contents of strains J18T, J11T and J9T were 63.4, 68.7 and 64.5 mol%, respectively. The major polyamines were putrescine and 2-hydroxyputescine, which were detected in all three strains. DNA–DNA between the three tested strains and the reference strains much lower than 70 %, the recommended threshold value for the delineation of genomic species. The predominant respiratory quinine was ubiquinone-8 (Q-8) and the major cellular fatty acids were Summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C16 : 0. On the basis of phenotypic and genotypic data and DNA–DNA hybridization results, the three isolates are considered to represent three novel species of the genus Massilia , for which the names Massilia solisilvae sp. nov. for type strain J18T (=KEMB 9005-366T=JCM 31607T), Massilia terrae sp. nov. for type strain J11T (=KEMB 9005-360T=JCM 31606T) and Massilia agilis sp. nov. for type strain J9T (=KEMB 9005-359T=JCM 31605T) are proposed.
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Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments
More LessTwo aerobic, Gram-stain-negative, gliding and yellow-pigmented bacteria, designated strains 03SUJ6T and WM95T were isolated from freshwater sediment of Juam reservoir and freshwater of Woopo wetland, Republic of Korea, respectively. Cells of the two strains are motile by gliding and catalase- and oxidase-positive. The 16S rRNA gene sequence similarity between 03SUJ6T and WM95T was 97.7 %, but their DNA–DNA relatedness was 55.1 %. A maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that 03SUJ6T and WM95T each form independent lineages within the genus Sphingomonas . 03SUJ6T was related distantly to Sphingomonas daechungensis CH15-11T (97.4 % 16S rRNA gene sequence similarity), Sphingomonas ginsengisoli Gsoil 634T (97.3 %) and Sphingomonas astaxanthinifaciens DMS 22298T (97.1 %). Closest relatives of strain WM95T were S . daechungensis CH15-11T (98.2 %), Sphingomonas jaspsi DSM 18422T (97.6 %), Sphingomonas sediminicola Dae 20T (97.5 %), Sphingomonas lutea JS5T (97.4 %) and S . ginsengisoli Gsoil 634T (97.2 %). The major fatty acids of the two isolates were summed feature 8 and C16 : 0. The predominant isoprenoid quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. sym-Homospermidine was the major polyamine of the isolates. Phenotypic characteristics distinguished 03SUJ6T and WM95T from the related species of the genus Sphingomonas . On the basis of the evidence presented in this study, the novel species, Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov. are proposed for strain 03SUJ6T (=KCTC 23331T=JCM 17543T) and strain WM95T (=KACC 18738T=JCM 31399T), respectively.
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Sphingomonas crusticola sp. nov., isolated from biological soil crusts
More LessA yellow-pigmented, Gram-stain-negative, short-rod-shaped bacterial strain, MIMD3T, was isolated from biological soil crusts collected in Liangcheng, north-western China. Cell growth could be observed at 10–37 °C (optimum 25 °C), at pH 5–8 (optimum 6.6) and in the presence of 1 % (w/v) NaCl (optimum 0 %). The genomic DNA G+C content was 65.0 mol%. Analysis of 16S rRNA gene sequences showed that strain MIMD3T shared the highest similarity with Sphingomonas vulcanisoli KCTC 42454T (95.1 %), Sphingomonas oligophenolica JCM 12082T (94.8 %), Sphingomonas mali IFO 15500T (94.5 %), Sphingomonas . leidyi ATCC 15260T (94.4 %) and Sphingomonas formosensis CC-Nfb-2T (94.3 %). The strain had Q-10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. The major fatty acids of the strain were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 0 cyclo ω8c, C14 : 0 2-OH and C16 : 0. The main polar lipids of strain MIMD3T were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is concluded that strain MIMD3T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas crusticola sp. nov. is proposed. The type strain is MIMD3T (=KCTC 42801T=MCCC 1K01310T).
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Paraphaeobacter pallidus gen. nov., sp. nov., isolated from seawater
More LessA Gram-stain-negative, aerobic, rod-shaped bacterium with a single polar flagellum, designated strain DCSW07T, was isolated from the surface water of the Bohai Sea, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DCSW07T shared highest similarity (96.97 %) with Phaeobacter gallaeciensis DSM 26640T, formed a lineage within the family Rhodobacteraceae and was distinct from the most closely related genera Phaeobacter and Pseudooceanicola (96.6–96.8 and 95.8–96.2 % 16S rRNA gene sequence similarity, respectively). Optimal growth occurred in the presence of 6 % (w/v) NaCl, at pH 6.0 and at 28 °C. Strain DCSW07T contained phosphatidylcholine, phosphatidylethanolamine, an unidentified phospholipid and two unidentified polar lipids as the major polar lipids, and C18 : 1ω7c as the main fatty acid (>10 % of the total). The DNA G+C content of strain DCSW07T was 64.8 mol%. On the basis of this polyphasic study, strain DCSW07T is considered to represent a novel species of a new genus in the Roseobacter clade of the family Rhodobacteraceae , for which the name Paraphaeobacter pallidus gen. nov., sp. nov. is proposed. The type strain of Paraphaeobacter pallidus is DCSW07T (=KCTC 52369T=MCCC 1K03197T=JCM 31458T=CGMCC 1.15762T).
