- Volume 70, Issue 7, 2020
Volume 70, Issue 7, 2020
- Editorial
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Lists of names of prokaryotic Candidatus taxa
More LessWe here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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- Validation List
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- Notification List
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- List of Changes in Taxonomic Opinion
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- New taxa
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- Actinobacteria
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Vaginimicrobium propionicum gen. nov., sp. nov., a novel propionic acid bacterium derived from human vaginal discharge
A Gram-stain-positive anaerobic rod-shaped bacterium, designated strain Marseille-P3275T, was isolated using culturomics from the vaginal discharge of healthy French woman. Marseille-P3275T was non-motile and did not form spores. Cells had neither catalase nor oxidase activity. The major fatty acids were C16 : 0 (29 %), C18:1ω9 (18 %), and iso-C15 : 0 (17 %). The genomic DNA G+C content was 50.64 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that Marseille-P3275T was related to members of the family Propionibacteriaceae (between 90.32–92.92 % sequence similarity) with formation of a clade with the monospecific genus Propionimicrobium (type species Propionimicrobium lymphophilum ). On the basis of these phylogenetic and phenotypic differences, Marseille-P3275T was classified in a novel genus, Vaginimicrobium, as Vaginimicrobium propionicum gen. nov., sp. nov. The type strain is Marseille-P3275T (=CSUR P3275T=CECT 9677T).
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Arcanobacterium bovis sp. nov., isolated from the milk of a cow with mastitis
A polyphasic taxonomic study was performed on an unidentified Arcanobacterium -like Gram-stain-positive bacterium designated strain C605018/01/1T isolated from a milk sample collected from the udder of a cow at post mortem. Comparative 16S rRNA gene sequencing showed that the bacterium belonged to the genus Arcanobacterium and was most closely related to the type strain of Arcanobacterium pluranimalium (99.76 %); sequence similarities to all other Arcanobacterium species were below 97 %. The wet-lab DNA–DNA hybridization values among strain C605018/01/1T and A. pluranimalium DSM 13483ᵀ were low, 16.9 % (reciprocal, 49.8 %). Pertaining to the whole genome sequence with a total length of 2.02 Mb and 1654 protein counts, the novel strain C605018/01/01T displayed a G+C content of 51.6 % mol%. The presence of the major menaquinone MK-9(H4) supported the affiliation of this strain to the genus Arcanobacterium . The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol-mannoside and unidentified glycolipid and aminophospholipids. Based on these results it is proposed that strain C605018/01/1T should be classified as representing a novel species, Arcanbacterium bovis sp. nov. The type strain C605018/01/1T (CCUG 45425T=DSM 107286T=BCCM/LMG 30783T)
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Phytoactinopolyspora mesophila sp. nov., isolated from a saline–alkaline soil
A novel moderately halophilic, filamentous actinobacterium, designated as XMNu-373T, was isolated from a saline–alkaline soil sample collected from the Mongolia Plateau, Dongwu County, Inner Mongolia Autonomous Region, PR China. The isolate grew optimally at 28‒37 °C, pH 7.0‒8.0 and with 2–5 % (w/v) NaCl. The substrate mycelia fragmented into rod-like elements, and the white aerial mycelia formed spore chains at maturity. The predominant menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, three unidentified phosphoglycolipids, an unidentified aminophospholipid, two phosphatidylinositol mannosides, four unidentified phospholipids, phosphatidylglycerol and two unidentified lipids. The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content was 66.2 mol%. It shared high 16S rRNA gene sequence similarities to Phytoactinopolyspora halotolerans YIM 96448T (96.1 %) and Phytoactinopolyspora endophytica EGI 60009T (96.0 %). Phylogenetic trees based on 16S rRNA gene sequences revealed that strain XMNu-373T resided in the clade of family Jiangellaceae , and it formed a monophyletic branch distinct from four other recognized type species in the subclade of the genus Phytoactinopolyspora . On the basis of polyphasic taxonomic evidence, strain XMNu-373T represents a novel species of the genus Phytoactinopolyspora , for which the name Phytoactinopolyspora mesophila sp. nov. is proposed. The type strain is XMNu-373T (=JCM 33740T=CGMCC 4.7654T).
