- Volume 64, Issue Pt_12, 2014
Volume 64, Issue Pt_12, 2014
- Notification List
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 64, part 9, of the IJSEM
More LessThis listing of names of prokaryotes published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
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- New Taxa
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- Proteobacteria
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Colwellia aquaemaris sp. nov., isolated from the Cynoglossus semilaevis culture tank in a recirculating mariculture system
More LessA Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated S1T, was isolated from the Cynoglossus semilaevis culture pond in a recirculating mariculture system in Tianjin, China. The taxonomy of strain S1T was studied by using a polyphasic approach. Cells of strain S1T were non-spore-forming, curved rods, 0.4–0.6 µm wide and 1.2–2.0 µm long, and motile by means of a single polar flagellum. The strain was positive for oxidase and catalase activities. Strain S1T was able to grow at 4–30 °C (optimum, 25 °C), at pH 5.5–10.0 (optimum, pH 6.5–7.5) and in the presence of 1–5 % (w/v) NaCl (optimum, 2 %). Strain S1T contained Q-8 as the sole respiratory quinone and C16 : 1ω7c/C16 : 1ω6c and C16 : 0 as the predominant cellular fatty acids. The genomic DNA G+C content was 40.1 mol% (T m). Phylogenetic analysis based on 16S rRNA gene sequences placed strain S1T in the genus Colwellia , and it formed a distinct lineage in the phylogenetic tree together with Colwellia meonggei MA1-3T, Colwellia aestuarii SMK-10T, Colwellia polaris 537T and Colwellia chukchiensis BCw111T, with 97.7, 96.1, 95.9 and 95.0 % 16S rRNA gene sequence similarity to these strains, respectively. DNA–DNA relatedness of strain S1T to Colwellia meonggei MA1-3T was 23.5±3.6 %. On the basis of the phylogenetic and phenotypic evidence, strain S1T is considered to represent a novel species of the genus Colwellia , for which the name Colwellia aquaemaris sp. nov. is proposed. The type strain is S1T ( = CGMCC 1.12165T = JCM 18479T).
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Altererythrobacter aestiaquae sp. nov., isolated from seawater
More LessA Gram-stain-negative, coccoid- or oval-shaped, gliding bacterial strain, designated HDW-31T, belonging to the class Alphaproteobacteria , was isolated from seawater of the Yellow Sea, Korea, and was subjected to a taxonomic study using a polyphasic approach. Strain HDW-31T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HDW-31T fell within the clade comprising the genus Altererythrobacter , clustering with the type strains of Altererythrobacter luteolus and Altererythrobacter gangjinensis , with which strain HDW-31T exhibited 97.0 and 96.0 % sequence similarity values, respectively. Sequence similarities to the type strains of the other recognized species of the genus Altererythrobacter were 93.5–96.0 %. The DNA G+C content was 57.9 mol% and mean DNA–DNA relatedness between strain HDW-31T and the type strain of A. luteolus was 5.3 %. Strain HDW-31T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0 as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, a sphingoglycolipid, two unidentified glycolipids and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain HDW-31T is distinguishable from recognized species of the genus Altererythrobacter . On the basis of the data presented, strain HDW-31T is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter aestiaquae sp. nov. is proposed. The type strain is HDW-31T ( = KCTC 42006T = CECT 8527T).
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Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense
Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247T, BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus Bradyrhizobium with the closest neighbours being the type strains of Bradyrhizobium paxllaeri (98.8 % similarity), Bradyrhizobium icense (98.8 %), Bradyrhizobium lablabi (98.7 %), Bradyrhizobium jicamae (98.6 %), Bradyrhizobium elkanii (98.6 %), Bradyrhizobium pachyrhizi (98.6 %) and Bradyrhizobium retamae (98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S–23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05T ( = LMG 24129T) to be the most closely related type strain (95.7 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C16 : 0 and summed feature 8 (18 : 1ω6c/18 : 1ω7c)], DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus Bradyrhizobium . Results of DNA–DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus Bradyrhizobium . Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) placed the novel species in a new branch within the genus Bradyrhizobium . Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247T ( = HAMBI 3599T).
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Asticcacaulis endophyticus sp. nov., a prosthecate bacterium isolated from the root of Geum aleppicum
A strictly aerobic, light-yellow-coloured, stalked bacterium, designated strain ZFGT-14T, was isolated from the root of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi province, north-west China, and was subjected to a taxonomic study using a polyphasic approach. This novel isolate grew at 7–33 °C (optimum 25–28 °C) and pH 6.0–10.0 (optimum pH 7.0–8.0). Flexirubin-type pigments were not produced. Cells were Gram-stain-negative, rod-shaped and motile with a single polar flagellum. The predominant respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C19 : 0 cyclo ω8c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and the major polar lipids were phosphatidylglycerol and glycolipids. The DNA G+C content was 57.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFGT-14T was most closely related to the genus Asticcacaulis and had low sequence similarity (95.0–95.9 %) with all species with validly published names within the genus Asticcacaulis . Based on the phenotypic, phylogenetic and genotypic data, strain ZFGT-14T is considered to represent a novel species of the genus Asticcacaulis , for which the name Asticcacaulis endophyticus sp. nov. is proposed. The type strain is ZFGT-14T ( = CCTCC AB 2013012T = KCTC 32296T = LMG 27605T).
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Ascidiaceihabitans donghaensis gen. nov., sp. nov., isolated from the golden sea squirt Halocynthia aurantium
More LessA Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated RSS1-M3T, was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. Strain RSS1-M3T grew optimally at 30 °C, at pH 7.0–8.0 and in presence of 2.0 % (w/v) NaCl. Strain RSS1-M3T exhibited the highest 16S rRNA gene sequence similarity (96.55 %) to the type strain of Pelagicola litoralis . Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS1-M3T clustered with the type strains, or proposed type strains, of Planktotalea frisia , Pacificibacter maritimus , Roseovarius marinus and Halocynthiibacter namhaensis , showing sequence similarity of 94.88–96.32 %. Strain RSS1-M3T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids. The polar lipid profile of strain RSS1-M3T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified aminolipid and one unidentified lipid as major components, could be distinguished from those of the phylogenetically related genera. The DNA G+C content of strain RSS1-M3T was 55.8 mol%. On the basis of the phylogenetic, chemotaxonomic and phenotypic properties, strain RSS1-M3T is considered to represent a novel species of a new genus within the class Alphaproteobacteria , for which the name Ascidiaceihabitans donghaensis gen. nov., sp. nov. is proposed. The type strain is RSS1-M3T ( = KCTC 42118T = CECT 8599T).