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Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil
Within the frame of a biotechnological screening, we isolated two Pseudomonas strains from forest soil. 16S rRNA gene sequence analysis indicated that strain CCOS 864T shared 99.8 % similarity with Pseudomonas donghuensis HYST, while strain CCOS 865T shared 99.0 % similarity with Pseudomonas putida DSM 291T and lower similarity with other P. putida group type strains. Based on multilocus sequence analysis, the two strains were genotypically distinct from each other, each forming a separate clade. Strains CCOS 864T and CCOS 865T were Gram-stain-negative, motile and rod-shaped, growing at a temperature range of 4–37 °C. Strain CCOS 864T could be phenotypically distinguished from P. putida group species by the combination of gelatinase-positive reaction and positive growth on N-acetyl-d-glucosamine, p-hydroxyphenylacetic acid and inosine but lack of fluorescein production on King’s B medium, while strain CCOS 865T could be distinguished from P. putida group species by the combination of positive growth with saccharic acid and negative growth with p-hydroxyphenylacetic acid and l-pyroglutamic acid. The major polar lipid for both strains was phosphatidylethanolamine; the major quinone was ubiquinone Q-9. DNA–DNA hybridization and average nucleotide identities confirmed the novel species status for the two strains. The DNA G+C contents of CCOS 864T and CCOS 865T were 62.1 and 63.8 mol%, respectively. The phenotypic, phylogenetic and DNA–DNA relatedness data support the suggestion that CCOS 864T and CCOS 865T represent two novel Pseudomonas species. The names Pseudomonas wadenswilerensis sp. nov. (type strain CCOS 864T=LMG 29327T) and Pseudomonas reidholzensis sp. nov. (type strain CCOS 865T=LMG 29328T) are proposed.
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Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil
More LessA light yellow-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain K-3-6T, capable of degrading aliphatic hydrocarbons was isolated from oil-contaminated soil of Biratnagar, Morang, Nepal. It was able to grow at 15–45 °C, at pH 5.0–9.5 and with 0–6 % (w/v) NaCl. Based on 16S rRNA gene sequence analysis, strain K-3-6T belongs to the genus Sphingobium and is closely related to Sphingobium olei IMMIB HF-1T (98.4 % similarity), Sphingobium abikonense NBRC 16140T (98.3 %), Sphingobium rhizovicinum CC-FH12-1T (97.9 %), Sphingobium lactosutens DS20T (97.9 %), Sphingobium amiense NBRC 102518T (97.2 %), Sphingobium phenoxybenzoativorans SC_3T (97.2 %) and Sphingobium fontiphilum Chen16-4T (97.0 %). The predominant respiratory quinone was ubiquinone-10 and the major polyamine was spermidine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, sphingoglycolipid and phosphatidylmonomethylethanolamine. The predominant fatty acids of strain K-3-6T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C14 : 0, C16 : 0 and C14 : 0 2-OH. The genomic DNA G+C content was 65.6 mol%. Levels of DNA–DNA relatedness between strain K-3-6T and S. olei IMMIB HF-1T, S. abikonense NBRC 16140T, S. lactosutens DS20T, S. rhizovicinum CC-FH12-1T, S. amiense NBRC 102518T and S. fontiphilum Chen16-4T were 34.0, 33.3, 28.7, 26.3, 29.0 and 22.3 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-3-6T represents a novel species of the genus Sphingobium , for which the name Sphingobium naphthae sp. nov. is proposed. The type strain is K-3-6T (=KEMB 9005-449T=KACC 19001T=JCM 31713T).
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Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root
More LessA novel Gram-stain-negative, aerobic, rod-shaped strain designated 166T was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, PR China. The 16S rRNA gene sequence analysis indicated that strain 166T belongs to the genus Rhizobium and is closely related to Rhizobium cellulosilyticum ALA10B2T and Rhizobium yantingense H66T with sequence similarities of 98.8 and 98.3 %, respectively. According to atp D and rec A sequence analysis, the highest sequence similarity between strain 166T and R. cellulosilyticum ALA10B2T is 93.8 and 84.7 %, respectively. However, the new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to R. cellulosilyticum DSM 18291T (20.8±2.3 %) and Rhizobium yantingense CCTCC AB 2014007T (47.2±1.4 %). The DNA G+C content of strain 166T was 59.8 mol%. The main polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified aminophospholipid and an unidentified aminolipid. The major fatty acids of strain 166T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The results of the physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 166T from the type strains of closely related species, R. cellulosilyticum DSM 18291T and R. yantingense CCTCC AB 2014007T. Strain 166T represents a novel species within the genus Rhizobium , for which the name Rhizobium wenxiniae sp. nov. is proposed, with the type strain 166T (=CGMCC 1.15279T=DSM 100734T).
