- Volume 65, Issue Pt_5, 2015
Volume 65, Issue Pt_5, 2015
- Notification List
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 65, part 2, 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). t1
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- NEW TAXA
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- Archaea
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Halomicroarcula salina sp. nov., isolated from a marine solar saltern
More LessHalophilic archaeal strain YGHS18T was isolated from the Yinggehai marine solar saltern near Shanya city of Hainan Province, China. Cells from the strain were observed to be pleomorphic rods, stained Gram-negative, and formed red-pigmented colonies on solid media. Strain YGHS18T was found to be able to grow at 20–50 °C (optimum 37 °C), with 0.9–4.8 M NaCl (optimum 2.1 M) and at pH 5.5–9.0 (optimum pH 7.0). The cells lysed in distilled water and the minimum NaCl concentration to prevent cell lysis was found to be 0.9 M. The major polar lipids of the strain were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, glucosyl mannosyl glucosyl diether and a diglycosyl diether (DGD-2). Strain YGHS18T possessed two heterogeneous 16S rRNA genes (rrnA and rrnB) and both were related to those of members of the genera Haloarcula (93.1–96.9 % sequence similarity) and Halomicroarcula (92.7–96.1 % similarity). The rrnA gene (orthologous gene) of strain YGHS18T clustered phylogenetically with members of the genus Halomicroarcula while the rrnB gene formed a paraphyly with members of the genera Halomicroarcula and Haloarcula . The rpoB′ gene of strain YGHS18T was related phylogenetically to species of the genera Halomicroarcula (91.6–92.7 % sequence similarity) and Haloarcula (91.5–92.4 % similarity). EF-2 gene analysis revealed that strain YGHS18T was related phylogenetically to species of the genus Halomicroarcula (92.2–92.9 % sequence similarity) rather than to those of the genus Haloarcula (90.9–91.7 % similarity). The DNA G+C content of strain YGHS18T was determined to be 64.5 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YGHS18T ( = CGMCC 1.12128T = JCM 18369T) represents a novel species of the genus Halomicroarcula , for which the name Halomicroarcula salina sp. nov. is proposed.
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Halococcus agarilyticus sp. nov., an agar-degrading haloarchaeon isolated from commercial salt
Two agar-degrading halophilic archaeal strains, 62ET and 197A, were isolated from commercial salt samples. Cells were non-motile cocci, approximately 1.2–2.0 µm in diameter and stained Gram-negative. Colonies were pink-pigmented. Strain 62ET was able to grow with 24–30 % (w/v) NaCl (optimum, 27 %), at pH 6.5–8.5 (optimum, pH 7.5) and at 22–47 °C (optimum, 42 °C). The 16S rRNA gene sequences of strains 62ET and 197A were identical, and the level of DNA–DNA relatedness between them was 90 and 90 % (reciprocally). The closest relative was Halococcus saccharolyticus JCM 8878T with 99.7 % similarity in 16S rRNA orthologous gene sequences, followed by Halococcus salifodinae JCM 9578T (99.6 %), while similarities with other species of the genus Halococcus were equal to or lower than 95.1 %. The rpoB′ gene tree strongly supported that the two strains were members of the genus Halococcus . Mean DNA–DNA relatedness between strain 62ET and H. saccharolyticus JCM 8878T and H. salifodinae JCM 9578T was 46 and 44 %, respectively. The major polar lipids were archaeol derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, and sulfated diglycosyl archaeol-1. Several unidentified glycolipids were present. Based on the phenotypic and phylogenetic analyses, the isolates are considered to represent a novel species of the genus Halococcus , for which the name Halococcus agarilyticus sp. nov. is proposed. The type strain is 62ET ( = JCM 19592T = KCTC 4143T).
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Halocalculus aciditolerans gen. nov., sp. nov., an acid-tolerant haloarchaeon isolated from commercial salt
Three halophilic archaeal strains, MH2-243-1T, MH2-93-1 and MH2-91-1 were isolated from commercial salt samples from Japan, Australia, and Bolivia. Strain MH2-243-1T was able to grow in the presence of 12–30 % (w/v) NaCl (optimum, 18 % NaCl), at pH 4.5–7.0 (optimum, pH 6.0) and at 20–60 °C (optimum, 40 °C). Strains MH2-91-1 and MH2-93-1 grew in slightly different ranges. The orthologous 16S rRNA gene sequences of the three strains were almost identical (99.8–99.9 % similarities), and the closest relative was Salarchaeum japonicum JCM 16327T with 94.2–94.3 % 16S rRNA gene sequence similarities, followed by strains of members of the closely related genera Halobacterium and Halarchaeum . The RNA polymerase subunit B′ gene (rpoB′) sequence also showed the highest similarity (86.6 %) to that of Salarchaeum japonicum JCM 16327T. The DNA G+C contents of strains MH2-243-1T, MH2-93-1 and MH2-91-1 were 68.5, 68.8 and 68.3 mol%, respectively. DNA–DNA relatedness values amongst the three strains were 97–99 %. The polar lipids of the three strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and at least seven unidentified glycolipids. The polar lipid composition differed from those of Salarchaeum japonicum and species of the genera Halobacterium and Halarchaeum . Based on the phenotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of a new genus, for which the name Halocalculus aciditolerans gen. nov., sp. nov. is proposed. The type strain of the type species is MH2-243-1T ( = JCM 19596T = KCTC 4149T) isolated from solar salt produced in Japan. MH2-93-1 ( = JCM 19595) and MH2-91-1 ( = JCM 19594) are additional strains of the type species.
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- Actinobacteria
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Corynebacterium pelargi sp. nov., isolated from the trachea of white stork nestlings
A Gram-stain-positive, pleomorphic, oxidase-negative, non-motile isolate from the trachea of a white stork from Poland, designated strain 136/3T, was subjected to a comprehensive taxonomic investigation. A comparative analysis of the 16S rRNA gene sequence showed highest similarities to Corynebacterium mustelae , Corynebacterium pseudotuberculosis , Corynebacterium vitaeruminis and Corynebacterium ulcerans (96.0–96.3 %). The quinone system consisted of major amounts of MK-8(H2), minor amounts of MK-9(H2) and traces of MK-8 and MK-9. The polar lipid profile of strain 136/3T contained phosphatidylinositol and phosphatidylinositol-mannoside as major lipids and phosphatidylglycerol and an acidic glycolipid in moderate amounts. In addition small amounts of diphosphatidylglycerol, a phospholipid, an aminolipid and two lipids of unknown group affiliation were found. The polyamine pattern was composed of the major components spermidine and spermine. Putrescine, 1,3-diaminopropane, cadaverine, sym-homospermidine and tyramine were found in minor or trace amounts. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. In the fatty acid profile straight-chain, saturated and mono-unsaturated fatty acids predominated (C18 : 1ω9c, C16 : 1ω7c, C16 : 0, C18 : 0). Corynemycolic acids were detected. Physiological traits as well as unique traits of the polar lipid profile and the fatty acid pattern distinguished strain 136/3T from the most closely related species. All these results indicate that strain 136/3T represents a novel species of the genus Corynebacterium for which we propose the name Corynebacterium pelargi sp. nov. The type strain is 136/3T ( = CIP 110778T = CCM 8517T = LMG 28174T).
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Actinomadura darangshiensis sp. nov., isolated from a volcanic cone
More LessAn actinobacterium, designated strain DLS-70T, was isolated from a soil sample from the surface of a rock on the peak of Darangshi Oreum (a volcanic cone) in Jeju, Republic of Korea. Substrate mycelium was produced abundantly on most of the media tested. Spiral chains of spores with warty surface developed on the aerial hyphae. A phylogenetic tree based on 16S rRNA gene sequences showed that strain DLS-70T belonged to the genus Actinomadura and was most closely related to Actinomadura bangladeshensis DSM 45347T (98.9 % sequence similarity), Actinomadura madurae DSM 43067T (98.8 %) and Actinomadura chokoriensis DSM 45346T (98.6 %). Chemotaxonomic observations supported the assignment of the isolate to the genus Actinomadura . DNA–DNA relatedness values between strain DLS-70T and the type strains of the closest phylogenetic relatives were less than 20 %. On the basis of data from this polyphasic study, strain DLS-70T ( = KCTC 29224T = DSM 45941T) is considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura darangshiensis sp. nov. is proposed.