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Reclassification of Streptomyces diastaticus subsp. ardesiacus, Streptomyces gougerotii and Streptomyces rutgersensis
More LessWe investigated the taxonomic relationships among Streptomyces diastaticus subsp. ardesiacus , Streptomyces diastaticus subsp. diastaticus , Streptomyces gougerotii and Streptomyces rutgersensis . The 16S rRNA gene sequence similarity between S. diastaticus subsp. ardesiacus and S. diastaticus subsp. diastaticus was 97.7 %, whereas S. diastaticus subsp. diastaticus , S. gougerotii and S. rutgersensis showed 100 % nucleotide sequence identity. In addition, S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis formed a single clade in the phylogenetic tree. Digital DNA–DNA relatedness between S. diastaticus subsp. diastaticus and S. diastaticus subsp. ardesiacus was only 22.8%, indicative of different species. In comparison, DNA–DNA relatedness values for S. diastaticus subsp. diastaticus , S. gougerotii and S. rutgersensis ranged from 95.8 to 97.2 %, suggesting the three taxa belong to the same genomospecies. Previously reported phenotypic data also supported synonymy. Therefore, we propose that S. diastaticus subsp. ardesiacus should be classified as an independent species, Streptomyces ardesiacus sp. nov. The type strain is NBRC 13412T (=ATCC 3315T=CBS 713.72T=DSM 40496T=ISP 5496T=JCM 4745T=NBRC 3714T=NRRL B-1241T=RIA 1373T). Our data also suggests that S. rutgersensis and S. gougerotii should be reclassified as later heterotypic synonyms of S. diastaticus .
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Actinokineospora pegani sp. nov., an endophytic actinomycete isolated from the surface-sterilized root of Peganum harmala L.
More LessA novel Gram-positive, aerobic and motile endophytic actinomycete, designated TRM 65233T, was isolated from the root of Peganum harmala L. collected from Xinjiang Uygur Autonomous Region of China. The isolate had white aerial mycelium and brown substrate mycelium on Gause’s synthetic agar. Growth occurred at 10–40 °C, pH 6–9 with NaCl concentration of 0–6 % (w/v). Strain TRM 65233T contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell hydrolysates included glucose and galactose as the major whole-cell sugars. The menaquinones were MK-9 (H4) and MK-7. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phospholipids, phosphatidylinositol and one unidentified lipid. Strain TRM 65233T showed the highest 16S rRNA gene sequence similarity to Actinokineospora cianjurensis BTCC B-558T (98.13 %), Actinokineospora auranticolor IFO 16518T (98.06 %), Actinokineospora spheciospongiae EG49T (97.99 %), Actinokineospora baliensis ID03-0561T (97.97 %), Actinokineospora mzabensis PAL84T (97.95 %) and Actinokineospora bangkokensis 44EHWT (97.06 %). The isolate was distinguished from these phylogenetically related strains by digital DNA–DNA hybridization and average nucleotide identity analyses and by a range of physiological and biochemical characteristics. The G+C content of the genomic DNA was 72.6 mol%. On the basis of polyphasic taxonomic data, strain TRM 65233T represents a novel species of the genus Actinokineospora , for which the name Actinokineospora pegani sp. nov. is proposed. The type strain is TRM 65233T (KCTC 49342=CCTCC AA 2019050).