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Massilia agri sp. nov., isolated from reclaimed grassland soil
More LessA light yellow-coloured, Gram-stain-negative, motile and rod-shaped bacterium, designated strain K-3-1T, was isolated from reclaimed grassland soils of Belbari, Morang, Nepal. It was able to grow at 4–45 °C, at pH 5.0–10.0, and at 0–2 % (w/v) NaCl concentrations. This strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain K-3-1T belongs to the genus Massilia and is closely related to Massilia consociata CCUG 58010T (98.3 % sequence similarity), Massilia tieshanensis TS3T (98.1 % sequence similarity), Massilia kyonggiensis TSA1T (98.1 % sequence similarity), Massilia yuzhufengensis Y1243-1T (98.1 % sequence similarity), Massilia haematophila CCUG 38318T (98.0 % sequence similarity), Massilia varians CCUG 35299T (97.9 % sequence similarity), Massilia niastensis 5516 S-1T (97.6 % sequence similarity) and Massilia alkalitolerans YIM 31775T (97.5 % sequence similarity). The predominant respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids of strain K-3-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C12 : 0, C10 : 0 3-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The genomic DNA G+C content of this novel strain was 66.8 mol%. The DNA–DNA relatedness between strain K-3-1T and its closest reference strains were significantly lower than the threshold value of 70 %. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-3-1T represents a novel species of the genus Massilia , for which the name Massilia agri sp. nov. is proposed. The type strain is K-3-1T (=KEMB 9005-446T=KACC 19000T=JCM 31661T).
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Altererythrobacter halimionae sp. nov. and Altererythrobacter endophyticus sp. nov., two endophytes from the salt marsh plant Halimione portulacoides
Two Gram-negative, rod-shaped, motile bacterial strains, named CPA5T and BR75T, were isolated from the halophyte Halimione portulacoides. Both presented optimum growth at 30 °C, pH 7.0–7.5 and 1–2 % NaCl (w/v) for strain CPA5T, and pH 7.5–8.0 and 2 % NaCl (w/v) for strain BR75T. Phylogenetic analyses based on 16S rRNA gene sequences affiliated both strains to the genus Altererythrobacter. CPA5T presented highest 16S rRNA gene sequence similarity with Altererythrobacter aestuarii KYW147T (96.5 %), followed by Altererythrobacter namhicola KYW48T (95.9 %), Novosphingobium indicum H25T (95.6 %) and Altererythrobacter oceanensis Y2T (95.5 %). BR75T displayed highest similarity with Altererythrobacter marensis MSW-14T (96.5 %), followed by Altererythrobacter xinjiangensis S3-63T, Altererythrobacter luteolus SW-109T and Altererythrobacter indicus MSSRF26T (96.1 %). Neither strain contained Bacteriochlorophyll a. The main fatty acids observed for CPA5T were C17 : 1ω6c and summed features 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and 8 (C18 : 1 ω7c and/or C18 : 1ω6c). The latter summed feature was the dominant fatty acid observed for strain BR75T as well. The major polar lipids were phosphatidylethanolamine, unidentified phospholipids and unidentified glycolipids for both strains. The predominant ubiquinone was Q-10 for both strains, and the DNA G+C contents were 63.4 mol% and 58.3 mol% for CPA5T and BR75T, respectively. Based on phenotypic and genotypic results, both strains represent novel species belonging to the genus Altererythrobacter for which the names Altererythrobacter halimionae sp. nov. (type strain CPA5T=CECT 9130T=LMG 29519T) and Altererythrobacter endophyticus sp. nov (type strain BR75T=CECT 9129T=LMG 29518T) are proposed.