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Comamonas humi sp. nov., isolated from soil
More LessA bacterial strain, designated GAU11T, was isolated from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic, non-motile rods. The 16S rRNA gene sequence of strain GAU11T showed high similarity to those of Comamonas zonglianii BF-3T (98.8 %), Pseudacidovorax intermedius CC21T (96.4 %), Acidovorax caeni R-24608T (96.2 %), Alicycliphilus denitrificans K601T (96.2 %), Pseudorhodoferax soli TBEA3T (95.9 %) and Comamonas terrigena LMG 1253T (95.9 %). Strain GAU11T contained ubiquinone 8 as the sole ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Its major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain GAU11T was 68.2 mol%. The DNA–DNA relatedness between strain GAU11T and C. zonglianii DSM 22523T was 52 or 68 % (reciprocal value). Phenotypic characterization indicated that strain GAU11T represents a member of the genus Comamonas , but at the same time distinguished it from C. zonglianii DSM 22523T. From polyphasic characterization, this strain should be classified as representing a novel species of the genus Comamonas , for which the name Comamonas humi sp. nov. (type strain GAU11T = JCM 19903T = DSM 28451T) is proposed.
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Mizugakiibacter sediminis gen. nov., sp. nov., isolated from a freshwater lake
More LessA novel, moderately thermophilic, bacterial strain (skMP5T) was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. Growth was observed at temperatures ranging from 25 to 52 °C, with optimum growth observed at 48–50 °C. The pH range for growth was pH 5.0–8.2, with optimum growth at pH 6.0–7.0. The G+C content of genomic DNA was 72 mol%. The major components in the fatty acid profile were iso-C17 : 0 and iso-C17 : 1ω9c. The predominant isoprenoid quinone of the strain was ubiquinone Q-8. The strain was facultatively anaerobic, and reduced nitrate to nitrite under anoxic conditions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was a member of the family Xanthomonadaceae within the class Gammaproteobacteria , showing highest sequence similarity with Tahibacter aquaticus RaM5-2 (93.6 %) and Metallibacterium scheffleri DKE6T (93.3 %). On the basis of phylogenetic and phenotypic properties, strain skMP5T represents a novel species of a new genus, Mizugakiibacter sediminis gen. nov., sp. nov. The type strain of the type species is skMP5T ( = DSM 27098T = NBRC 109608T).
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Marinobacterium mangrovicola sp. nov., a marine nitrogen-fixing bacterium isolated from mangrove roots of Rhizophora mangle
More LessA nitrogen-fixing marine bacterium, designated strain Gal22T, was isolated from mangrove roots of Rhizophora mangle. Cells were Gram-stain-negative rods, motile with a single polar flagellum. Growth was observed at 4–42 °C, pH 5.5 to 10 and with 0–18 % (w/v) NaCl. Strain Gal22T was positive for catalase and oxidase. Q-8 was the predominant lipoquinone. The DNA G+C content was 57.0 mol%. Based on phylogenetic analysis of 16S rRNA gene, strain Gal22T belongs to the genus Marinobacterium . The closely related strains were shown to be Marinobacterium lutimaris DSM 22012T and Marinobacterium litorale IMCC1877T with 99 % and 96 % 16S rRNA gene sequence similarity, respectively. DNA–DNA relatedness analysis indicated that strain Gal22T was different from M. lutimaris DSM 22012T. On the basis of genotypic, morphological and biochemical characteristics, a novel species, Marinobacterium mangrovicola sp. nov. (type strain, Gal22T = DSM 27697T = CIP 110653T), is proposed.
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Arenimonas maotaiensis sp. nov., isolated from fresh water
More LessA translucent, white, Gram-reaction-negative, facultatively anaerobic, non-flagellated, slightly curved or curved bacterial strain, designated YT8T, was isolated from the fresh water of the Maotai section of Chishui River, China. Cells were catalase-positive and oxidase-positive. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain YT8T is a member of the genus Arenimonas with similarity to other members of this genus ranging from 93.7 to 95.0 %. The major isoprenoid quinone was ubiquinone 8 (Q-8), major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, two unidentified phospholipids and two unidentified polar lipids, while major fatty acids were iso-C15 : 0, iso-C14 : 0 and anteiso-C15 : 0. The DNA G+C content of strain YT8T was 66.6 mol%. On the basis of phenotypic, phylogenetic and genotypic features studied, strain YT8T is suggested to represent a novel species of the genus Arenimonas , for which the name Arenimonas maotaiensis sp. nov. is proposed. The type strain is YT8T ( = CGMCC 1.12726T = JCM 19710T).
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Acinetobacter gandensis sp. nov. isolated from horse and cattle
We previously reported the presence of an OXA-23 carbapenemase in an undescribed species of the genus Acinetobacter isolated from horse dung at the Faculty of Veterinary Medicine, Ghent University, Belgium. Here we include six strains to corroborate the delineation of this taxon by phenotypic characterization, DNA–DNA hybridization, 16S rRNA gene and rpoB sequence analysis, % G+C determination, MALDI-TOF MS and fatty acid analysis. The nearly complete 16S rRNA gene sequence of strain UG 60467T showed the highest similarities with those of the type strains of Acinetobacter bouvetii (98.4 %), Acinetobacter haemolyticus (97.7 %), and Acinetobacter schindleri (97.2 %). The partial rpoB sequence of strain UG 60467T showed the highest similarities with ‘Acinetobacter bohemicus’ ANC 3994 (88.6 %), A. bouvetii NIPH 2281 (88.6 %) and A. schindleri CIP 107287T (87.3 %). Whole-cell MALDI-TOF MS analyses supported the distinctness of the group at the protein level. The predominant fatty acids of strain UG 60467T were C12 : 0 3-OH, C12 : 0, C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). Strains UG 60467T and UG 60716 showed a DNA–DNA relatedness of 84 % with each other and a DNA–DNA relatedness with A. schindleri LMG 19576T of 17 % and 20 %, respectively. The DNA G+C content of strain UG 60467T was 39.6 mol%. The name Acinetobacter gandensis sp. nov. is proposed for the novel taxon. The type strain is UG 60467T ( = ANC 4275T = LMG 27960T = DSM 28097T).
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Amylibacter marinus gen. nov., sp. nov., isolated from surface seawater
More LessA Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, designated strain 2-3T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. This strain grew well with starch. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Rhodobacteraceae and that the strain was related most closely to the genus Pacificibacter (94.0 % sequence similarity to the type strain). The DNA G+C content was 52.4 mol%. The major fatty acids were C18 : 1ω7c, C14 : 0 and C16 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. The major isoprenoid quinone was Q-10. Strain 2-3T did not grow at 4 or 35 °C, while the type strain of the type species of the genus Pacificibacter grows at both temperatures. From the taxonomic data obtained in this study, it is proposed that strain 2-3T be placed into a novel genus and species named Amylibacter marinus gen. nov., sp. nov. in the family Rhodobacteraceae . The type strain of Amylibacter marinus is 2-3T ( = NBRC 110140T = LMG 28364T).