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Microbacterium shaanxiense sp. nov., isolated from the nodule surface of soybean
More LessA Gram-stain-positive, non-motile, catalase- and oxidase-positive rod, designated CCNWSP60T, was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. 16S rRNA gene sequence analysis clearly showed that the isolate belonged to the genus Microbacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP60T was most closely related to Microbacterium murale DSM 22178T (98.8 % similarity), Microbacterium aerolatum DSM 14217T (98.3 %), Microbacterium ginsengiterrae DSM 24823T (98.0 %) and Microbacterium profundi DSM 22239T (97.8 %). However, the DNA–DNA relatedness values of strain CCNWSP60T to M. murale DSM 22178T, M. aerolatum DSM 14217T, M. ginsengiterrae DSM 24823T and M. profundi DSM 22239T were 48 %, 43 %, 28 % and 41 %, respectively. Growth of strain CCNWSP60T occurred at 4–40 °C and at pH 5.0–9.0. The NaCl range for growth was 0–4 % (w/v). The predominant menaquinone of strain CCNWSP60T was MK-13; MK-12 was also detected. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid and one unidentified phospholipid. The diagnostic diamino acid of the peptidoglycan was ornithine. The acyl type of the peptidoglycan was glycolyl. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The DNA G+C content of the type strain was 67.4 mol%. As the physiological and biochemical characteristics as well as the DNA–DNA relatedness between strain CCNWSP60T and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species Microbacterium shaanxiense is proposed to accommodate it. The type strain is CCNWSP60T ( = DSM 28301T = ACCC 19329T = JCM 30164T).
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Microbacterium populi sp. nov., isolated from Populus×euramericana bark
More LessFive non-spore-forming, aerobic and Gram-stain-positive bacterial strains, 10-107-8T, 1C-4, NHI3_6, 4107_1_2, and 3D-3, were isolated from Populus×euramericana bark collected in Puyang City, Henan Province, PR China. The isolates grew at 15–40 °C and pH 5–10. The optimum temperature and pH for growth were 30 °C and pH 8.0, respectively. Chemotaxonomic features included MK-10 and MK-11 as major menaquinones (type strain); predominating iso- and anteiso-branched cellular fatty acids; diphosphatidylglycerol and phosphatidylglycerol as major polar lipids (type strain); ornithine as the principal diamino acid of the cell-wall peptidoglycan (type strain); glycolyl type as cell-wall acyl type; and DNA G+C content of 66.8–67.6 mol%. These features were consistent with classification in the genus Microbacterium . Analysis of 16S rRNA gene sequence data indicated that the five isolates belonged to the genus Microbacterium and were closely related to Microbacterium halotolerans . A high 16S rRNA gene sequence similarity of 96.97 % to M. halotolerans YIM 70130T was observed. The five isolates showed less than 96.20 % 16S rRNA gene sequence similarity to the other species of the genus Microbacterium with validly published names. DNA–DNA relatedness of the five isolates with M. halotolerans JCM 13013T ranged from 35.62 % to 44.36 %. Considering the results of 16S rRNA gene sequence analysis and the physiological and biochemical characteristics, we propose that the five strains should be assigned to a novel species of the genus Microbacterium . The name proposed for the five strains is Microbacterium populi sp. nov., and the type strain is 10-107-8T ( = CFCC 11275T = KCTC 29152T).
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Micromonospora costi sp. nov., isolated from a leaf of Costus speciosus
More LessAn endophytic actinobacterial strain, CS1-12T, was isolated from a leaf of Costus speciosus. Single spores were observed directly on the substrate mycelia. The cell-wall peptidoglycan of this strain exhibited meso-diaminopimelic acid and 3-OH-meso-diaminopimelic acid. Arabinose, glucose, ribose, xylose and rhamnose were detected as whole-cell sugars. The diagnostic phospholipids of this strain were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The predominant menaquinones were MK-10(H6), MK-10(H8), MK-9(H4) and MK-10(H4). The main components of the cellular fatty acids (>10 %) were iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 72.8 mol%. 16S rRNA gene sequence analysis data showed that strain CS1-12T should be classified in the genus Micromonospora and that it is closely related to Micromonospora fulviviridis DSM 43906T (99.3 %). The physiological, biochemical and chemotaxonomic properties, including the DNA–DNA hybridization results, indicated that strain CS1-12T could be judged a novel species of the genus Micromonospora , for which the name Micromonospora costi sp. nov. is proposed. The type strain is CS1-12T ( = BCC 58124T = NBRC 109518T).
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Streptomyces albiflavescens sp. nov., an actinomycete isolated from soil
More LessTwo actinobacterial strains, m20T and z8, were isolated from soil taken from rainforest areas/tropic forest region, Yunnan Province, south-west China. The 16S rRNA gene sequence similarities and DNA–DNA relatedness values between strains m20T and z8 were 100 and 88.2 %, respectively, which indicated that these two strains should be classified as the same species. The taxonomic position of the strains was determined by a polyphasic approach. Morphological and chemotaxonomic features of the strains were consistent with those of the genus Streptomyces . A phylogenetic tree based on 16S rRNA gene sequences showed that strains m20T and z8 formed an evolutionary branch within the genus Streptomyces and shared relatively high 16S rRNA gene sequence similarity values with other members of this genus, including ‘Streptomyces siamensis’ NBRC 108799 (98.95 %), Streptomyces graminilatus NBRC 108882T (98.25 %), Streptomyces seoulensis NBRC 16668T (98.11 %), Streptomyces peucetius ATCC 29050T (98.11 %) and Streptomyces hygroscopicus subsp. ossamyceticus ATCC 15420T (98.11 %). DNA–DNA relatedness values between strain m20T and the five above-mentioned strains were 56.3, 55.1, 52.8 , 50.1 and 48.4 %, respectively. On the basis of phenotypic, genotypic and phylogenetic properties, strains m20T and z8 could be distinguished from phylogenetically related members of the genus Streptomyces . The isolates thus merit species status within the genus Streptomyces , for which the name http://dx.doi.org/10.1601/nm.6817 Streptomyces albiflavescens sp. nov. is proposed. The type strain is m20T ( = CGMCC 4.7111T = KCTC 29196T). Strain z8 ( = CGMCC 4.7112 = KCTC 29197) is a reference strain.
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Nesterenkonia populi sp. nov., an actinobacterium isolated from Populus euphratica
An alkaliphilic and moderately halophilic actinobacterium, designated strain GP10-3T, was isolated from Populus euphratica collected from the southern edge of Taklimakan desert, Xinjiang, China. Cells of this strain were Gram-stain-positive, non-motile and non-spore-forming short rods. Strain GP10-3T grew optimally at 37 °C on LB agar media in the presence of 5–10 % (w/v) NaCl at pH 9.0. The menaquinones were MK-7, MK-8 and MK-9. The major fatty acids (>10 %) were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The peptidoglycan type was variation A4α, l-Lys-l-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylglycolipid, phosphatidylcholine, phosphatidylinositol, glycolipid and an unidentified phospholipid. The DNA G+C content was 67.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain GP10-3T belonged to the genus Nesterenkonia , sharing 94.6–96.9 % sequence similarity with the type strains of species within this genus with validly published names. Based on the evidence of the polyphasic taxonomic study, strain GP10-3T represents a novel species of the genus Nesterenkonia , for which the name Nesterenkonia populi sp. nov. is proposed. The type strain is GP10-3T ( = DSM 27959T = KCTC 29119T).
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Actinomycetospora rhizophila sp. nov., an actinomycete isolated from rhizosphere soil of a peace lily (Spathi phyllum Kochii)
A novel actinomycete, designated strain NEAU-B-8T, was isolated from the rhizosphere soil of a peace lily (Spathi phyllum Kochii) collected from Heilongjiang province, north-east China. Key morphological and physiological characteristics as well as chemotaxonomic features of strain NEAU-B-8T were congruent with the description of the genus Actinomycetospora , such as the major fatty acids, the whole-cell hydrolysates, the predominant menaquinone and the phospholipid profile. The 16S rRNA gene sequence analysis revealed that strain NEAU-B-8T shared the highest sequence similarities with Actinomycetospora lutea JCM 17982T (99.3 % 16S rRNA gene sequence similarity), Actinomycetospora chlora TT07I-57T (98.4 %), Actinomycetospora straminea IY07-55T (98.3 %) and Actinomycetospora chibensis TT04-21T (98.2 %); similarities to type strains of other species of this genus were lower than 98 %. The phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-B-8T formed a distinct branch with A. lutea JCM 17982T that was supported by a high bootstrap value of 97 % in the neighbour-joining tree and was also recovered with the maximum-likelihood algorithm. However, the DNA–DNA relatedness between strain NEAU-B-8T and A. lutea JCM 17982T was found to be 50.6±1.2 %. Meanwhile, strain NEAU-B-8T differs from other most closely related strains in phenotypic properties, such as maximum NaCl tolerance, hydrolysis of aesculin and decomposition of urea. On the basis of the morphological, physiological, chemotaxonomic, phylogenetic and DNA–DNA hybridization data, we conclude that strain NEAU-B-8T represents a novel species of the genus Actinomycetospora , named Actinomycetospora rhizophila sp. nov. The type strain is NEAU-B-8T. ( = CGMCC 4.7134T = DSM 46673T).