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Mesorhizobium oceanicum sp. nov., isolated from deep seawater
A novel Gram-staining-negative, oval-shaped (0.4–0.6×0.8–1.0 µm), non-motile strain without flagella, designated B7T, was isolated from deep seawater in the South China Sea. Strain B7T was able to grow at 25–40 °C (optimum 35 °C), at pH 5.5–9.0 (optimum pH 7.0) and with 0–8 % (w/v) NaCl (optimum 3 %). Chemotaxonomic analysis showed that the predominant isoprenoid quinone was Q-10 and the dominant fatty acids were C19 : 0 cyclo 8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The polar lipids of strain B7T were diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unknown aminophospholipid, one unknown glycolipid and three unknown lipids. The DNA G+C content of the genomic DNA was 65.1 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain B7T belongs to the genus Mesorhizobium with similarities ranging from 96.2 to 97.5 %. Phylogenetic analyses of housekeeping genes recA, atpD and glnII indicated that strain B7T represented a distinct evolutionary lineage with the genus Mesorhizobium . OrthoANI values between strain B7T and related strains of the genus Mesorhizobium (<80 %) were lower than the threshold value of 95 % ANI relatedness for species demarcation. Therefore, strain B7T is concluded to represent a novel species of the genus Mesorhizobium , for which the name Mesorhizobium oceanicumsp. nov. is proposed. The type strain is B7T (=KCTC 42783T=MCCC 1K02305T).
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Reclassification of Xuhuaishuia manganoxidans Wang et al. 2015 as a later heterotypic synonym of Brevirhabdus pacifica Wu et al. 2015 and emendation of the species description
A polyphasic taxonomic study was undertaken to clarify the exact position of type strain DY6-4T of Xuhuaishuia manganoxidans . A combination of physiological properties of X. manganoxidans DY6-4T was consistent with those of type strain 22DY15T of Brevirhabdus pacifica . The 16S rRNA gene sequence analyses indicated that X. manganoxidans DY6-4T and B. pacifica 22DY15T shared 100 % similarity and formed a monophyletic group. The close relationship between the two strains was underpinned by the results of chemotaxonomic characteristics, including the fatty acids, quinone and polar lipids. The digital DNA–DNA hybridization and average nucleotide identity values between the two strains were 99.90 and 99.98 %, respectively. Based on these results, we propose that Xuhuaishuia manganoxidans is a later heterotypic synonym of Brevirhabdus pacifica .
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Defluviimonas nitratireducens sp. nov., isolated from surface seawater
More LessA bacterial strain, designated DL5-4T, was isolated from the surface seawater of Dalian Bay and characterized using a polyphasic taxonomy approach. Cells of DL5-4T were Gram-staining-negative, non-motile and short-rod-shaped. Growth was observed at 8–40 °C (optimum 28–30 °C), at pH 6–9 (optimum pH 7) and in 0–7 % NaCl (optimum 1–3 %, w/v). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that DL5-4T formed an independent branch with members of the genus Defluviimonas , sharing high similarities with five related type strains, Defluviimonas aquaemixtae CDM-7T (96.6 %), Defluviimonas denitrificans DSM 18921T (96.0 %), Defluviimonas indica 20V17T (95.8 %), Defluviimonas aestuarii BS14T (95.8 %) and Defluviimonas alba cai42T (94.5 %). The predominant fatty acid was summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The isoprenoid quinone was identified as Q-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four phospholipids, an aminolipid and an unknown lipid. The DNA G+C content was 63.8 mol%. The results of the phenotypic, phylogenetic and chemotaxonomic analyses clearly indicated that DL5-4T represents a novel species of the genus Defluviimonas , for which the name Defluviimonas nitratireducens sp. nov. is proposed, with type strain DL5-4T (=MCCC 1A06955T=LMG 29616T).
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Sphingomonas silvisoli sp. nov., isolated from forest soil
More LessA novel Gram-stain-negative, aerobic, non-motile and short-rod-shaped bacterium, designated RP18T, was isolated from forest soil in Gwang-ju, Republic of Korea. Growth occurred at 15–30 °C (optimum 30 °C), pH 6.0–7.0 (optimum pH 7.0), and was inhibited in the presence of normal saline. According to the 16S rRNA gene sequence, strain RP18T showed the highest sequence similarity to Sphingomonas kyeonggiensis THG-DT81T (96.0 %), followed by Sphingomonas pituitosa EDIVT (95.4 %) and Sphingomonas dokdonensis DS-4T (95.2 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RP18T was clustered with Sphingomonas gimensis 9PNM-6T and Sphingomonas jejuensis MS-31T under the genus Sphingomonas . The G+C content of the genomic DNA of strain RP18T was 61.5 mol%. The major cellular fatty acids (>6 % of the total) were C16 : 0, C14 : 0 2-OH, C17 : 1ω6с, summed feature 3 (C16 : 1ω7с and/or C16 : 1ω6с) and summed feature 8 (C18 : 1ω7с and/or C18 : 1ω6с). Ubiquinone-10 (Q-10) and sym-homospermidine were detected as the predominant respiratory quinone and major compound in the polyamine pattern, respectively. The major polar lipids of the isolate consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phospholipid and sphingoglycolipid. Based on phylogenetic analysis and physiological and biochemical characterization, strain RP18T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas silvisoli sp. nov. is proposed. The type strain is RP18T (=KACC 18914T=JCM 31801T).