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Amphritea ceti sp. nov., isolated from faeces of Beluga whale (Delphinapterus leucas)
More LessA Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated RA1T, was isolated from faeces collected from Beluga whale (Delphinapterus leucas) in Yeosu aquarium, South Korea. Strain RA1T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain RA1T joins the cluster comprising the type strains of three species of the genus Amphritea , with which it exhibited 95.8–96.0 % sequence similarity. Sequence similarities to the type strains of other recognized species were less than 94.3 %. Strain RA1T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain RA1T were phosphatidylethanolamine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain RA1T was 47.4 mol%. The differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain RA1T is separated from other species of the genus Amphritea . On the basis of the data presented, strain RA1T is considered to represent a novel species of the genus Amphritea , for which the name Amphritea ceti sp. nov. is proposed. The type strain is RA1T ( = KCTC 42154T = NBRC 110551T).
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Granulosicoccus marinus sp. nov., isolated from Antarctic seawater, and emended description of the genus Granulosicoccus
More LessA Gram-staining-negative, motile by flagella, non-pigmented, poly-β-hydroxybutyrate-producing, strictly aerobic and sphere-shaped bacterium, IMCC3490T, was isolated from a coastal seawater sample from the Antarctic Peninsula. Optimal growth of strain IMCC3490T was observed at 20 °C, pH 8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain IMCC3490T belonged to the genus Granulosicoccus in the family Granulosicoccaceae . The strain was closely related to Granulosicoccus antarcticus IMCC3135T (98.8 % 16S rRNA gene sequence similarity) and Granulosicoccus coccoides Z 271T (98.5 %). The DNA–DNA relatedness values between IMCC3490T and type strains of the two species of the genus were far lower than 70 %, which indicated strain IMCC3490T is a novel genomic species of the genus Granulosicoccus . The major fatty acids of strain IMCC3490T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The isoprenoid quinone detected was ubiquinone-8 (Q-8) and predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 61.0 mol%. On the basis of phylogenetic analyses, DNA–DNA relatedness values and phenotypic data, it is suggested that strain IMCC3490T represents a novel species of the genus Granulosicoccus , for which the name Granulosicoccus marinus sp. nov. is proposed. The type strain is IMCC3490T ( = KACC 17483T = NBRC 109704T). An emended description of the genus Granulosicoccus is also provided.
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Brucella papionis sp. nov., isolated from baboons (Papio spp.)
Two Gram-negative, non-motile, non-spore-forming coccoid bacteria (strains F8/08-60T and F8/08-61) isolated from clinical specimens obtained from baboons (Papio spp.) that had delivered stillborn offspring were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence similarities, both strains, which possessed identical sequences, were assigned to the genus Brucella . This placement was confirmed by extended multilocus sequence analysis (MLSA), where both strains possessed identical sequences, and whole-genome sequencing of a representative isolate. All of the above analyses suggested that the two strains represent a novel lineage within the genus Brucella . The strains also possessed a unique profile when subjected to the phenotyping approach classically used to separate species of the genus Brucella, reacting only with Brucella A monospecific antiserum, being sensitive to the dyes thionin and fuchsin, being lysed by bacteriophage Wb, Bk2 and Fi phage at routine test dilution (RTD) but only partially sensitive to bacteriophage Tb, and with no requirement for CO2 and no production of H2S but strong urease activity. Biochemical profiling revealed a pattern of enzyme activity and metabolic capabilities distinct from existing species of the genus Brucella . Molecular analysis of the omp2 locus genes showed that both strains had a novel combination of two highly similar omp2b gene copies. The two strains shared a unique fingerprint profile of the multiple-copy Brucella-specific element IS711. Like MLSA, a multilocus variable number of tandem repeat analysis (MLVA) showed that the isolates clustered together very closely, but represent a distinct group within the genus Brucella . Isolates F8/08-60T and F8/08-61 could be distinguished clearly from all known species of the genus Brucella and their biovars by both phenotypic and molecular properties. Therefore, by applying the species concept for the genus Brucella suggested by the ICSP Subcommittee on the Taxonomy of Brucella, they represent a novel species within the genus Brucella , for which the name Brucella papionis sp. nov. is proposed, with the type strain F8/08-60T ( = NCTC 13660T = CIRMBP 0958T).
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Description of Comamonas serinivorans sp. nov., isolated from wheat straw compost
More LessA Gram-stain-negative bacterium, designated SP-35T, was isolated from compost and was subjected to a taxonomic study. This isolate was short-rod-shaped and non-spore-forming. Phylogenetic analysis based on 16S rRNA sequence comparison indicated the isolate was related to the genus Comamonas . 16S rRNA gene sequence analysis showed that its closest neighbours were the type strains Comamonas odontotermitis Dant 3-8T (96.8 % similarity), Comamonas testosteroni DSM 50244T (96.5 %), Comamonas guangdongensis CY01T (95.9 %) and Comamonas composti YY287T (95.6 %). Using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics we could clearly distinguish strain SP-35T from type strains of the genus Comamonas . The genomic DNA G+C content of strain SP-35T was 63.1 mol%. The predominant cellular fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidlyglycerol. Differences in phenotypic and phylogenetic characteristics support the classification of strain SP-35T as a representative of a novel species in the genus Comamonas , for which the name Comamonas serinivorans sp. nov. is proposed. The type strain is SP-35T ( = DSM 26136T = JCM 18194T).
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Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov.
More LessA taxonomic study was carried out on strain P73T, which was isolated from deep-sea sediment of the Indian Ocean by enrichment of polycyclic aromatic hydrocarbons. The strain was able to degrade biphenyl, naphthalene, 2-methylnaphthalene, 2,6-dimethylnaphthalene, acenaphthene, anthracene, phenanthrene, dibenzothiophene, dibenzofuran, fluorene, 4-methyldibenzothiophene and fluoranthene, but not pyrene or chrysene. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P73T formed a clade with the genera Celeribacter and Huaishuia within the family Rhodobacteraceae , with highest sequence similarity of 96.98 % to Celeribacter neptunius H 14T, followed by Huaishuia halophila ZXM137T (96.42 %). The bacterium was Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at salinities from 0.5 to 12 % and at temperatures from 10 to 41 °C. The principal fatty acids (>10 %) of strain P73T were summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0ω8c cyclo. The sole respiratory quinone was Q-10. The major lipids were phosphatidylglycerol, one unknown aminolipid, one unknown phospholipid and one unknown lipid; a second unknown phospholipid and one unknown glycolipid were present as minor components. The G+C content of the chromosomal DNA was 66.0 mol%. The combined genotypic and phenotypic data show that strain P73T represents a novel species of the genus Celeribacter , for which the name Celeribacter indicus sp. nov. is proposed. The type strain is P73T ( = MCCC 1A01112T = LMG 27600T = DSM 27257T). Phylogenetic study and existing phenotypic information also show that Huaishuia halophila should be transferred to the genus Celeribacter as Celeribacter halophilus comb. nov. (type strain ZXM137T = MCCC 1A06432T = CGMCC 1.8891T = LMG 24854T).