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- Archaea
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Halobacterium bonnevillei sp. nov., Halobaculum saliterrae sp. nov. and Halovenus carboxidivorans sp. nov., three novel carbon monoxide-oxidizing Halobacteria from saline crusts and soils
More LessThree novel carbon monoxide-oxidizing Halobacteria were isolated from Bonneville Salt Flats (Utah, USA) salt crusts and nearby saline soils. Phylogenetic analysis of 16S rRNA gene sequences revealed that strains PCN9T, WSA2T and WSH3T belong to the genera Halobacterium , Halobaculum and Halovenus , respectively. Strains PCN9T, WSA2T and WSH3T grew optimally at 40 °C (PCN9T) or 50 °C (WSA2T, WSH3T). NaCl optima were 3 M (PCN9T, WSA2T) or 4 M NaCl (WSH3T). Carbon monoxide was oxidized by all isolates, each of which contained a molybdenum-dependent CO dehydrogenase. G+C contents for the three respective isolates were 66.75, 67.62, and 63.97 mol% as derived from genome analyses. The closest phylogenetic relatives for PCN9T, WSA2T and WSH3T were Halobacterium noricense A1T, Halobaculum roseum D90T and Halovenus aranensis EB27T with 98.71, 98.19 and 95.95 % 16S rRNA gene sequence similarities, respectively. Genome comparisons of PCN9T with Halobacterium noricense A1T yielded an average nucleotide identity (ANI) of 82.0% and a digital DNA–DNA hybridization (dDDH) value of 25.7 %; comparisons of WSA2T with Halobaculum roseum D90T yielded ANI and dDDH values of 86.34 and 31.1 %, respectively. The ANI value for a comparison of WSH3T with Halovenus aranensis EB27T was 75.2 %. Physiological, biochemical, genetic and genomic characteristics of PCN9T, WSA2T and WSH3T differentiated them from their closest phylogenetic neighbours and indicated that they represent novel species for which the names Halobaculum bonnevillei, Halobaculum saliterrae and Halovenus carboxidivorans are proposed, respectively. The type strains are PCN9T (=JCM 32472=LMG 31022=ATCC TSD-126), WSA2T (=JCM 32473=ATCC TSD-127) and WSH3T (=JCM 32474=ATCC TSD-128).
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- Bacteroidetes
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Patiriisocius marinistellae gen. nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov.
More LessA marine strain, designated KK4T, was isolated from the surface of a starfish, Patiria pectinifera, which was collected from seawater off the coast of Hokkaido, Japan. Strain KK4T is a Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium that forms yellow-pigmented colonies. A phylogenetic relationship analysis, based on 16S rRNA gene sequences, revealed that strain KK4T was closely related to Ulvibacter marinus IMCC12008T, Ulvibacter antarcticus IMCC3101T and Ulvibacter litoralis KMM 3912T, with similarities of 96.9, 95.8 and 95.6 %, respectively, but low sequence similarities (<94 %) among other genera in the family Flavobacteriaceae . Genomic similarities between strain KK4T and the three Ulvibacter type strains based on average nucleotide identity and digital DNA–DNA hybridization values were lower than the species delineation thresholds. Moreover, phylogenetic tree based on genome sequences showed that strain KK4T was clustered with U. marinus IMCC12008T and formed a branch independent from the cluster including type species of the genera Ulvibacter , Marixanthomonas , Marinirhabdus , Aureitalea and Aequorivita . Amino acid identity values between strain KK4T/ U. marinus IMCC12008T and the neighbour type species/strains were 61.9–68.2% and 61.5–67.4 %, which were lower than the genus delineation threshold, implying the novel genus status of strain KK4T. Strain KK4T growth occurred at pH 6.0–9.0, 4–30 °C and in NaCl concentrations of 0.5–5.0 %, and optimally at pH 7.0, 25 °C and 3.0 %, respectively. Unlike Ulvibacter strains, strain KK4T could assimilate glucose, mannose, galactose and acetate. The major quinone and fatty acids were menaquinone-6 and iso-C15 : 0 (27.5 %), iso-C15 : 1 G (22.5 %) and iso-C17 : 0 3-OH (12.8 %), respectively. Based on genetic, phylogenetic and phenotypic properties, strain KK4T represents a novel species of the genus Patiriisocius, for which the name Patiriisocius marinistellae gen. nov., sp. nov. is proposed. The type strain is KK4T (=JCM 33344T=KCTC 72225T). In addition, based on the current data, Ulvibacter marinus should be reclassified as Patiriisocius marinus comb. nov.