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Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked species of the genus and emendation of the genus Henriciella
Two Gram-negative, heterotrophic, aerobic, prosthecated, marine bacteria, designated strains MCS23T and MCS27T, were isolated from seawater samples. NaCl was required for growth. The major polar lipid detected in strain MCS27T was phosphatidylglycerol, whereas those detected in MCS23T were phosphatidylglycerol, sulfoquinovosyl diacylglycerol and 1,2-diacyl-3-α-d-glucuronopyranosyl-sn-glycerol taurineamide. The most abundant cellular fatty acids were C18 : 1ω7 and C16 : 0, hydroxyl-fatty acids were 3-OH C12 : 0 in both strains and 3-OH C11 : 0 in MCS23T. Strains MCS23T and MCS27T had DNA G+C contents of 57.0 and 55.0 mol%, respectively. The two strains shared 99.3 % 16S rRNA gene sequence similarity; levels of similarity with the type strains of species of the genus Henriciella were 99.4–97.8 % but DNA–DNA hybridizations were 53 % or lower. Besides their 16S rRNA gene sequences, the novel strains can be differentiated from other species of the genus Henriciella by cell morphology, lipid and fatty acid patterns and enzyme activities. The data obtained led to the identification of two novel species, for which the names Henriciella barbarensis sp. nov. (type strain MCS23T=LMG 28705T=CCUG 66934T) and Henriciella algicola sp. nov. (type strain MCS27T=LMG 29152T=CCUG 67844T) are proposed. As these two novel species are the first prosthecate species in the genus Henriciella , an emended genus description is also provided.
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Roseibium sediminis sp. nov., isolated from sea surface sediment
A Gram-stain-negative, rod-shaped, facultatively aerobic strain, motile by a monotrichous (polar or lateral) flagellum, designated BSS09T, was isolated from surface sediment of the Bohai Sea, PR China. Growth was observed at 10–45 °C (optimum 32 °C), in the presence of 1.0–7.0 % (w/v) NaCl (optimum 4.0 %) and at pH 5.0–8.0 (optimum pH 6.0). Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain BSS09T belonged to the genus Roseibium and showed the highest sequence similarity of 96.5 % to Roseibium hamelinense JCM 10544T. The significant dominant fatty acid was C18 : 1ω7c. The polar lipids comprised one phosphatidylcholine, one phosphatidylmonomethylethanolamine, one unidentified aminolipid, one phosphatidylglycerol, one phosphatidylethanolamine and one unidentified polar lipid. The major respiratory quinone was Q-10. The DNA G+C content of strain BSS09T was 57.1 mol%. On the basis of evidence from this polyphasic study, strain BSS09T is proposed to represent a novel species of the genus Roseibium , for which the name Roseibium sediminis sp. nov. is proposed. The type strain is BSS09T (=KCTC 52373T=MCCC 1K03201T).
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Alteromonas aestuariivivens sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, JDTF-113T, was isolated from a tidal flat in Jindo, an island of South Korea. Strain JDTF-113T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, revealed that strain JDTF-113T fell within the clade enclosing the type strains of species of the genus Alteromonas . Strain JDTF-113T exhibited 16S rRNA gene sequence similarity values of 97.1–98.1 % to the type strains of Alteromonas lipolytica , Alteromonas litorea , Alteromonas mediterranea , Alteromonas confluentis , Alteromonas hispanica , Alteromonas genovensis and Alteromonas marina , and of 94.8–96.9 % to those of the other species of the genus Alteromonas . Strain JDTF-113T contained Q-8 as the predominant ubiquinone and C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 1ω7c as the major fatty acids. The major polar lipids of strain JDTF-113T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified glycolipid. The DNA G+C content of strain JDTF-113T was 51.1 mol% and its mean DNA–DNA relatedness values with the type strains of seven closely phylogenetically related species of the genus Alteromonas were was 10–23 %. The differential phenotypic properties and phylogenetic and genetic distinctiveness support strain JDTF-113T being separated from species of the genus Alteromonas with validly published names . On the basis of the data presented, strain JDTF-113T is considered to represent a novel species of the genus Alteromonas , for which the name Alteromonas aestuariivivens sp. nov. is proposed. The type strain is JDTF-113T (=KCTC 52655T=NBRC 112708T).