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Erythrobacter lutimaris sp. nov., isolated from a tidal flat sediment
More LessA Gram-stain-negative, non-motile, coccoid- or oval-shaped bacterial strain, designated S-5T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea and was subjected to a polyphasic taxonomic study. Strain S-5T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining analysis based on 16S rRNA gene sequences showed that strain S-5T fell within the clade comprising the species of the genus Erythrobacter , clustering with the type strains of Erythrobacter pelagi , Erythrobacter citreus and Erythrobacter seohaensis with which it exhibited the highest 16S rRNA gene sequence similarity (96.0–96.7 %). The DNA G+C content was 66.0 mol%. Strain S-5T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω6c as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid and two unidentified lipids. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain S-5T is distinguishable from other species of the genus Erythrobacter . On the basis of the data presented, strain S-5T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter lutimaris sp. nov. is proposed. The type strain is S-5T ( = KCTC 42109T = CECT 8624T).
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Defluviimonas aquaemixtae sp. nov., isolated from the junction between a freshwater spring and the ocean
More LessA Gram-stain-negative, coccoid- or short-rod-shaped and non-gliding bacterial strain, designated CDM-7T, was isolated from the zone where the ocean meets a freshwater spring at Jeju island, South Korea, and was subjected to a polyphasic taxonomic study. Strain CDM-7T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain CDM-7T falls within the clade comprising species of the genus Defluviimonas, clustering with the type strain of Defluviimonas aestuarii , with which it exhibited the highest 16S rRNA gene sequence similarity value (98.4 %). The 16S rRNA gene sequence similarity values between strain CDM-7T and the type strains of Defluviimonas denitrificans and Defluviimonas indica were 97.1 and 96.2 %, respectively. The genomic DNA G+C content was 66.8 mol% and the mean DNA–DNA relatedness values between strain CDM-7T and the type strains of D. aestuarii and D. denitrificans were 15.6±2.5 and 6.7±3.2 %, respectively. Strain CDM-7T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain CDM-7T is distinguishable from other species of the genus Defluviimonas . On the basis of the data presented, strain CDM-7T is considered to represent a novel species of the genus Defluviimonas , for which the name Defluviimonas aquaemixtae sp. nov. is proposed. The type strain is CDM-7T ( = KCTC 42108T = CECT 8626T).
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- Bacteroidetes
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Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert
More LessA Gram-stain-negative, short rod-shaped, non-motile, non-spore-forming bacterial strain, designated H7T, was isolated from the Gobi desert, Xinjiang Province of China. The temperature, NaCl and pH ranges for growth were 8–40 °C (optimum 30 °C), 0–5 % (w/v) NaCl and pH 6–10 (optimum pH 7), respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H7T belonged to the genus Sphingobacterium and showed highest sequence similarity (91 %) to Sphingobacterium composti DSM 18850. The genomic DNA G+C content was 44.3 mol%. MK-7 was identified as the predominant respiratory quinone. Strain H7T contained C16 : 1ω7c and/or C16 : 1ω6c, iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids. These data support the affiliation of strain H7T to the genus Sphingobacterium while phenotypic data indicated it is a representative strain of a novel species for which the name Sphingobacterium gobiense sp. nov. is proposed. The type strain is H7T ( = ACCC 05757T = KCTC 32293T).
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Microbacter margulisiae gen. nov., sp. nov., a propionigenic bacterium isolated from sediments of an acid rock drainage pond
More LessA novel anaerobic propionigenic bacterium, strain ADRIT, was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4–0.6×1–1.7 µm), non-motile and non-spore-forming rods. Cells possessed a Gram-negative cell-wall structure and were vancomycin-resistant. Strain ADRIT utilized yeast extract and various sugars as substrates and formed propionate, lactate and acetate as major fermentation products. The optimum growth temperature was 30 °C and the optimum pH for growth was pH 6.5, but strain ADRIT was able to grow at a pH as low as 3.0. Oxidase, indole formation, and urease and catalase activities were negative. Aesculin and gelatin were hydrolysed. The predominant cellular fatty acids of strain ADRIT were anteiso-C15 : 0 (30.3 %), iso-C15 : 0 (29.2 %) and iso-C17 : 0 3-OH (14.9 %). Major menaquinones were MK-8 (52 %) and MK-9 (48 %). The genomic DNA G+C content was 39.9 mol%. Phylogenetically, strain ADRIT was affiliated to the family Porphyromonadaceae of the phylum Bacteroidetes . The most closely related cultured species were Paludibacter propionicigenes with 16S rRNA gene sequence similarity of 87.5 % and several species of the genus Dysgonomonas (similarities of 83.5–85.4 % to the type strains). Based on the distinctive ecological, phenotypic and phylogenetic characteristics of strain ADRIT, a novel genus and species, Microbacter margulisiae gen. nov., sp. nov., is proposed. The type strain is ADRIT ( = JCM 19374T = DSM 27471T).
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Flavisolibacter rigui sp. nov., isolated from freshwater of an artificial reservoir and emended description of the genus Flavisolibacter
More LessA non-motile and rod-shaped bacterium, designated strain 02SUJ3T, was isolated from freshwater collected from the Juam Reservoir (Republic of Korea). Cells were Gram-stain-negative, aerobic, oxidase-negative and catalase-positive. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The strain contained MK-7 as the major isoprenoid quinone. The main polar lipid was phosphatidylethanolamine. The DNA G+C content was 46.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain 02SUJ3T forms an independent lineage within the genus Flavisolibacter with low sequence similarity to Flavisolibacter ginsengiterrae Gsoil 492T and Flavisolibacter ginsengisoli Gsoil 643T (95.7 %). Phenotypic characteristics distinguished strain 02SUJ3T from members of the genus Flavisolibacter . On the basis of the evidence presented in this study, strain 02SUJ3T is considered to represent a novel species, for which the name Flavisolibacter rigui sp. nov. is proposed. The type strain is 02SUJ3T ( = JCM 17515T = KCTC 23328T). An emended description of the genus Flavisolibacter is also provided.
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Pedobacter rivuli sp. nov., isolated from a freshwater stream
More LessA Gram-staining-negative, rod-shaped, red strain, HME8457T, was isolated from a freshwater stream located in the Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8457T formed a lineage within the genus Pedobacter . Strain HME8457T was most closely related to species of the genus Pedobacter : Pedobacter daechungensis Dae 13T (96.4 % sequence similarity), Pedobacter lentus DS-40T (95.3 %), Pedobacter terricola DS-45T (94.9 %), Pedobacter glucosidilyticus 1-2T (94.2 %) and ‘Pedobacter soyangensis’ HME6451 (93.6 %). The major fatty acids were iso-C15 : 0 (28.8 %), summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 21.7 %), iso-C17 : 0 3-OH (7.7 %) and anteiso-C15 : 0 (6.2 %). The only respiratory quinone was MK-7. Polar lipid analysis revealed the presence of phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. Sphingolipid was present. The DNA G+C content was 33.3 mol%. On the basis of the evidence presented in this study, strain HME8457T represents a novel species of the genus Pedobacter , for which the name Pedobacter rivuli sp. nov. is proposed; the type strain is HME8457T ( = KACC 17312T = CECT 8291T).