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Glycomyces tarimensis sp. nov., an actinomycete isolated from a saline-alkali habitat
More LessA novel actinomycete strain, designated TRM 45387T, was isolated from a saline-alkali soil in Xinjiang Province (40° 22′ N 79° 08′ E), north-west China. The isolate was characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain TRM 45387T belonged to the genus Glycomyces and was closely related to Glycomyces arizonensis DSM 44726T (96.59 % 16S rRNA gene sequence similarity). The G+C content of the DNA was 71.26 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid, and xylose, glucose, galactose, arabinose and ribose as the major whole-cell sugars. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositolmannosides. The predominant menaquinone was MK-10(H6). The major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. On the basis of the evidence from this polyphasic study, a novel species, Glycomyces tarimensis sp. nov., is proposed. The type strain of Glycomyces tarimensis is TRM 45387T ( = CCTCC AA 2014007T = JCM 30184T).
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Prauserella isguenensis sp. nov., a halophilic actinomycete isolated from desert soil
Two actinomycete strains, designated H225T and H137, were isolated from two soil samples collected from the arid region of Ahbas at Béni-Isguen (Mzab), located in the Algerian Sahara. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel strains should be assigned to the genus Prauserella of the family Pseudonocardiaceae , and they were therefore subjected to a polyphasic taxonomic study. These two strains contained meso-diaminopimelic acid as the diagnostic diamino acid and arabinose and galactose as major whole-cell sugars. The diagnostic phospholipid was phosphatidylethanolamine. The predominant menaquinone was MK-9(H4), and the major fatty acid was iso-C16 : 0. DNA–DNA hybridization values between strain H225T and its closest phylogenetic neighbours, namely Prauserella flava DSM 45265T, Prauserella alba DSM 44590T, Prauserella aidingensis DSM 45266T, Prauserella salsuginis DSM 45264T and Prauserella sediminis DSM 45267T, were clearly below the 70 % threshold used for species delineation. The genomic DNA G+C content of strains H225T and H137 was 70.4 mol%. On the basis of phenotypic and genotypic data, strains H225T and H137T are considered to represent a novel species of the genus Prauserella , for which the name Prauserella isguenensis sp. nov. is proposed. The type strain is H225T ( = DSM 46664T = CECT 8577T).
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Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil
A rod- or coccus-shaped, non-spore-forming actinobacterium, designated strain SC8A-24T, was isolated from a soil sample collected from the rhizosphere of Alhagi sparsifolia on the southern edge of the Taklimakan desert, Xinjiang, China, and examined by a polyphasic approach to clarify its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain SC8A-24T grew optimally without NaCl at 28–30 °C and pH 7.0–8.0. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SC8A-24T belonged to the genus Nocardioides and shared the highest 16S rRNA gene sequence similarity with Nocardioides salarius CL-Z59T (96.51 %), N. pyridinolyticus OS4T (96.43 %) and N. ginsengagri BX5-10T (96.37 %). The DNA G+C content of strain SC8A-24T was 71 mol%. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid, and MK-8(H4) was the predominant menaquinone. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The major fatty acids were C17 : 1ω8c, 10-methyl C17 : 0 and C18 : 1ω9c. On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain SC8A-24T represents a novel species of the genus Nocardioides , for which the name Nocardioides deserti sp. nov. is proposed. The type strain is SC8A-24T ( = DSM 26045T = CGMCC 4.7183T).
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- Firmicutes and related organisms
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Bacillus encimensis sp. nov. isolated from marine sediment
A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium designated SGD-V-25T was isolated from Veraval sediment sample, India. Strain SGD-V-25T was capable of growing at 25–50 °C (optimum 37 °C), pH 6–12 (optimum pH 7.0) and with 0–5 % (w/v) NaCl. The taxonomic position of this strain was deduced using a polyphasic approach and the 16S rRNA gene sequence analysis showed that the isolate belongs to the phylum Firmicutes , forming the cluster with Bacillus badius MTCC 1548T, with which it shares highest similarity of 99.1 % with 13 nt differences. Other type strains of the genus Bacillus showed less than 96 % similarity. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The polar lipid profile of strain SGD-V-25T showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phsophoglycolipid and two aminophospholipids. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, C16 : 1ω11c and C16 : 0. The genomic DNA G+C content of strain SGD-V-25T was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization, strain SGD-V-25T could be clearly distinguished from closely related members of the genus Bacillus , and the name Bacillus encimensis sp. nov., is proposed to accommodate this strain. The type strain is SGD-V-25T ( = NCIM 5513T = DSM 28241T).
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Anaerosolibacter carboniphilus gen. nov., sp. nov., a strictly anaerobic iron-reducing bacterium isolated from coal-contaminated soil
A strictly anaerobic, mesophilic, iron-reducing bacterial strain, IRF19T, was isolated from coal-contaminated soil in the Republic of Korea. IRF19T cells were straight, rod-shaped, Gram-staining-negative and motile by means of flagella. The optimum pH and temperature for their growth were determined to be pH 7.5–8.0 and 40 °C, while the optimum range was pH 6.5–10.0 and 20–45 °C, respectively. Strain IRF19T did not require NaCl for growth but it tolerated up to 2 % (w/v). Growth was observed with yeast extract, d-glucose, d-fructose, d-ribose, d-mannitol, d-mannose, l-serine, l-alanine and l-isoleucine. Fe(III), elemental sulfur, thiosulfate and sulfate were used as electron acceptors. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain IRF19T is affiliated to the family Clostridiaceae and is most closely related to Salimesophilobacter vulgaris Zn2T (93.5 % similarity), Geosporobacter subterraneus VNs68T (93.2 %) and Thermotalea metallivorans B2-1T (92.3 %). The major cellular fatty acids of strain IRF19T were C14 : 0, iso-C15 : 0 and C16 : 0, and the profile was distinct from those of the closely related species. The major respiratory quinone of strain IRF19T was menaquinone MK-5 (V-H2). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and two unknown polar lipids. The G+C content of the genomic DNA of strain IRF19T was determined to be 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic results, strain IRF19T is considered to represent a novel species of a novel genus of the family Clostridiaceae , for which we propose the name Anaerosolibacter carboniphilus gen. nov., sp. nov., with the type strain IRF19T ( = KCTC 15396T = JCM 19988T).
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Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis)
A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T was able to grow with 0–13 % (w/v) NaCl (optimum 2–5 %), at pH 5.5–10.0 (optimum pH 7.5) and at 5–50 °C (optimum 30–35 °C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 100118T belonged to the genus Bacillus , and was most closely related to Bacillus litoralis SW-211T (98.9 % 16S rRNA gene sequence similarity), Bacillus halosaccharovorans E33T (98.3 %), Bacillus niabensis 4T19T (97.8 %) and Bacillus herbersteinensis D-1,5aT (97.1 %). The combination of results from the phylogenetic analysis, DNA–DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118T represents a novel species of the genus Bacillus , for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118T ( = CCTCC AB 2010452T = DSM 24486T = JCM 17523T).
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Exiguobacterium enclense sp. nov., isolated from sediment
A Gram-stain-positive bacterium, designated strain NIO-1109T, was isolated from a marine sediment sample from Chorao Island, Goa, India. Phenotypic and chemotaxonomic characteristics and data from phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1109T was related to the genus Exiguobacterium . Strain NIO-1109T exhibited >98.0 % 16S rRNA gene sequence similarity with respect to Exiguobacterium indicum HHS 31T (99.5 %) and Exiguobacterium acetylicum NCIMB 9889T (99.1 %); the type strains of other species showed <98 % similarity. Levels of DNA–DNA relatedness between strain NIO-1109T and E. acetylicum DSM 20416T and E. indicum LMG 23471T were less than 70 % (33.0±2.0 and 37±3.2 %, respectively). Strain NIO-1109T also differed from these two closely related species in a number of phenotypic traits. Based on phenotypic, chemotaxonomic and phylogenetic data, strain NIO-1109T is considered to represent a novel species of the genus Exiguobacterium , for which the name Exiguobacterium enclense sp. nov. is proposed. The type strain is NIO-1109T ( = NCIM 5457T = DSM 25128T = CCTCC AB 2011124T).