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Umboniibacter caenipelagi sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated SCTF-16T, was isolated from a tidal flat on the Yellow Sea, South Korea. Strain SCTF-16T grew optimally at 30 °C, at pH 7.0–7.5 and in the presence of 2.0 % (w/v) NaCl. In the neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences, strain SCTF-16T clustered with the type strains of two species of the genus Umboniibacter . Strain SCTF-16T exhibited 16S rRNA gene sequence similarities of 99.6 and 97.1 % to the type strains of Umboniibacter roseus and Umboniibacter marinipuniceus , respectively, and of less than 93.4 % to the type strains of the other recognized species. Strain SCTF-16T contained Q-7 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C13 : 0 as the major fatty acids. The major polar lipids detected in strain SCTF-16T were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain SCTF-16T was 50.0 mol%, and its mean DNA–DNA relatedness values with the type strains of U. roseus and U. marinipuniceus were 31 and 9 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain SCTF-16T is separated from the two recognized species of the genus Umboniibacter . On the basis of the data presented, strain SCTF-16T is considered to represent a novel species of the genus Umboniibacter , for which the name Umboniibacter caenipelagi sp. nov. is proposed. The type strain is SCTF-16T (=KCTC 52628T=NBRC 112760T).
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Henriciella pelagia sp. nov., isolated from seawater
More LessStrain LA220T, isolated from seawater of the Eastern Pacific Ocean, was subjected to a polyphasic taxonomic study. Cells of the strain were Gram-stain-negative, aerobic, motile and short rod-shaped. On the basis of 16S rRNA gene sequence analysis, strain LA220T showed high similarity to Henriciella litoralis SD10T (98.5 %), Henriciella marina DSM 19595T (98.3 %) and Henriciella aquimarin a P38T (97.5 %), and exhibited less than 97.0 % 16S rRNA gene sequence similarity with respect to the type strains of other Hyphomonadaceae species. Phylogenetic analyses revealed that strain LA220T fell within the cluster of the genus Henriciella. The average nucleotide identity and in silico DNA–DNA hybridization values between strain LA220T and the type strains of Henriciella species were 74.8–76.8 and 18.4–20.8 %, respectively. The sole respiratory quinone was ubiquinone-10 (Q-10). The principal fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The major polar lipids were three unidentified glycolipids. The DNA G+C content was 59.9 mol%. Phylogenetic distinctiveness, chemotaxonomic differences and phenotypic properties revealed that strain LA220T could be differentiated from recognized Henriciella species. Therefore, strain LA220T is considered to represent a novel species of the genus Henriciella , for which the name Henriciella pelagia sp. nov. (type strain LA220T=CGMCC 1.15928T=KCTC 52577T) is proposed.
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Erythrobacter aquimixticola sp. nov., isolated from the junction between the ocean and a freshwater spring
More LessA Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated JSSK-14T, was isolated from the place where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain JSSK-14T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 1.0–2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain JSSK-14T fell within the clade comprising the type strains of species of the genus Erythrobacter . Strain JSSK-14T exhibited 16S rRNA gene sequence similarity values of 97.09–98.42 % to the type strains of Erythrobacter gangjinensis , Erythrobacter atlanticus and Erythrobacter luteus and of 94.31–96.97 % to the type strains of the other species of the genus Erythrobacter . Strain JSSK-14T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain JSSK-14T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The DNA G+C content of strain JSSK-14T was 63.5 mol%, and its mean DNA–DNA relatedness values with the type strains of Erythrobacter gangjinensis , Erythrobacter atlanticus and Erythrobacter luteus were 13–25 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain JSSK-14T is separated from recognized species of the genus Erythrobacter . On the basis of the data presented, strain JSSK-14T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter aquimixticola sp. nov. is proposed. The type strain is JSSK-14T (=KCTC 52764T=NBRC 112765T).
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Sphingomonas gotjawalisoli sp. nov., isolated from soil of a lava forest
A bacterial strain, designated SN6-9T, was isolated from soil of the Gotjawal, lava forest, located in Jeju, Republic of Korea. Strain SN6-9T was Gram-stain-negative, motile, oxidase- and catalase-negative, yellow-pigmented and rod-shaped. It contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids, Q-10 as the predominant isoprenoid quinone, sym-homospermidine as the major polyamine and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and two unidentified phospholipids as the polar lipids. The DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a separate lineage in the genus Sphingomonas . Based on the results from this polyphasic taxonomic study, it is concluded that strain SN6-9T represents a novel species in the genus Sphingomonas . The name Sphingomonas gotjawalisoli sp. nov. is proposed; the type strain is SN6-9T (=KCTC 52405T=NRRL B-65395T).