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Echinicola soli sp. nov., isolated from alkaline saline soil
More LessStrains of Echinicola , thought to play vital roles in the environment for their high enzyme production capacity during decomposition of polysaccharides, are ubiquitous in hypersaline environments. A Gram-negative, non-spore forming, gliding, aerobic bacterial strain, designated LN3S3T, was isolated from alkaline saline soil sampled in Tumd Right Banner, Inner Mongolia, northern PR China. Strain LN3S3T grew at 10–40 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 8.0) and with 0–12.5 % NaCl (optimum, 2.0 %). A phylogenetic tree based on the 16S rRNA gene sequences showed that strain LN3S3T clustered with Echinicola rosea JL3085T and Echinicola strongylocentroti MEBiC08714T, sharing 97.0, 96.7 and <96.50 % of 16S rRNA gene sequence similarities to E. rosea JL3085T, E. strongylocentroti MEBiC08714T and all other type strains. MK-7 was the major respiratory quinone, while phosphatidylethanolamine, two unidentified phospholipids, an unidentified aminophospholipid, an unidentified lipid and two unidentified aminolipids were the major polar lipids. Its major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The genome consisted of a circular 5 550 304 bp long chromosome with a DNA G+C content of 44.0 mol%. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values of strain LN3S3T to E. rosea JL3085T and E. strongylocentroti MEBiC08714T were 82.5 and 81.5 %, 87.5 and 86.0 %, and 39.1 and 35.1 %, respectively. Based on physiological, genotypic and phylogenetic analyses, strain LN3S3T could be discriminated from its phylogenetic relatives. Echinicola soli sp. nov. is therefore proposed with strain LN3S3T (=CGMCC 1.17081T=KCTC 72458T) as the type strain.
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Sunxiuqinia indica sp. nov., isolated from deep sea
More LessA Gram-stain-negative, facultative anaerobic, red-pigmented, rod-shaped and non-motile strain (RC1_OXG_1FT) was isolated from deep sea water of the Indian Ocean. It was able to grow at pH 5–8 (optimum, pH 7), at 5–37 °C (optimum, 30 °C), and at salinity (% NaCl, w/v) of 0.5–5 % (optimum, 1–2 %). Catalase- and oxidase-positive. It had highest 16S rRNA gene similarity (96.7 %) to ‘ Sunxiuqinia dokdonensis ’ DH1T, followed by Sunxiuqinia faeciviva JAM-BA0302T (96.6 %), Sunxiuqinia elliptica CGMCC 1.9156T (96.2 %), Sunxiuqinia rutila HG677T (96.0 %) and species (less than 92.3 %) of other genera. It belongs to the genus Sunxiuqinia within the phylum Bacteroidetes , based on the phylogenetic analysis. The results of digital DNA–DNA hybridization and average nucleotide identity analyses indicated that the strain belonged to a novel species. Its genome size is 5,250, 885 bp, with DNA G+C content of 40.5 mol%. Genome analysis revealed that the strain possessed many genes involved in polysaccharide degradation, especially hemicellulose degradation, indicating that the strain could maintain its normal metabolism by using recalcitrant organic matter in the oligotrophic deep sea environment. Its principal fatty acids were anteiso-C15 : 0 and iso-C15 : 0 and the major polar lipids were phosphatidylethanolamine, two unidentified glycolipids, three unidentified phospholipids and two unidentified polar lipids. The isoprenoid quinone was MK-7. Based on the phenotypic, chemotaxonomic and genotypic data, the strain represents a novel species within the genus Sunxiuqinia , for which the name Sunxiuqinia indica sp. nov. is proposed. The type strain is RC1_OXG_1FT (=MCCC 1A13858T=KCTC 62805T).