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Hymenobacter roseus sp. nov., isolated from sand
More LessStrain JC245T was isolated from a sand sample, and appeared as dark pink colonies on agar plates with cells staining Gram-negative. Catalase and oxidase activities were positive. Casein was hydrolysed while chitin, gelatin and starch were not. Major (>5 %) fatty acids were iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 1ω5c, C16 : 1ω6c/C16 : 1ω7c, anteiso-C17 : 1 B/iso-C17 : 1 I and iso-C17 : 0 3-OH. Strain JC245T contained phosphatidylethanolamine and two unidentified lipids as the major polar lipids, with minor amounts of four unidentified lipids and an unidentified amino lipid. Bacterial hopane derivatives and adenosylhopane were the major hopanoids. Hydroxyflexixanthin was identified as one of the major carotenoids of strain JC245T along with five unidentified carotenoids. The genomic DNA G+C content was 52.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC245T represents a member of the genus Hymenobacter within the family Cytophagaceae of the phylum Bacteroidetes . Strain JC245T shared the highest 16S rRNA gene sequence similarity with Hymenobacter roseosalivarius AA-718T (98.3 %) and other members of the genus Hymenobacter (<95.1 %). However, strain JC245T showed 21±2 % relatedness (based on DNA–DNA hybridization) with H. roseosalivarius DSM 11622T. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC245T as a representative of a novel species in the genus Hymenobacter , for which the name Hymenobacter roseus sp. nov. is proposed. The type strain is JC245T ( = KCTC 42090T = LMG 28260T).
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Epilithonimonas xixisoli sp. nov., isolated from wetland bank-side soil
More LessA novel Gram-staining-negative, non-motile and rod-shaped bacterial strain containing flexirubin-type pigments, designated S31T, was isolated from bank-side soil of the Xixi wetland in Zhejiang province, China. Growth occurred at 10–37 °C (optimum, 32 °C), pH 6–8 (optimum, pH 7) and with 0–2 % (w/v) NaCl (optimum, 1 %). Strain S31T shared highest 16S rRNA gene sequence similarities with Epilithonimonas lactis H1T (96.2 %) and Chryseobacterium molle DW3T (96.4 %). Phylogenetic analysis suggested that strain S31T was a member of the genus Epilithonimonas . The dominant respiratory quinone was MK-6 and the DNA G+C content was 33.3 mol%. The major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and anteiso-C15 : 0. The major polar lipids of strain S31T were phosphatidylethanolamine, three unidentified aminolipids and four unidentified polar lipids. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S31T represents a novel species of the genus Epilithonimonas , for which the name Epilithonimonas xixisoli sp. nov. (type strain S31T = CGMCC 1.12802T = NBRC 110387T) is proposed.
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Flavobacterium gyeonganense sp. nov., isolated from freshwater, and emended descriptions of Flavobacterium chungangense, Flavobacterium aquidurense, Flavobacterium tructae and Flavobacterium granuli
More LessA Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated HME7524T, was isolated from freshwater of Gyeong-an stream in Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME7524T formed a distinct lineage within the genus Flavobacterium and exhibited high sequence similarity with Flavobacterium chungangense CJ7T (96.9 %), Flavobacterium aquidurense WB-1.1.56T (96.9 %), Flavobacterium tructae 435-08T (96.9 %) and Flavobacterium granuli Kw05T (96.9 %). The major fatty acids of strain HME7524T were iso-C15 : 0 (26.5 %) and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 17.4 %). The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and three unidentified polar lipids. The major respiratory quinone was MK-6. The DNA G+C content of strain HME7524T was 34.2 mol%. On the basis of the evidence presented in this study, strain HME7524T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium gyeonganense sp. nov., is proposed. The type strain is HME7524T ( = KACC 17688T = CECT 8365T). Emended descriptions of Flavobacterium chungangense , Flavobacterium aquidurense , Flavobacterium tructae and Flavobacterium granuli are also provided.
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- Firmicutes and Related Organisms
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Paenibacillus susongensis sp. nov., a mineral-weathering bacterium
More LessA Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterial strain, designated M327T, was isolated from the weathered surfaces of rock (mica schist) from Susong, Anhui Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M327T belonged to the genus Paenibacillus and was related most closely to Paenibacillus terrigena A35T (98.6 % similarity) and Paenibacillus selenitireducens ES3-24T (98.3 %). Strain M327T contained meso-diaminopimelic acid in the cell wall and MK-7 as the major menaquinone. The main fatty acids of strain M327T were anteiso-C15 : 0 and iso-C16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown aminophospholipids and an unknown lipid. The total DNA G+C content of strain M327T was 48.6 mol%. Based on the low level of DNA–DNA relatedness (ranging from 26.6 to 33.1 %) to these type strains of species of the genus Paenibacillus and unique phenotypic characteristics, it is suggested that strain M327T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus susongensis sp. nov. is proposed. The type strain is M327T ( = CCTCC AB 2014058T = LMG 28236T = JCM 19951T).
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Lactobacillus gorillae sp. nov., isolated from the faeces of captive and wild western lowland gorillas (Gorilla gorilla gorilla)
Four strains of Gram-staining-positive, anaerobic rods were isolated from the faeces of western lowland gorillas (Gorilla gorilla gorilla). Three strains, KZ01T, KZ02 and KZ03, were isolated at the Kyoto City Zoo, Japan, and one strain, GG02, was isolated in the Moukalaba-Doudou National Park, Gabon. These strains were investigated taxonomically. These strains belonged to the Lactobacillus reuteri phylogenetic group according to phylogenetic analysis based on 16S rRNA gene sequences and specific phenotypic characteristics. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains KZ01T, KZ02, KZ03 and GG02 formed a single monophyletic cluster and had a distinct line of descent. Based on sequence similarity of the 16S rRNA gene, Lactobacillus fermentum JCM 1173T (96.6 %) was the closest neighbour to these novel strains, although it was clear that these strains belonged to a different species. Partial pheS sequences also supported these relationships. DNA–DNA relatedness between strain KZ01T and L. fermentum JCM 1173T was less than 22 % and the DNA G+C content of strain KZ01T was 50.7 mol%. The cell-wall peptidoglycan type was A4β (l-Orn–d-Asp) and the major fatty acids were C16 : 0, C18 : 1ω9c and C19 : 1 cyclo 9,10. Therefore, based on phylogenetic, phenotypic and physiological evidence, these strains represent a novel species of the genus Lactobacillus , for which the name Lactobacillus gorillae sp. nov. is proposed. The type strain is KZ01T ( = JCM 19575T = DSM 28356T).