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Roseomonas hibiscisoli sp. nov., isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus)
More LessA Gram-stain-negative, aerobic, non-motile and coccoid to short-rod-shaped bacterial strain (THG-N2.22T) was isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus). Growth occurred at 20–40 °C (optimum 28 °C), at pH 5–9 (optimum 7) and with 0–4 % (w/v) NaCl (optimum 1 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-N2.22T were identified as Roseomonas rhizosphaerae YW11T (98.5 % similarity), Roseomonas rubra S5T (98.5 %), Roseomonas cervicalis ATCC 49957T (98.2 %), Roseomonas aestuarii JC17T (97.8 %), Roseomonas oryzae JC288T (97.3 %) and Roseomonas ludipueritiae 170/96T (97.3 %); levels of similarity with the type strains of other Roseomonas species were lower than 97.0 %. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, three unidentified phospholipids and three unidentified lipids. The major quinone was ubiquinone-10. The major fatty acids were C16 : 0, C18 : 1 2-OH, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain THG-N2.22T was 64.1 mol%. DNA–DNA hybridization values between strain THG-N2.22T and R. rhizosphaerae YW11T, R. rubra S5T, R. cervicalis ATCC 49957T, R. aestuarii JC17T, R. oryzae JC288T and R. ludipueritiae 170/96T were 43.1 % (30.2 %, reciprocal analysis), 39.0 % (24.7 %), 34.4 % (15.2 %), 18.0 % (14.5 %), 14.7 % (9.7 %) and 11.0 % (5.6 %), respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA–DNA hybridization data, strain THG-N2.22T represents a novel species of the genus Roseomonas , for which the name Roseomonas hibiscisoli sp. nov. is proposed. The type strain is THG-N2.22T (=KACC 18935T=CCTCC AB 2016176T).
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Desulfosarcina widdelii sp. nov. and Desulfosarcina alkanivorans sp. nov., hydrocarbon-degrading sulfate-reducing bacteria isolated from marine sediment and emended description of the genus Desulfosarcina
More LessIn previous studies, two hydrocarbon-degrading sulfate-reducing bacteria, strains PP31T and PL12T, were obtained from oil-polluted marine sediments of Shuaiba, Kuwait. They had been reported as organisms capable of anaerobic degradation of p-xylene and n-alkanes, respectively. The 16S rRNA gene sequence of strain PP31T showed 98.8 % sequence similarities to that of Desulfosarcina variabilis ‘Montpellier’T. Strains PL12T had 97.8 % of sequence similarity to Desulfosarcina ovata oXys1T. They both have been partially characterized, but not been validly published as new species of the genus Desulfosarcina . In this study, additional characterizations of these strains were made to describe them as two new species of the genus Desulfosarcina . Major cellular fatty acids of strain PP31T were C15 : 0 (25.9 %) and anteiso-C15 : 0 (22.3 %), whereas those of strain PL12T were C15 : 0 (21.3 %), C16 : 0 (17.8 %) and anteiso-15 : 0 (11.6 %). The phylogenetic tree based on 16S rRNA gene revealed that these isolates should not be classified as any of the known species in the genus Desulfosarcina . On the basis of phenotypic and phylogenetic analyses, these two sulfate reducers are proposed to form two novel species of the genus Desulfosarcina : Desulfosarcina widdelii sp. nov. (PP31T=JCM 31729T=DSM 103921T) and Desulfosarcina alkanivorans sp. nov. (PL12T=JCM 31728T=DSM 103901T). In addition, emended description of the genus Desulfosarcina is presented in this study.
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Spiribacter aquaticus sp. nov., a novel member of the genus Spiribacter isolated from a saltern
More LessA moderately halophilic bacterium, designated strain SP30T, was isolated from a solar saltern located in Santa Pola, Alicante, on the East coast of Spain. It was a Gram-stain-negative, strictly aerobic bacterium, able to grow in 7.5–25 % (w/v) NaCl and optimally in 12.5 % (w/v) NaCl. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that the novel isolate is a member of the genus Spiribacter , with the most closely related species being Spiribacter roseus SSL50T (99.9 % sequence similarity) and Spiribacter curvatus UAH-SP71T (99.4 % sequence similarity). The 16S rRNA gene sequence similarity with the type species Spiribacter salinus M19-40T was 96.6 %. The DNA–DNA relatedness value between strain SP30T and S. roseus SSL50T and S. curvatus UAH-SP71T was 40 and 55 %, respectively; these values are lower than the 70 % threshold accepted for species delineation. The major fatty acids were C16:0, C18 : 1ω7c, C19 : 0 cyclo ω8c and C12 : 0. Similarly to other species of the genus Spiribacter , strain SP30Twas observed as curved rods and spiral cells. Metabolic versatility was reduced to the utilization of a few organic compounds as the sole carbon and energy sources, as with other members of Spiribacter. However, it differed in terms of colony pigmentation (brownish-yellow instead of pink) and in having a higher growth rate. Based on these data and on the phenotypic, genotypic and chemotaxonomic characterization, we propose the classification of strain SP30T as a novel species within the genus Spiribacter , with the name Spiribacter aquaticus sp. nov. The type strain is SP30T (=CECT 9238T=LMG 30005T).