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- Proteobacteria
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Phenotypic characterization of Sodalis praecaptivus sp. nov., a close non-insect-associated member of the Sodalis-allied lineage of insect endosymbionts
A Gram-stain-negative bacterium, isolated from a human wound was previously found to share an unprecedentedly close relationship with Sodalis glossinidius and other members of the Sodalis-allied clade of insect symbionts. This relationship was inferred from sequence analysis of the 16S rRNA gene and genomic comparisons and suggested the strain belonged to a novel species. Biochemical and genetic analyses supported this suggestion and demonstrated that the organism has a wide repertoire of metabolic properties, which is consistent with the presence of a relatively large gene inventory. Among members of the Sodalis-allied clade, this is the first representative that has sufficient metabolic capabilities to sustain growth in minimal media. On the basis of the results of this study, we propose that this organism be classified as a representative of a novel species, Sodalis praecaptivus sp. nov. (type strain HST = DSM 27494T = ATCC BAA-2554T).
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Serratia glossinae Geiger et al. 2010 is a later synonym of Serratia fonticola Gavini et al. 1979
More LessSerratia glossinae DSM 22080T was compared with Serratia fonticola ATCC 29844T to clarify the taxonomic relationship of both species. 16S rRNA gene sequence comparisons demonstrated that these species share 99.6 % sequence similarity. Investigation of substrate utilization profiles displayed no striking differences from the type strains of both species. DNA–DNA hybridizations between both strains showed 100 % (99.9 %) similarity. Therefore, the reclassification of S. glossinae as a later synonym of S. fonticola is proposed, based upon the estimated phylogenetic position derived from 16S rRNA gene sequence data, biochemical data and DNA–DNA hybridization results.
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N ovosphingobium fluoreni sp. nov., isolated from rice seeds
More LessA yellow-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterium designated strain HLJ-RS18T, which could degrade fluorene, was isolated from rice seeds collected from Heilongjiang Province, China. Similarities of full-length of 16S rRNA gene sequences between strain HJL-RS18T and the type strains of the genus Novosphingobium with validly published names ranged from 93.8 to 97.1 %. Phylogenetic analysis with maximum-likelihood and neighbour-joining methods revealed that strain HLJ-RS18T belonged to genus Novosphingobium and strain HLJ-RS18T formed a distinct clade to Novosphingobium chloroacetimidivorans BUT-14T (96.9 % similarity based on 16S rRNA gene). DNA–DNA hybridization of HLJ-RS18T and BUT-14T showed a low relatedness value of 22.4±0.9 %, which indicated that strain HLJ-RS18T represents a novel species of the genus Novosphingobium . The genomic DNA G+C content of strain HLJ-RS18T was 62 mol%. Ubiquinone Q-10 was the major respiratory quinone. Spermidine was the predominant polyamine. Polar lipids consisted mainly of aminophospholipid, phosphatidylglycerol, phosphatidylethanolamine, phospholipid and sphingoglycolipid. The predominant fatty acid composition of HLJ-RS18T were summed 8 (C18 : 1ω7c and/or C18 : 1ω6c, 61.5 %), C16 : 0 (14.2 %), summed 3 (C16 : 1ω7c and/or C16 : 1ω6c, 13.5 %) and C14 : 0 2-OH (6.8 %). Phylogenetic analysis, DNA–DNA hybridization, chemotaxonomic data and phenotypic characteristics support the conclusion that HLJ-RS18T represents a novel species within the genus Novosphingobium . Therefore, we propose the species Novosphingobium fluoreni sp. nov. with HLJ-RS18T ( = DSM 27568T = ACCC19180T) as the type strain.
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Psychrobacter oceani sp. nov., isolated from marine sediment
A novel marine bacterium, designated strain 4k5T, was isolated from a sediment sample of the Pacific Ocean. The strain was Gram-stain-negative, strictly aerobic, non-motile, oxidase-positive and catalase-positive and required Na+ for growth. Its major isoprenoid quinone was ubiquinone 8 (Q-8), and its cellular fatty acid profile consisted mainly of C18 : 1v9c (71.4 %), C16 : 1v7c (9.1 %) and C18 : 0. The DNA G+C content was 45.3 mol%. 16S rRNA gene sequence analysis suggested that strain 4k5T is a member of the genus Psychrobacter . Strain 4k5T exhibited the closely phylogenetic affinity to Psychrobacter pacificensis IFO 16270T (99.4 % 16S rRNA gene sequence similarity), P. piscatorii T-3-2T (97.7 %), P. nivimaris 88/2-7T (97.7 %), P. celer SW-238T (97.7 %), P. aestuarii SC35T (97.6 %) and P. vallis CMS39T (97.6 %). DNA–DNA hybridization between strain 4k5T and P. pacificensis NBRC 103191T, P. piscatorii JCM 15603T. P. nivimaris DSM 16093T, P. celer JCM 12601T, P. aestuarii JCM 16343T and P. vallis DSM 15337T was 42.5, 47.0, 38.1, 23.7, 9.0 and 27.4 %, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on the 16S rRNA gene sequence and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Psychrobacter oceani sp. nov. is proposed. The type strain is 4k5T ( = JCM 30235T = NCIMB 14948T).
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P uniceibacterium sediminis sp. nov., from intertidal sediment
More LessThe Gram-stain-negative, rod-shaped bacterial strain designated RU-1-R-18T was isolated from intertidal sediment on Sakhalin Island in Russia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RU-1-R-18T was related to the genus Puniceibacterium and shared highest sequence similarities with the type strain Puniceibacterium antarcticum KACC 16875T (97.9 %). The predominant cellular fatty acid was C18 : 1ω7c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and seven unidentified polar lipids. The genomic DNA G+C content of strain RU-1-R-18T was 59.1 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain RU-1-R-18T represents a novel species of the genus Puniceibacterium , for which the name Puniceibacterium sediminis sp. nov. is proposed (type strain RU-1-R-18T = LMG 28384T = DSM 29052T).
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Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.
Strains originating from various sources and classified as members of the genus Citrobacter within the family Enterobacteriaceae were characterized by sequencing internal portions of genes rpoB, fusA, pyrG and leuS, 16S rRNA gene sequencing, average nucleotide identity (ANI) of genomic sequences and biochemical tests. Phylogenetic analysis based on the four housekeeping genes showed that the 11 species of the genus Citrobacter with validly published names are well demarcated. Strains CIP 55.13T and CIP 55.9 formed a distinct branch associated with Citrobacter youngae . The ANI between CIP 55.9 and CIP 55.13T was 99.19 %, whereas it was 94.75 % between CIP 55.13T and strain CIP 105016T of the species C. youngae , the most closely related species. Biochemical characteristics consolidated the fact that the two isolates represent a separate species, for which the name Citrobacter pasteurii sp. nov. is proposed. The type strain is CIP 55.13T ( = DSM 28879T = Na 1aT).
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Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng
More LessA novel bacterial strain, designated DCY94T, was isolated from forest soil cultivated with ginseng in Vietnam. The strain was Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped and catalase- and oxidase-positive. 16S rRNA gene sequence analysis demonstrated that strain DCY94T was closely related to Paracoccus sphaerophysae Zy-3T (97.5 % 16S rRNA gene sequence similarity) and Paracoccus caeni MJ17T (96.9 %). The fatty acid profile of strain DCY94T contained a predominant amount of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 88.4 %) and moderate to small quantities of C8 : 0 3-OH (1.0 %), C10 : 0 3-OH (2.8 %) and C18 : 0 (5.2 %). Phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified glycolipid were major polar lipids; one unidentified aminolipid, one unidentified aminophospholipid, one unidentified phospholipid and four unidentified polar lipids were minor components. The polyamine pattern comprised the major compounds putrescine and spermidine and minor amounts of sym-homospermidine and spermine. The ubiquinone of the strain was Q-10 and the G+C content of its genomic DNA was 68.3 mol%. All these results support the placement of strain DCY94T within the genus Paracoccus . Levels of DNA–DNA relatedness between strain DCY94T and P. sphaerophysae HAMBI 3106T and P. caeni KCTC 22480T were 52 and 50 %, respectively. The results of phylogenetic analysis, phenotypic tests, chemotaxonomic characterization and DNA–DNA relatedness studies distinguished strain DCY94T from the closest recognized species of the genus Paracoccus , suggesting that this strain represents a novel species, for which the name Paracoccus panacisoli sp. nov. is proposed. The type strain is DCY94T ( = KCTC 42086T = JCM 30337T).