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Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia
A Gram-staining-positive, spore-forming, obligately anaerobic, acetogenic bacterium, designated LAM1030T, was isolated from methanogenic consortia enriched from biogas slurry collected from the large-scale anaerobic digester of Modern Farming Corporation in Hebei Province, China. Cells of strain LAM1030T were motile, straight or spiral-rod-shaped. Strain LAM1030T could utilize glucose, fructose, maltose, galactose, lactose, sucrose, cellobiose, mannitol, pyruvate, succinic acid and tryptophan as the sole carbon source. Acetic acid, isovaleric acid and butanoic acid were the main products of glucose fermentation. Sodium sulfite was used as an electron acceptor. Growth of strain LAM1030T was completely inhibited by the addition of ampicillin, tetracycline, gentamicin or erythromycin at a concentration of 20 µg ml−1. The main polar lipids of strain LAM1030T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, 11 unknown glycolipids and two unknown phospholipids. No respiratory quinone was detected. The major fatty acids of strain LAM1030T were C16 : 0 (21.1 %), C14 : 0 (10.3 %), summed feature 9 (including C16:0 10-methyl and/or iso-C17:1 ω9c) (11.3% ), summed feature 3 (including C16:1 ω7c and/or C16:1 ω6c) (10.6% ) and iso-C15 : 0 (6.6 %). Analysis of the 16S rRNA gene sequence indicated that strain LAM1030T belonged to the genus Clostridium and was most closely related to Clostridium subterminale DSM 6970T, Clostridium thiosulfatireducens DSM 13105T and Clostridium sulfidigenes DSM 18982T, with 97.0, 96.9 and 96.8 % similarity, respectively. The G+C content of the genomic DNA of strain LAM1030T was 31.2±0.3 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characterization, strain LAM1030T is suggested to represent a novel species of the genus Clostridium , for which the name Clostridium huakuii sp. nov. is proposed. The type strain is LAM1030T ( = ACCC 00698T = JCM 19186T).
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Domibacillus enclensis sp. nov., isolated from marine sediment, and emended description of the genus Domibacillus
More LessA novel red-pigmented bacterial strain, designated NIO-1016T, was isolated from a sediment sample from Chorao Island, India and was investigated by a polyphasic taxonomic approach. The strain was Gram-reaction-positive, strictly aerobic, motile and catalase-positive and produced spherical to slightly ellipsoidal endospores with subterminal position on swollen sporangia. The genomic DNA G+C content was 46.9 mol%. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and C16 : 0. The predominant quinones were MK-6 (89.3 %) and MK-7 (8.7 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, and an unidentified phospholipid. meso-Diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan and the major whole-cell sugars were glucose and ribose. The closest phylogenetic neighbours were identified as Domibacillus robiginosus DSM 25058T (98.0 % similarity) and Domibacillus indicus DSM 28032T (97.2 % similarity), other species of the genus Bacillus displayed below 96 % similarity. Phylogenetic, physiological, biochemical and morphological differences between strain NIO-1016T and its closest neighbours indicate that this strain represents a novel species in the genus Domibacillus in the family Bacillaceae for which the name Domibacillus enclensis sp. nov. is proposed with the type species NIO-1016T ( = DSM 25145T = NCIM 5462T = CCTCC AB 2011121T).
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Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae
More LessA halophilic actinomycete, strain R4S8T, was isolated from soil of Inche-Broun hypersaline wetland in the north of Iran. The isolate grew aerobically at temperatures of 30–50 °C (optimum 40 °C), pH 6–10 (optimum pH 7.0) and in the presence of 1–15 % (w/v) NaCl (optimum 3–5 %). It formed short and straight to moderately flexuous aerial mycelium without motile elements. The cell wall of strain R4S8T contained meso-diaminopimelic acid as the diamino acid without any diagnostic sugars. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylmonomethylethanolamine two unknown phospholipids and one unknown aminophospholipid. It synthesized anteiso-C15 : 0 (44.8 %), iso-C15 : 0 (28.8 %) and iso-C14 : 0 (8.5 %) as major fatty acids. MK-6 was the predominant respiratory quinone. The G+C content of the genomic DNA was 52.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R4S8T belongs to the family Thermoactinomycetaceae and showed the closest 16S rRNA gene sequence similarity with Desmospora activa IMMIB L-1269T (95.5 %) and Marininema mesophilum SCSIO 10219T (95.3 %). On the basis of phylogenetic analysis and phenotypic characteristics, strain R4S8T represents a novel species in a new genus within the family Thermoactinomycetaceae , for which the name Salinithrix halophila gen. nov., sp. nov. is proposed. The type strain of the type species is R4S8T ( = IBRC-M 10813T = CECT 8506T).
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Microbacterium petrolearium sp. nov., isolated from an oil-contaminated water sample
A Gram-staining-positive, rod-shaped, aerobic bacterium, designated strain LAM0410T, was isolated from an oil-contaminated water sample from the Dagang Oilfield, PR China. The temperature and pH ranges for growth were 4 °C to 50 °C and pH 4.4 to pH 12.0, respectively. The strain did not need NaCl for growth, but could tolerate a concentration of up to 12 % (w/v). Cell wall hydrolysates from the isolate showed that the diamino acid was ornithine. The cell wall sugars contained ribose and galactose. The glycan moiety of the cell wall contained N-glycolyl residues. The major respiratory quinones were MK-10, MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and nine unknown glycolipids. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Microbacterium and was closely related to Microbacterium sediminis MCCC 1A06153T and Microbacterium murale DSM 22178T with 97.5 % and 97.4 % sequence similarities, respectively; while the DNA–DNA hybridization values were 33.1±3.4 % and 21.8±1.6 %, respectively. The DNA G+C content was 67.4 mol%, as determined by the T m method. Based on its phenotypic and genotypic properties, strain LAM0410T represents a novel species of the genus Microbacterium , for which the name Microbacterium petrolearium sp. nov. is proposed; the type strain is LAM0410T ( = ACCC 00719T = JCM 19612T).
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Reclassification of Staphylococcus jettensis De Bel et al. 2013 as Staphylococcus petrasii subsp. jettensis subsp. nov. and emended description of Staphylococcus petrasii Pantucek et al. 2013
The type and clinical strains of two recently described coagulase-negative species of the genus Staphylococcus, Staphylococcus petrasii and Staphylococcus jettensis , were compared using dnaJ, tuf, gap, hsp60 and rpoB gene sequences, DNA–DNA hybridization, ribotyping, repetitive sequence-based PCR fingerprinting and extensive biochemical characterization. Based on the results, the species description of S. petrasii has been emended and S. jettensis should be reclassified as a novel subspecies within S. petrasii for which the name Staphylococcus petrasii subsp. jettensis subsp. nov. is proposed. The type strain is SEQ110T ( = LMG 26879T = CCUG 62657T = DSM 26618T = CCM 8494T).