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Novosphingobium humi sp. nov., isolated from soil of a military shooting range
More LessA Gram-stain-negative, strictly aerobic bacterium, designated R1-4T, was isolated from soil from a military shooting range in the Republic of Korea. Cells were non-motile short rods, oxidase-positive and catalase-negative. Growth of R1-4T was observed at 15–45 °C (optimum, 30 °C) and pH 6.0–9.0 (optimum, pH 7.0). R1-4T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c), cyclo-C19 : 0ω8c and C16 : 0 as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, an unknown glycolipid and four unknown lipids were detected as polar lipids. The major polyamine was spermidine. The G+C content of the genomic DNA was 64.4 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that R1-4T formed a tight phylogenetic lineage with Novosphingobium sediminicola HU1-AH51T within the genus Novosphingobium . R1-4T was most closely related to N. sediminicola HU1-AH51T with a 98.8 % 16S rRNA gene sequence similarity. The DNA–DNA relatedness between R1-4T and the type strain of N. sediminicola was 37.8±4.2 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that R1-4T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium humi sp. nov. is proposed. The type strain is R1-4T (=KACC 19094T=JCM 31879T).
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- Eukaryotic Micro-organisms
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Cyberlindnera tropicalis f.a., sp. nov., a novel yeast isolated from tropical regions
Two yeast strains, DMKU-WBBC14 and UFMG-CM-Y3283, were isolated from soil in Samutprakarn province in the central part of Thailand and from rotting wood in an Amazonian forest site in the Roraima State in Brazil, respectively. The two strains showed identical sequences of the D1/D2 domain of the large subunit (LSU) rRNA gene and different sequences by three nucleotide substitutions of the internal transcribed spacer (ITS) region. Therefore, these two strains represented a single species which was most closely related to Cyberlindnera mengyuniae CBS 10845T. The nucleotide sequence differences between the two strains of the novel species and the type strain Cyberlindnera mengyuniae CBS 10845T were 10 substitutions in the D1/D2 region of the LSU rRNA gene and 46 substitutions in the ITS region. DMKU-WBBC14 and UFMG-CM-Y3283 differed in growth temperature profiles. Moreover, they also exhibited different carbon assimilation profiles and growth temperature profiles from the type strain of Cyberlindnera mengyuniae, CBS 10845T. The name Cyberlindnera tropicalis f.a., sp. nov. is proposed. The type strain is DMKU-WBBC14T (=CBS 14558T=TBRC 6562T). The Mycobank number is MB 819722.
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Occultifur plantarum f.a., sp. nov., a novel cystobasidiomycetous yeast species
Nine strains representing a single anamorphic novel yeast species in dispersed tropical and subtropical habitats were isolated from sugarcane leaf tissue (DMKU-SE24, DMKU-SE45T, DMKU-SE129 and DMKU-SE134) and corn leaf tissue (DMKU-CE36) in Thailand, phylloplane and rhizoplane of sugarcane in Brazil (IMUFRJ 52018 and IMUFRJ 52019), bromeliad leaf tissue in Brazil (IMUFRJ 51954) and plant leaf in Japan (IPM31-24). These strains showed identical or only 1 nt substitution in the sequences of the D1/D2 region of the LSU rRNA gene and 0–5 nt substitutions in the internal transcribed spacer (ITS) region. Phylogenetic analysis based on the combined sequences of the ITS and the D1/D2 regions showed that the eight of these strains represented a single species in the genus Occultifur that was distinct from related species. Occultifur kilbournensis was the most closely related species, but with 0.9–1.2 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, and 2.4–2.6 % nucleotide substitutions in the ITS region. They are therefore considered to represent a novel species of the genus Occultifur although the formation of basidia was not observed. The name Occultifur plantarum f.a., sp. nov. is proposed. The type strain is DMKU-SE45T (=CBS 14554T=TBRC 6561T).
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Two novel Lipomycetaceous yeast species, Lipomyces okinawensis sp. nov. and Lipomyces yamanashiensis f.a., sp. nov., isolated from soil in the Okinawa and Yamanashi prefectures, Japan
More LessFour novel Lipomyces strains were isolated from soil collected in the Okinawa and Yamanashi prefectures, Japan. Based on their morphological and biochemical characteristics, along with sequence typing using the D1/D2 domain of the LSU rRNA, internal transcribed spacer (ITS) region including 5.8S rRNA, and translation elongation factor 1 alpha gene (EF-1α), the four strains were shown to represent two novel species of the genus Lipomyces, described as Lipomyces okinawensis sp. nov. (type strain No.3-a(35)T=NBRC 110620T=CBS 14747T) and Lipomyces yamanashiensis f.a., sp. nov. (type strain No.313T=NBRC 110621T=CBS 14748T).
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Volumes and issues
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