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Alteromonas gracilis sp. nov., a marine polysaccharide-producing bacterium
A novel exopolysaccharide-producing bacterium, designated strain 9a2T, was isolated from Pacific Ocean sediment. The strain was Gram-stain-negative, motile, strictly aerobic, oxidase- and catalase-positive, and required NaCl for growth. Its major isoprenoid quinone was ubiquinone-8 (Q-8), and its cellular fatty acid profile consisted mainly of C16 : 1ω7c, C18 : 1ω9c and C16 : 0. The DNA G+C content was 46.6 mol%. 16S rRNA gene sequence analysis suggested that strain 9a2T is a member of the genus Alteromonas . Strain 9a2T exhibited closest phylogenetic affinity to Alteromonas macleodii NBRC 102226T (99.3 % 16S rRNA gene sequence similarity), A. marina SW-47T (99.3 %), A. litorea TF-22T (99.0 %), A. australica H17T (98.7 %), A. simiduii BCRC 17572T (98.5 %), A. stellipolaris LMG 21861T (98.3 %) and A. hispanica F-32T (98.2 %). The DNA–DNA reassociation values between strain 9a2T and A. macleodii JCM 20772T, A. marina JCM 11804T, A. litorea JCM 12188T, A. australica CIP 109921T, A. simiduii JCM 13896T, A. stellipolaris LMG 21861T and A. hispanica LMG 22958T were below 70 %. Strain 9a2T contained phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid. Owing to differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on 16S rRNA gene sequences and DNA–DNA relatedness data, the isolate merits classification as representing a novel species, for which the name Alteromonas gracilis sp. nov. is proposed. The type strain of this species is 9a2T ( = JCM 30236T = NCIMB 14947T).
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Sulfuriferula multivorans gen. nov., sp. nov., isolated from a freshwater lake, reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov., and description of Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.
More LessA sulfur-oxidizing bacterium, strain TTNT, was isolated from a Thioploca sample obtained from a freshwater lake in Japan. The isolate shared 97.1 % 16S rRNA gene sequence similarity with an obligately aerobic chemolithoautotroph, ‘Thiobacillus plumbophilus’ Gro7T. Cells were rods, motile, and Gram-stain-negative. The G+C content of the genomic DNA was approximately 66 mol%. Strain TTNT grew over a temperature range of 8–32 °C (optimum 22–25 °C), an NaCl concentration range of 0–133.3 mM (optimum 0–3.3 mM) and a pH range of 5.3–8.6 (optimum pH 6.4–7.0). Strain TTNT was facultatively anaerobic and could utilize nitrate as an electron acceptor. The isolate oxidized tetrathionate, thiosulfate and elemental sulfur as the sole energy sources for autotrophic growth, and could also grow heterotrophically on a number of organic substrates. Based on its phylogenetic and phenotypic properties, strain TTNT represents a novel species of a novel genus, for which the name Sulfuriferula multivorans gen. nov., sp. nov. is proposed. The type strain is TTNT ( = NBRC 110683T = DSM 29343T). Along with this, the reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov. (type strain Gro7T = NBRC 107929T = DSM 6690T) is proposed. Based on the data obtained in this study, we describe the designations Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.
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Pseudohalocynthiibacter aestuariivivens gen. nov., sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-motile, aerobic and coccoid, ovoid or rod-shaped bacterial strain, designated BS-W9T, was isolated from a tidal flat of the South Sea, South Korea. Strain BS-W9T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. Phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain BS-W9T clustered with the type strain of Halocynthiibacter namhaensis , showing a highest sequence similarity of 97.3 %. It exhibited sequence similarity values of less than 95.6 % to the type strains of other species with validly published names. Strain BS-W9T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids of strain BS-W9T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain BS-W9T were distinguished from those of the type strains of H. namhaensis and other phylogenetically related genera. The DNA G+C content of strain BS-W9T was 53.2 mol% and its mean DNA–DNA relatedness value with H. namhaensis RA2-3T was 14 %. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain BS-W9T is considered to represent a novel genus and species within the family Rhodobacteraceae , for which the name Pseudohalocyntiibacter aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Pseudohalocyntiibacter aestuariivivens is BS-W9T ( = KCTC 42348T = CECT 8726T).
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Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator
More LessA Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512T) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512T was shown to belong to the genus Rhizobium and to be most closely related to Rhizobium endophyticum CCGE 2052T (98.4 %), Rhizobium tibeticum CCBAU 85039T (98.1 %), Rhizobium grahamii CCGE 502T (98.0 %) and Rhizobium mesoamericanum CCGE 501T (98.0 %). The phylogenetic relationships of ChimEc512T were confirmed by sequencing and analyses of recA and atpD genes. DNA–DNA relatedness values of strain ChimEc512T with R. endophyticum CCGE 2052T, R. tibeticum CCBAU 85039T, R. mesoamericanum CCGE 52T, Rhizobium grahamii CCGE 502T, Rhizobium etli CCBAU 85039T and Rhizobium radiobacter KL09-16-8-2T were 27, 22, 16, 18, 19 and 11 %, respectively. The DNA G+C content of strain ChimEc512T was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus Rhizobium . The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512T was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA–DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512T from species of the genus Rhizobium with validly published names. Strain ChimEc512T, therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain ChimEc512T ( = DSM 26575 = CIP 110550T).
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Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus
More LessA polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing marine bacterium, designated strain PQ-2T, was isolated from marine biofilm collected from a boat shell at a harbour of Zhoushan island in Zhejiang Province, PR China. Strain PQ-2T is Gram-stain-negative, yellow-pigmented, non-motile and short rod-shaped. Optimal growth of strain PQ-2T was observed at 32 °C, at pH 7.0 and in 2 % (w/v) NaCl. The 16S rRNA gene sequence of strain PQ-2T showed highest similarity to Croceicoccus marinus E4A9T (96.3 %) followed by Novosphingobium malaysiense MUSC 273T (95.6 %) and Altererythrobacter marinus H32T (95.6 %). Phylogenetic analysis with all species of the family Erythrobacteraceae with validly published names revealed that strain PQ-2T formed a phyletic line with Croceicoccus marinus E4A9T that was distinct from other members of the family Erythrobacteraceae . The sole respiratory quinone was ubiquinone 10 (Q-10). The predominant fatty acids were C18 : 1ω7c, C17 : 1ω6c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 61.7 mol%. In the polar lipid profile, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one unidentified phospholipid and one sphingoglycolipid were the major compounds; and another sphingoglycolipid was present in a minor amount. Based on the genotypic and phenotypic data, strain PQ-2T represents a novel species of the genus Croceicoccus , for which the name Croceicoccus naphthovorans sp. nov. is proposed. The type strain is PQ-2T ( = CGMCC 1.12805T = NBRC 110381T). In addition, emended descriptions for the genus Croceicoccus and the species C. marinus are given.
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Marinomonas mangrovi sp. nov., isolated from mangrove sediment
More LessA Gram-stain-negative, Na+-requiring bacterial strain, designated B20-1T, was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1T belonged to the genus Marinomonas , sharing highest sequence similarities with Marinomonas rhizomae IVIA-Po-145T (97.6 %), Marinomonas dokdonensis DSW10-10T (97.0 %) and Marinomonas foliarum IVIA-Po-155T (96.9 %). The predominant cellular fatty acids of strain B20-1T were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1T was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1T ( = DSM 28136T = LMG 28077T) as the type strain.
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Bradymonas sediminis gen. nov., sp. nov., isolated from coastal sediment, and description of Bradymonadaceae fam. nov. and Bradymonadales ord. nov.
More LessA novel Gram-stain-negative, rod-shaped, gliding, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated FA350T, was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Strain FA350T showed growth on modified nutrient agar supplemented with 0.1 % d-(+)-trehalose and with distilled water replaced by seawater. Optimal growth occurred at 33 °C and pH 8.5 with 4 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA350T belongs to a novel bacterial order in the class Deltaproteobacteria , and the most closely related type strains belong to the order Desulfuromonadales , with 85.1–85.6 % 16S rRNA gene sequence similarity. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and two unknown phospholipids. Major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω10c and menaquinone MK-7 was the sole respiratory quinone. The DNA G+C content of strain FA350T was 60.3 mol%. The isolate and closely related environmental clones formed a novel order-level clade in the class Deltaproteobacteria . Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain FA350T may represent a novel order of the Deltaproteobacteria . Here, we propose the name Bradymonas sediminis gen. nov., sp. nov. to accommodate strain FA350T. The type strain of Bradymonas sediminis is FA350T ( = DSM 28820T = CICC 10904T); Bradymonadales ord. nov. and Bradymonadaceae fam. nov. are also proposed to accommodate the novel taxon.