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- Actinobacteria
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Nesterenkonia rhizosphaerae sp. nov., an alkaliphilic actinobacterium isolated from rhizosphere soil in a saline-alkaline desert
An alkaliphilic actinobacterial strain, designated EGI 80099T, was isolated from a rhizosphere soil sample of Reaumuria soongorica found in the desert soils of Fukang, Xinjiang, north-west China. Cells of strain EGI 80099T were Gram-stain-positive, non-motile, non-endospore-forming cocci. The predominant menaquinones were MK-7, MK-8 and MK-9. The major cellular fatty acids (>10 %) were anteiso-C15 : 0 and anteiso-C17 : 0. Analysis of the cell wall showed the presence of peptidoglycan of the type l-Lys–Gly–l-Glu, variation A4α. Cells of the isolate contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unknown phospholipid and an unidentified glycolipid as polar lipids. The genomic DNA G+C content was 63.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80099T belongs to the genus Nesterenkonia , sharing 95.68–97.37 % sequence similarities with the type strains of recognized species within this genus. DNA–DNA hybridization of strain EGI 80099T with the type strains of species that showed the highest sequence similarities, Nesterenkonia aethiopica DSM 17733T (97.37 %), Nesterenkonia flava CAAS 251T (97.23 %) and Nesterenkonia xinjiangensis YIM 70097T (97.02 %), gave relatedness values of 8.7–62.2 %. Data from DNA–DNA hybridizations and physiological and biochemical tests indicated that strain EGI 80099T represents a novel species of the genus Nesterenkonia , for which the name Nesterenkonia rhizosphaerae sp. nov. is proposed. The type strain is EGI 80099T ( = BCRC 16947T = JCM 19129T).
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Saccharothrix carnea sp. nov., an actinobacterium isolated from soil
A novel actinobacterium, designated strain NEAU-yn17T, was isolated from a soil sample collected at the wastewater discharge site of a pesticide factory in Harbin, northern China, and characterized using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-yn17T were consistent with the description of the genus Saccharothrix , such as the spore arrangement, the diamino acid of the peptidoglycan, the whole-cell hydrolysates, the predominant menaquinone and the phospholipid profile. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-yn17T should also be classified in the genus Saccharothrix , with Saccharothrix saharensis DSM 45456T (99.52 % sequence similarity) and Saccharothrix xinjiangensis JCM 12329T (99.04 %) as the nearest phylogenetic relatives. A combination of DNA–DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-yn17T can be distinguished from its closest relatives. Therefore, strain NEAU-yn17T represents a novel species of the genus Saccharothrix , for which the name Saccharothrix carnea sp. nov. is proposed. The type strain is NEAU-yn17T ( = CGMCC 4.7097T = DSM 45878T).
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Streptomyces burgazadensis sp. nov., isolated from soil
A novel actinobacterial strain, designated Z1R7T, was isolated from a soil sample collected from Burgazada, in the Marmara Sea (Turkey), and the strain identity was determined using a polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces and it formed a distinct phyletic line in the 16S rRNA gene tree, together with the type strains Streptomyces specialis GW41-1564T (95.76 %), Streptomyces mayteni YIM 60475T (95.64 %), Streptomyces hainanensis YIM 47672T (95.53 %), Streptomyces hoynatensis S1412T (95.29 %), Streptomyces avicenniae MCCC 1A01535T (94.74 %), Streptomyces sedi YIM 65188T (94.59 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (94.68 %). Chomotaxonomic data revealed that strain Z1R7T possesed MK-9 (H8) as the predominant menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid, and galactose, glucose and ribose as whole cell sugars. Diphosphatidylglycerol, phoshphatidylethanolamine and phosphatidylinositol were the predominant polar lipids; iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0 were the major fatty acids, and the genomic DNA G+C content was 69.4 mol%. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z1R7T ( = KCTC 29434T = DSM 42126T) should be classified in the genus Streptomyces as Streptomyces burgazadensis sp. nov.
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Gryllotalpicola soli sp. nov., isolated from soil
A novel Gram-stain-positive, short rod-shaped, non-flagellated and mesophilic strain, KIS12-7T, isolated from a soil sample collected from Daecheong-Island in Ongjin County, Republic of Korea, was studied using a polyphasic approach. Phylogenetic trees based on the 16S rRNA gene sequence revealed that the novel strain was a member of the genus Gryllotalpicola , showing more than 97.0 % sequence similarity with Gryllotalpicola daejeonensis RU-04T (98.0 %), Gryllotalpicola koreensis RU-16T (97.7 %) and Gryllotalpicola kribbensis PU-02T (97.3 %). However, DNA–DNA relatedness values demonstrated that strain KIS12-7T could be clearly distinguished from closely related species of the genus Gryllotalpicola . The cell-wall peptidoglycan of strain KIS12-7T was of the type B2 and the acyl type was acetyl. The predominant menaquinones were MK-11 and MK-10. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phosphoglycolipid, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The G+C content of the genomic DNA was 72.1 mol%. On the basis of the evidence presented, strain KIS12-7T is a representative of a novel species of the genus Gryllotalpicola , and the name Gryllotalpicola soli sp. nov. is proposed; the type strain is KIS12-7T ( = DSM 27182T = KACC 17302T = NBRC 109659T).
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Nocardioides daecheongensis sp. nov., isolated from soil
Strain KIS2-16T was isolated from a soil sample collected from Daecheong Island of Incheon region, South Korea. KIS2-16T was Gram-staining-positive, aerobic, non-spore-forming, non-motile, catalase-positive, oxidase-negative and mesophilic. On the basis of 16S rRNA gene sequence analysis, strain KIS2-16T represented a member of the genus Nocardioides , being most closely related to the type strains of species of the genus Nocardioides , Nocardioides maradonensis RP-B30T (97.8 % sequence similarity) and Nocardioides ultimimeridianus RP-B26T (97.0 %). The fatty acid profile of KIS2-16T was dominated by C18 : 1ω9c, C17 : 1ω8c, C16 : 0, C18 : 0 10-methyl (TBSA), C16 : 0 2-OH and C17 : 0 2-OH. The major isoprenoid quinone was MK-8(H4), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The peptidoglycan structure was A3γ-type with ll-diaminopimelic acid. The genomic DNA G+C content of KIS2-16T was 64.9 mol%. Strain KIS2-16T showed DNA–DNA hybridization values of less than 70 % with the closely related species of the genus Nocardioides . Based on phenotypic, genotypic and phylogenetic data, the isolate represents a novel species of the genus Nocardioides , for which the name Nocardioides daecheongensis sp. nov. (type strain KIS2-16T = DSM 27136T = KACC 17297T = NBRC 109597T) is proposed.
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Streptomyces lopnurensis sp. nov., an actinomycete isolated from soil
More LessA novel actinomycete, designated strain TRM 49590T, was isolated from a soil sample from Lop Nur in Xinjiang Province, China. Strain TRM 49590T was aerobic, Gram-staining-positive, with an optimum NaCl concentration for growth of 1.5 % (w/v) and an optimum temperature for growth of 28–37 °C. The aerial mycelium was sparse, cylindrical and smooth-surfaced with irregular branches on ISP medium 4. The whole-cell sugars of strain TRM 49590T were ribose and glucose. The diagnostic diamino acid contained ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6) and MK-9(H8), with MK-9(H4) and MK-10(H6) present in smaller amounts. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 62.2 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TRM 49590T belongs to the genus Streptomyces with a sequence similarity of 97.16 % with the most closely related species Streptomyces sodiiphilus . Based on these observations, strain TRM 49590T is proposed to represent a novel species of the genus Streptomyces for which the name Streptomyces lopnurensis sp. nov. is suggested. The type strain is TRM 49590T ( = CCTCC AA 2013018T = NRRL B59109T).