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Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013
More LessA Gram-stain-negative heterotrophic bacterium, designated GSD6T, capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6T was observed at 4–37 °C (optimum 30 °C), at pH 5.5–9.0 (optimum pH 6.5–7.5) and in the presence of 1–9 % (w/v) NaCl (optimum 2 %). Strain GSD6T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C17 : 0 10-methyl and C17 : 1ω8c as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6T formed a phylogenetic lineage with members of the genus Aliiglaciecola . Strain GSD6T was most closely related to Aliiglaciecola lipolytica E3T with a 16S rRNA gene sequence similarity of 97.4 %, but their DNA–DNA hybridization value was 39.1±7.1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6T represents a novel species of the genus Aliiglaciecola , for which the name Aliiglaciecola aliphaticivorans sp. nov. is proposed. The type strain is GSD6T ( = KACC 18129T = JCM 30133T). An emended description of the genus Aliiglaciecola is also proposed.
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Paenibacillus tibetensis sp. nov., a psychrophilic bacterium isolated from alpine swamp meadow soil
More LessA novel psychrophilic strain, SSB001T, was isolated from an alpine swamp meadow soil in Tibet, China, and identified as a representative of a novel phylogenetic subclade in the genus Paenibacillus , with Paenibacillus antarcticus (96.2 %), Paenibacillus macquariensis (96.53 %) and Paenibacillus glacialis (96.2 %) as the most closely related species on the basis of 16S rRNA gene sequence analyses. The strain was distinguished from defined species of the genus Paenibacillus by further study of rpoB gene sequences, phenotypic characterization, cellular fatty acid composition, quinones, polar lipids and meso-diaminopimelic acid in the peptidoglycan. Based upon these results, we propose the strain as a representative of a novel species named Paenibacillus tibetensis sp. nov., with SSB001T ( = ACCC 19728T = DSM 29321T) as the type strain. The DNA G+C content (mol%) of strain SSB001T was 40.18 mol% (HPLC).
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Mameliella phaeodactyli sp. nov., a member of the family Rhodobacteraceae isolated from the marine algae Phaeodactylum tricornutum
A novel Gram-staining-negative, aerobic, rod-shaped, non-motile, yellow bacterium designated strain KD53T, was isolated from a culture of the alga Phaeodactylum tricornutum from Xiamen, Fujian Province, China. 16S rRNA gene sequence comparison showed that strain KD53T was a member of the Roseobacter clade within the family Rhodobacteraceae , forming a distinct lineage with species of the genus Mameliella . The 16S rRNA gene sequence similarities between strain KD53T and other strains examined were all less than 97.0 %. Strain KD53T was found to grow optimally at 28 °C, at pH 7.5–8.0 and in the presence of 3 % (w/v) NaCl. The dominant fatty acids of strain KD53T were C18 : 1ω6c and/or C18 : 1ω7c, C18 : 0 and C16 : 0. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 65 mol% and the major respiratory quinone was ubiquinone 10 (Q-10). On the basis of phenotypic data and phylogenetic inference, strain KD53T represents a novel member of the genus Mameliella , then the name Mameliella phaeodactyli sp. nov. is proposed. The type strain is KD53T ( = MCCC 1K00273T = KCTC 42178T).
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Chelativorans intermedius sp. nov. and proposal to reclassify Thermovum composti as Chelativorans composti comb. nov.
More LessTwo Gram-stain-negative, non-endospore-forming, rod-shaped bacteria, strains CC-MHSW-5T and A1392, were isolated from water of coastal hot springs located in Taiwan and China, respectively, and investigated for their taxonomic position. The two strains shared identical 16S rRNA gene sequences, a DNA-DNA hybridization value >80 % and similar genomic DNA G+C contents (64.3 and 64.6 mol%), but showed different genomic fingerprint patterns generated by BOX-PCR and three random amplification polymorphic DNA PCRs. The strains shared highest 16S rRNA gene sequence similarities with the type strains of Chelativorans multitrophicus (96.7 and 96.1 %), Thermovum composti (96.2 and 96.1 %) and Chelativorans oligotrophicus (96.1 and 95.8 %). Phylogenetic trees (based on 16S rRNA and recA gene sequence comparisons) showed a distinct clustering of both strains with the type strains of species of the genus Chelativorans and T. composti Nis3T. The quinone systems of strains CC-MHSW-5T and Nis3T contained ubiquinone Q-10 as the major component. The major polyamine in both strains was sym-homospermidine. Putrescine, spermidine and, for strain CC-MHSW-5T, spermine were found in minor concentrations. Their polar lipid profiles consisted of phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The fatty acid profile contained major amounts of C18 : 1ω7c and C19 : 0 cyclo ω8c. On the basis of these results, the two strains are considered to represent a novel species of the genus Chelativorans , for which the name Chelativorans intermedius sp. nov. is proposed. The type strain is CC-MHSW-5T ( = CCM 8543T = LMG 28482T = DSM 29391T = CIP 110825T). Based on both genotypic and phenotypic characters, it is proposed that T. composti be reclassified within the genus Chelativorans as Chelativorans composti comb. nov.
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Blastomonas aquatica sp. nov., a bacteriochlorophyll-containing bacterium isolated from lake water
Yellow or orange-to-brown pigmented, ovoid or rod-shaped, Gram-negative staining, aerobic strains PE 4-5T and N5-10 m-1 were isolated from brackish water in Lake Peng Co and fresh to brackish water in Lake Namtso on the Tibetan Plateau, China. Bacteriochlorophyll a was produced by the isolates. The predominant cellular fatty acids were C16 : 1, C17 : 1 and C18 : 1 unsaturated fatty acids, C17 : 1ω6c (55.3 %), C17 : 1ω8c (13.0 %) and C18 : 1ω7c (10.4 %) for PE 4-5T and C18 : 1ω7c (54.7 %) and C16 : 1ω7c (18.0 %) for N5-10 m-1. The polar lipid profiles of strains PE 4-5T and N5-10 m-1 were composed of diphosphatidylglycerol, phosphatidylcholine (not detected in N5-10 m-1), phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unknown phospholipid. The predominant respiratory quinone was ubiquinone Q10 and the DNA G+C content was 66.0 mol% for both strains. The16S rRNA gene sequence of strain PE 4-5T shared 99.0 % similarity with that of N5-10 m-1, and 97.56 % similarity with those of Blastomonas natatoria LMG 17322T and Blastomonas ursincola DSM 9006T, respectively. The DNA–DNA hybridization relatedness between strains PE 4-5T and N5-10 m-1 was 79.0±1.0 %, but below 70 % with the type strains in the genus Blastomonas . Based on the variability of phylogenetic and phenotypic characteristics, the isolates should be classified as representatives of a novel species of the genus Blastomonas ; the name Blastomonas aquatica sp. nov. is proposed. The type strain is PE 4-5T ( = JCM 30179T = CGMCC 1.12851T).
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O leiagrimonas soli gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield
More LessA yellow-pigmented strain, designated strain 3.5XT, was isolated from oil-contaminated saline soil in Gudao, Shandong Province, China, and was characterized taxonomically. The results showed that the isolate was a Gram-stain-negative, aerobic, motile, rod-shaped cell with a polar flagellum. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family Xanthomonadaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. The closest relative of strain 3.5XT was Fulvimonas soli DSM 14263T (94 % similarity). The genomic DNA G+C content was 67 mol% by thermal denaturation and 66.3 mol% from genome sequences. The cells mainly consisted of branched fatty acids, with iso-C17 : 0, iso-C15 : 0, iso-C17 : 1ω9c and/or C16 : 010-methyl and iso-C11 : 0 as the major fatty acids. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol and phosphatidylethanolamine. In addition, ubiquinone Q-8 was the major component of the quinone system and the polyamine pattern contained the major compound spermidine plus minor amounts of putrescine and spermine. On the basis of phenotypic, genotypic and phylogenetic distinctiveness, it is proposed that the isolate represents a novel species in a novel genus, namely Oleiagrimonas soli gen. nov., sp. nov. The type strain is 3.5XT ( = NBRC 110685T = KCTC 42351T = CPCC 100614T).
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Sulfitobacter undariae sp. nov., isolated from a brown algae reservoir
More LessA Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, W-BA2T, was isolated from a brown algae reservoir in Wando of South Korea. Strain W-BA2T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain W-BA2T fell within the clade comprising the type strains of species of the genus Sulfitobacter , clustering coherently with the type strains of Sulfitobacter donghicola and Sulfitobacter guttiformis showing sequence similarity values of 98.0–98.1 %. Sequence similarities to the type strains of the other species of the genus Sulfitobacter were 96.0–97.4 %. Strain W-BA2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain W-BA2T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain W-BA2T was 55.0 mol% and its DNA–DNA relatedness values with the type strains of Sulfitobacter donghicola , Sulfitobacter guttiformis and Sulfitobacter mediterraneus were 16–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain W-BA2T is separated from other species of the genus Sulfitobacter . On the basis of the data presented, strain W-BA2T is considered to represent a novel species of the genus Sulfitobacter , for which the name Sulfitobacter undariae sp. nov. is proposed. The type strain is W-BA2T ( = KCTC 42200T = NBRC 110523T).
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Desulfuromonas carbonis sp. nov., an Fe(III)-, S0- and Mn(IV)-reducing bacterium isolated from an active coalbed methane gas well
More LessA novel, mesophilic, obligately anaerobic, acetate-oxidizing, dissimilatory iron-, sulfur-, and manganese-reducing bacterium, designated strain ICBMT, was obtained from an active, coalbed methane gas well in Indiana, USA. Strain ICBMT was a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium that was rich in c-type cytochromes and formed red colonies in solid medium. Strain ICBMT conserved energy to support growth from the oxidation of acetate, propionate, pyruvate, malate, fumarate, succinate and dl-lactate, concomitant with dissimilatory iron reduction. Strain ICBMT fermented fumarate yielding succinate and acetate. Strain ICBMT was able to grow in the temperature range of 10 °C to 37 °C, NaCl concentration range of 0 to 1.2 M, and pH range of 6.5 to 8.0. The physiological characteristics of strain ICBMT indicated that it belongs to the Desulfuromonas cluster. The G+C content of its genomic DNA was 61.2 mol%. The predominant cellular fatty acids were C16 : 0 (39.3 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (36.6 %). The closest cultured phylogenetic relative of strain ICBMT was Desulfuromonas michiganensis BB1T with only 95 % 16S rRNA gene sequence similarity. This confirmed that strain ICBMT is affiliated with the genus Desulfuromonas . On the basis of phenotypic and genotypic differences between strain ICBMT and other taxa of the genus Desulfuromonas , strain ICBMT represents a novel species for which the name Desulfuromonas carbonis sp. nov. is proposed (type strain ICBMT = DSM 29759T = JCM 30471T). Strain ICBMT is the first Fe(III)-, S0-, and Mn(IV)-reducing bacterium that was isolated from a coal bed.
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- Bacteroidetes
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Marivirga atlantica sp. nov., isolated from seawater and emended description of the genus Marivirga
A novel Gram-stain-negative, aerobic, orange-pigmented, non-flagellated, gliding, rod-shaped bacterium, designated strain SM1354T was isolated from surface seawater of the Atlantic Ocean. The strain hydrolysed gelatin and DNA but did not reduce nitrate. It grew at 4–40 °C and with 0.5–11 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain SM1354T belonged to the genus Marivirga with 96.0–96.2 % sequence similarities to known species of the genus Marivirga . The major fatty acids of strain SM1354T were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 03-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 02-OH). Polar lipids of strain SM1354T included phosphatidylethanolamine, three unidentified lipids and one unidentified aminolipid and aminophospholipid. The major respiratory quinone of strain SM1354T was menaquinone 7 (MK-7). The genomic DNA G+C content of strain SM1354T was 33.9±0.4 mol%. On the basis of the results of the polyphasic characterization in this study, it is proposed that strain SM1354T represents a novel species of the genus Marivirga , namely Marivirga atlantica sp. nov. The type strain of Marivirga atlantica is SM1354T ( = CCTCC AB 2014242T = JCM 30305T). An emended description of the genus Marivirga is also proposed.
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Algibacter amylolyticus sp. nov., isolated from intertidal sediment
More LessA Gram-reaction-negative, rod-shaped, yellow-pigmented, motile by gliding bacterial strain, designated RU-4-M-4T, was isolated from intertidal sediment of Sakhalin Island in Russia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RU-4-M-4T was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity with Algibacter pectinivorans KACC 14153T (97.2 %). The major cellular fatty acids were iso-C15 : 0 3-OH, C15 : 0 and iso-C15 : 1 G. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content of strain RU-4-M-4T was 36.4 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain RU-4-M-4T is a representative of a novel species of the genus Algibacter , for which we propose the name Algibacter amylolyticus sp. nov. (type strain RU-4-M-4T = LMG 28383T = DSM 29199T).
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Sediminicola arcticus sp. nov., a psychrophilic bacterium isolated from deep-sea sediment, and emended description of the genus Sediminicola
A Gram-stain-negative, rod-shaped and non-motile strain, designated PAMC 27266T, was isolated from deep-sea sediment of the Arctic Ocean. Analysis of the 16S rRNA gene sequence of strain PAMC 27266T showed closest affiliation with the genus Sediminicola . Phylogenetic analyses revealed that strain PAMC 27266T formed a robust clade with Sediminicola luteus CNI-3T, with which it shared 98.9 % 16S rRNA gene sequence similarity. Genomic relatedness analyses based on the average nucleotide identity and genome-to-genome distance showed that strain PAMC 27266T is clearly distinguished from S. luteus . Cells of strain PAMC 27266T grew optimally at 15 °C and pH 6.5–7.5 in the presence of 3.5 % (w/v) sea salts. The major polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and two unidentified lipids. The only respiratory quinone was menaquinone-6. The major cellular fatty acids (>10 %) were C16 : 1ω6c and/or C16 : 1ω7c and C15 : 0. The genomic DNA G+C content was 37.9 mol%. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data presented, we propose strain PAMC 27266T ( = KCCM 43038T = JCM 19894T) as the type strain of a novel species, with the name Sediminicola arcticus sp. nov.
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Rufibacter roseus sp. nov., isolated from radiation-polluted soil
A rose, Gram-stain-negative, aerobic, rod-shaped bacterium that was motile by gliding, and designated strain H359T, was isolated from radiation-polluted soil (with high Cs137) from the Xinjiang Uygur Autonomous Region of PR China and subjected to a polyphasic taxonomic analysis. The isolate grew optimally at 30 °C and pH 7.0. It grew with NaCl up to 4 % (w/v). 16S rRNA gene sequence analysis indicated that strain H359T belonged to the genus Rufibacter , a member of the family Cytophagaceae , with Rufibacter tibetensis CCTCC AB 208084T as its closest phylogenetic relative, having 96.1 % 16S rRNA gene sequence similarity to the type strain. Strain H359T contained menaquinone-7 (MK-7) as the predominant menaquinone, and the major fatty acids were iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c. The polar lipid profile had phosphatidylethanolamine as the major component. The DNA G+C content was 43.9 mol%. Based on phenotypic, genotypic and phylogenetic evidence, strain H359T represents a novel species of the genus Rufibacter , for which the name Rufibacter roseus sp. nov. is proposed. The type strain is H359T ( = CPCC 100615T = KCTC 42217T).
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Rufibacter immobilis sp. nov., isolated from a high-altitude saline lake
More LessTwo pinkish-red, Gram-stain-negative, non-motile aerobic bacterial strains (MCC P1T and MCC P2), capable of growing at low temperatures (15 °C), were isolated from water of a saline lake located in the western Himalayas of India. The strains were capable of growth in the presence of 0–2.0 % NaCl and at pH 6.5–9.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed the closest similarity of 96.3 % to the type strain of the only species of the genus Rufibacter , Rufibacter tibetensis CCTCC AB 208084T. Strains MCC P1T and MCC P2 shared 99.0 % 16S rRNA gene sequence similarity and 88.6 % DNA–DNA relatedness. The major cellular fatty acids were iso-C15 : 0, C17 : 1ω6c, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and summed feature 4 (anteiso-C17 : 1 B/iso-C17 : 1 I). Predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The respiratory quinone was MK-7. The DNA G+C content of the strains was 52.6–52.8 mol%. Based on morphological, physiological, chemotaxonomical and molecular characteristics, strains MCC P1T and MCC P2 represent a novel species of the genus Rufibacter , for which the name Rufibacter immobilis sp. nov. is proposed. The type strain is MCC P1T ( = MCC 2268T = CCTCC AB 2013351T).