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- Eukaryotic Micro-organisms
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Morphology, ontogenetic features and SSU rRNA gene-based phylogeny of a soil ciliate, Bistichella cystiformans spec. nov. (Protista, Ciliophora, Stichotrichia)
More LessThe morphology, ontogeny and SSU rRNA gene-based phylogeny of Bistichella cystiformans spec. nov., isolated from the slightly saline soil of a mangrove wetland in Zhanjiang, southern China, were investigated. The novel species was characterized by having five to eight buccal cirri arranged in a row, three to five transverse cirri, four macronuclear nodules aligned, and 17–32 and 20–34 cirri in frontoventral rows V and VI, respectively, both extending to the transverse cirri. The main ontogenetic features of the novel species were as follows: (1) the parental adoral zone of the membranelles is completely inherited by the proter; (2) the frontoventral and transverse cirri are formed in a six-anlagen mode; (3) basically, the frontal-ventral-transverse cirral anlagen II–V generate one transverse cirrus each at their posterior ends, while anlage VI provides no transverse cirrus; (4) both marginal rows and dorsal kineties develop intrakinetally, no dorsal kinety fragment is formed; and (5) the macronuclear nodules fuse into a single mass at the middle stage. Phylogenetic analyses based on the SSU rRNA gene showed that the novel species groups with the clade containing Bistichella variabilis, Parabistichella variabilis, Uroleptoides magnigranulosus and two species of the genus Orthoamphisiella. Given present knowledge, it was considered to be still too early to come to a final conclusion regarding the familial classification of the genus Bistichella; further investigations of key taxa with additional molecular markers are required.
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Morphology and phylogeny of three karyorelictean ciliates (Protista, Ciliophora), including two novel species, Trachelocerca chinensis sp. n. and Tracheloraphis dragescoi sp. n.
More LessThis paper investigates the morphology and infraciliature of three karyorelictean ciliates, Trachelocerca chinensis sp. n., Tracheloraphis dragescoi sp. n. and a rarely known form, Geleia acuta (Dragesco, 1960) Foissner, 1998, which were isolated from the intertidal zone of sandy beaches at Zhanjiang and Qingdao, China. Trachelocerca chinensis sp. n. is distinguished from related forms by having 26–30 somatic kineties, a narrow glabrous stripe and a single nuclear group composed of approximately four to six macronuclei and two micronuclei. Tracheloraphis dragescoi sp. n. can be recognized through its 14–22 somatic kineties, wide glabrous stripe and a single nuclear group composed of about four macronuclei. Phylogenetic analyses based on small-subunit (SSU) rRNA gene sequences indicated that the genera Trachelocerca and Tracheloraphis are closely related but that neither of them appears to be a clearly monophyletic group. Nonetheless, the monophyly of Trachelocerca is not rejected by the approximately unbiased (AU) test (P = 0.143, >0.05), although that of Tracheloraphis is rejected (P = 0.011, <0.05). Geleia acuta, meanwhile, branched with Geleia fossata and falls in the Geleia clade.
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- Other Bacteria
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Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans
More LessA group of strains representing species of the genus Leptospira, isolated from patients with leptospirosis in Mayotte (Indian Ocean), were previously found to be considerably divergent from other known species of the genus Leptospira . This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. Two strains from each serogroup currently identified within this novel species were studied. Spirochaete, aerobic, motile, helix-shaped strains grew well at 30–37 °C, but not at 13 °C or in the presence of 8-azaguanine. Draft genomes of the strains were also analysed to study the DNA relatedness with other species of the genus Leptospira . The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii , in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA–DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. The G+C content of the genomic DNA was 39.5 mol%. These isolates are considered to represent a novel species, for which the name Leptospira mayottensis sp. nov. is proposed, with 200901116T ( = CIP 110703T = DSM 28999T) as the type strain.
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Deinococcus citri sp. nov., isolated from citrus leaf canker lesions
More LessA Gram-stain-positive, strictly aerobic, non-motile, coccoid bacterium, designated NCCP-154T, was isolated from citrus leaf canker lesions and was subjected to a polyphasic taxonomic study. Strain NCCP-154T grew at 10–37 °C (optimum 30 °C) and at pH 7.0–8.0 (optimum pH 7.0). The novel strain exhibited tolerance of UV irradiation (>1000 J m−2). Based on 16S rRNA gene sequence analysis, strain NCCP-154T showed the highest similarity to Deinococcus gobiensis CGMCC 1.7299T (98.8 %), and less than 94 % similarity to other closely related taxa. The chemotaxonomic data [major menaquinone, MK-8; cell-wall peptidoglycan type, A3β (Orn–Gly2); major fatty acids, summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH; 35.3 %) followed by C16 : 0 (12.7 %), iso-C17 : 1ω9c (9.2 %), C17 : 1ω8c (7.4 %) and iso-C17 : 0 (6.9 %); major polar lipids made up of several unidentified phosphoglycolipids and glycolipids and an aminophospholipid, and mannose as the predominant whole-cell sugar] also supported the affiliation of strain NCCP-154T to the genus Deinococcus . The level of DNA–DNA relatedness between strain NCCP-154T and D. gobiensis JCM 16679T was 63.3±3.7 %. The DNA G+C content of strain NCCP-154T was 70.0 mol%. Based on the phylogenetic analyses, DNA–DNA hybridization and physiological and biochemical characteristics, strain NCCP-154T can be differentiated from species with validly published names. Therefore, it represents a novel species of the genus Deinococcus . The name Deinococcus citri sp. nov. is proposed, with the type strain NCCP-154T ( = JCM 19024T = DSM 24791T = KCTC 13793T).
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Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta
An anaerobic, psychrophilic bacterium, strain MO-SPC2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediments collected from off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. Cells were pleomorphic: spherical, annular, curved rod, helical and coccoid cell morphologies were observed. Motility only occurred in helical cells. Strain MO-SPC2T grew at 0–17 °C (optimally at 9 °C), at pH 6.0–8.0 (optimally at pH 6.8–7.2) and in 20–40 g NaCl l−1 (optimally at 20–30 NaCl l−1). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC2T were phosphatidylglycolipids, phospholipids and glycolipids. The major cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9. Isoprenoid quinones were not detected. The G+C content of the DNA was 32.3 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-SPC2T was affiliated with the genus Sphaerochaeta within the phylum Spirochaetes , and its closest relatives were Sphaerochaeta pleomorpha GrapesT (88.4 % sequence identity), Sphaerochaeta globosa BuddyT (86.7 %) and Sphaerochaeta coccoides SPN1T (85.4 %). Based on phenotypic characteristics and phylogenetic traits, strain MO-SPC2T is considered to represent a novel species of the genus Sphaerochaeta , for which the name Sphaerochaeta multiformis sp. nov. is proposed. The type strain is MO-SPC2T ( = JCM 17281T = DSM 23952T). An emended description of the genus Sphaerochaeta is also proposed.
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