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Belliella aquatica sp. nov., isolated from a saline lake
More LessA Gram-staining-negative bacterium, strain TS-T86T, was isolated from Lake Tuosu, a saline lake (salinity 5.4 %, w/w) in Qaidam basin, China. Its taxonomic position was determined by using a polyphasic approach. Strain TS-T86T was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Cells were non-spore-forming, non-motile rods, 0.4–0.6 µm wide and 1.2–2.3 µm long. Growth was observed in the presence of 0–9.0 % (w/v) NaCl (optimum, 2.0 %), at 4–35 °C (optimum, 25 °C) and at pH 7.0–10.5 (optimum, pH 8.5–9.0). Strain TS-T86T contained MK-7 as the predominant respiratory quinone. The major fatty acids (>10 %) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, an unknown phospholipid, six unidentified aminolipids and two uncharacterized lipids. The DNA G+C content was 35 mol% (T m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T86T was associated with the genus Belliella , and showed the highest sequence similarity to Belliella baltica BA134T (98.5 %) and then to Belliella kenyensis No.164T (95.7 %) and Belliella pelovolcani CC-SAL-25T (95.3 %). DNA–DNA relatedness of strain TS-T86T to Belliella baltica DSM 15883T was 32±3 %. It is concluded that strain TS-T86T represents a novel species of the genus Belliella , for which the name Belliella aquatica sp. nov. is proposed. The type strain is TS-T86T ( = CGMCC 1.12479T = JCM 19468T).
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Polaribacter undariae sp. nov., isolated from a brown alga reservoir
More LessA Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped or ovoid bacterial strain, designated W-BA7T, was isolated from a brown alga reservoir on the South Sea in South Korea. This strain grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-BA7T belonged to the genus Polaribacter , clustering coherently with the type strain of Polaribacter sejongensis, showing 99.3 % sequence similarity. Strain W-BA7T exhibited 16S rRNA gene sequence similarity of 93.4–98.6 % to the type strains of the other species of the genus Polaribacter . Strain W-BA7T contained MK-6 as the predominant menaquinone and iso-C15 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain W-BA7T were phosphatidylethanolamine, three unidentified lipids, one unidentified glycolipid, one unidentified aminolipid and one unidentified aminophospholipid. The DNA G+C content of strain W-BA7T was 31.9 mol%, and the mean DNA–DNA relatedness with the type strains of four phylogenetically related species of the genus Polaribacter was 12–27 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain W-BA7T is separated from recognized species of the genus Polaribacter . On the basis of the data presented, strain W-BA7T is considered to represent a novel species of the genus Polaribacter , for which the name Polaribacter undariae sp. nov. is proposed. The type strain is W-BA7T ( = KCTC 42175T = CECT 8670T).
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Leeuwenhoekiella polynyae sp. nov., isolated from a polynya in western Antarctica
A Gram-stain-negative, motile by gliding, rod-shaped bacterial strain, designated SOJ2014-1T was isolated from surface water of a polynya in the Antarctic Ocean. A comparative 16S rRNA gene sequence analysis showed that strain SOJ2014-1T belongs to the genus Leeuwenhoekiella and is most closely related to Leeuwenhoekiella marinoflava DSM 3653T (97.5 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA of strain SOJ2014-1T was 38.8 mol%. Its predominant cellular fatty acids were summed feature 3 (composed of C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G and summed feature 9 (composed of iso-C17 : 1ω9c and/or 10-methyl C16 : 0). DNA–DNA relatedness between strain SOJ2014-1T and close relatives, L. marinoflava DSM 3653T and Leeuwenhoekiella aequorea LMG 22550T, was below 49 %. The respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. The strain grew at 0–35 °C (optimum, 25 °C) with 0–14.0 % (w/v) NaCl (optimum, 1.0–5.0 %). It was strictly aerobic and had different carbohydrate utilization traits compared with L. marinoflava DSM 3653T. Based on the phenotypic, chemotaxonomic and phylogenetic analyses, strain SOJ2014-1T is proposed as a representative of a novel species, Leeuwenhoekiella polynyae. The type strain is SOJ2014-1T ( = KCTC 42185T = JCM 30387T).
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- Other Bacteria
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Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium
More LessA novel anoxygenic photoheterotrophic member of the phylum Acidobacteria , Chloracidobacterium thermophilum strain B sp. nov., was isolated from a cyanobacterial enrichment culture derived from microbial mats associated with Octopus Spring, Yellowstone National Park, WY. C. thermophilum sp. nov. was a Gram-stain-negative rod (diameter, approximately 0.8–1.0 µm; variable length, approximately 2.5 µm), which formed greenish-brown liquid suspension cultures. It was a moderately thermophilic microaerophile and grew in a defined medium at 51 °C (Topt; range 44 to 58 °C) and in the pH range 5.5 to 9.5 (pHopt = ~7.0). The DNA G+C content was 61.3 mol%, and phylogenetic analysis, based on the 16S rRNA sequence, showed that C. thermophilum sp. nov. belongs to subdivision 4 ( Acidobacteriaceae ) of the Acidobacteria . C. thermophilum sp. nov. was unable to synthesize branched-chain amino acids, l-lysine, and vitamin B12, which were required for growth. Although the organism lacked genes/enzymes for autotrophic carbon fixation, bicarbonate was required. Growth was stimulated by other amino acids and 2-oxoglutarate. Cells produced chlorosomes containing a diverse mixture of bacteriochlorophyll (BChl) c derivatives, and additionally, synthesized BChl a P, Chl a PD, and Zn-BChl a′P, which occurred in type-1 homodimeric reaction centres. The carotenoids included echinenone, canthaxanthin, lycopene, γ-carotene and β-carotene. C. thermophilum sp. nov. produced iso-diabolic acid as its major fatty acid and synthesized three hopanoids (diploptene, bacteriohopanetetrol and bacteriohopanetetrol cyclitol ether). Based upon its phenotypic and genotypic properties, the name Chloracidobacterium thermophilum gen. nov., sp. nov. is proposed for this isolate; the type strain is C. thermophilum strain BT (ATCC BAA-2647 = JCM 30199).
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Planctomicrobium piriforme gen. nov., sp. nov., a stalked planctomycete from a littoral wetland of a boreal lake
An aerobic, budding, non-pigmented and rosette-forming bacterium was isolated from a littoral wetland of a boreal lake located in Valaam Island, northern Russia, and designated strain P3T. Ellipsoidal to pear-shaped cells of this bacterium were covered with crateriform pits and possessed stalks suggesting a planctomycete morphotype. 16S rRNA gene sequence analysis confirmed that strain P3T was a member of the order Planctomycetales and belonged to a phylogenetic lineage defined by the genus Planctomyces , with 89 and 86 % sequence similarity to Planctomyces brasiliensis and Planctomyces maris , respectively. Strain P3T was a mildly acidophilic, mesophilic organism capable of growth at pH values between pH 4.2 and 7.1 (with an optimum at pH 6.0–6.5) and at temperatures between 10 and 30 °C (optimum at 20–28 °C). Most sugars, a number of polysaccharides and several organic acids were the preferred growth substrates. Compared with Planctomyces brasiliensis and Planctomyces maris , which require NaCl for growth, strain P3T was salt-sensitive and did not develop at NaCl concentrations above 0.5 % (w/v). The major fatty acids were C16 : 0 and C16 : 1ω7c; the cells also contained significant amounts of C18 : 1ω7c and C18 : 0. The major intact polar lipids were diacylglycerol-O-(N,N,N-trimethyl)homoserine (DGTS) lipids; the major neutral lipids were long-chain 1,(ω-1)-diols and C31 : 9 hydrocarbon. The quinone was MK-6, and the G+C content of the DNA was 59.0 mol%. Strain P3T differed from Planctomyces brasiliensis and Planctomyces maris by cell morphology, substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Planctomicrobium piriforme gen. nov., sp. nov., is proposed. The type strain is P3T ( = DSM 26348T = VKM B-2887T).
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- Eukaryotic Micro-organisms
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Occultifur tropicalis f.a., sp. nov., a novel cystobasidiomycetous yeast species isolated from tropical regions
Five strains representing a single novel anamorphic yeast species were isolated from sugar cane. Two strains were from tissue (DMKU-SE38, DMKU-SE59T) and two from the external surface (DMKU-SP385, DMKU-SP403) of leaves collected in Thailand and the fifth (IMUFRJ 52020) from the rhizoplane of sugar cane in an organically cultivated field in Brazil. On the basis of sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, they were classified as representing a single species of the genus Occultifur. The sequences of the D1/D2 region of the LSU rRNA genes and the ITS regions of the five strains were either identical or differed from each other by only one nucleotide substitution. The novel species was related most closely to Occultifur brasiliensis f.a. CBS 12687T but with 0.7–1.0 % nucleotide substitutions (4–6 nt) in the D1/D2 region of the LSU rRNA gene and 2.5–2.7 % nucleotide substitutions (14–15 nt) in the ITS region. The name Occultifur tropicalis f.a., sp. nov. is proposed. The type strain is DMKU-SE59T ( = BCC 61184T = NBRC 109696T = CBS 13389 T).
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 71 (2020 - 2021)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 1 (1951)