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Pontibacter mangrovi sp. nov., isolated from mangrove sediment
More LessA Gram-stain-negative, short-rod-shaped and pink-pigmented bacterial strain (HB172049T) was isolated from mangrove sediment. Cells grew at 10–45 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.0) and with 0.5–9.0 % (w/v) NaCl (optimum, 2–5 %). Analysis of the 16S rRNA gene sequence revealed that the isolate had highest sequence similarities to Pontibacter mucosus DSM 100162T (96.5 %) and Pontibacter korlensis X14-1T (96.5 %). The values of average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization between the isolate and its close neighbours were, respectively, less than 80.1, 81.7 and 23.2 %. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-7 and the predominant cellular fatty acids were summed feature 4 and iso-C15 : 0 (42.2 and 24.6 %, respectively). The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified polar lipids. The genomic DNA G+C content was 52.6 mol%. Based on polyphasic taxonomic characterization, it is proposed that strain HB172049T belongs to the genus Pontibacter and represents a novel species, for which the name Pontibacter mangrovi sp. nov. is proposed. The type strain is HB172049T (=CGMCC 1.16729T=JCM 33333T).
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Flavobacterium salilacus sp. nov., isolated from surface water of a hypersaline lake, and descriptions of Flavobacterium salilacus subsp. altitudinum subsp. nov. and Flavobacterium salilacus subsp. salilacus subsp. nov.
Two yellow-pigmented, Gram-stain-negative, aerobic, rod-shaped bacteria were isolated from the water of the hypersaline Chaka Salt Lake (strain SaA2.12T) and sediment of Qinghai Lake (strain LaA7.5T), PR China. According to the 16S rRNA phylogeny, the isolates belong to the genus Flavobacterium , showing the highest 16S rRNA sequence similarities to Flavobacterium arcticum SM1502T(97.6–97.7 %) and Flavobacterium suzhouense XIN-1T(96.5–96.6 %). Moreover, strains SaA2.12T and LaA7.5T showed 99.73 % 16S rRNA sequence similarity to each other. Major fatty acids, respiratory quinones and polar lipids detected in these isolates were iso-C15 : 0, menaquinone-6 and phosphatidylethanolamine, respectively. Strains SaA2.12T and LaA7.5T showed significant unique characteristics between them as well as between the closest phylogenetic members. The highest digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between SaA2.12T and its closest neighbours were 25.3 and 82.8 %, respectively; whereas these values (highest) between LaA7.5T and its closest members were 25.2 and 82.8 %, respectively. The dDDH and ANI values between strains SaA2.12T and LaA7.5T were calculated as 75.9 and 97.2 %, respectively. Therefore, based on polyphasic data, we propose that strain SaA2.12T represents a novel species with the name Flavobacterium salilacus sp. nov., with the type strain SaA2.12T (=KCTC 72220T=MCCC 1K03618T) and strain LaA7.5T as a subspecies within novel Flavobacterium salilacus with the name Flavobacterium salilacus subsp. altitudinum subsp. nov., with the type strain LaA7.5T (=KCTC 72806T=MCCC 1K04372T). These propositions automatically create Flavobacterium salilacus subsp. salilacus subsp. nov. with SaA2.12T (=KCTC 72220T=MCCC 1K03618T) as the type strain.
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Raineyella fluvialis sp. nov., an actinobacterium isolated from freshwater sediment
A novel, facultatively anaerobic actinobacterium, designated strain CBA3103T, was isolated from sediment of the Geum River in South Korea. Phylogenetic analysis indicated that strain CBA3103T is most closely related to Raineyella antarctica LZ-22T (98.47 % 16S rRNA gene sequence similarity). The genome of strain CBA3103T was 3 649 865 bp with a DNA G+C content of 69.6 mol%. The average nucleotide identity value between strain CBA3103T and R. antarctica LZ-22T was 79.22 %. Cells of strain CBA3103T were Gram-positive, rod-shaped, 0.6–0.9 µm wide and 1.4–2.4 µm long. Growth occurred at 15–40 °C (optimum, 35 °C), at pH 6.0–7.0 (optimum, pH 7.0) and with 0–2 % NaCl (w/v) (optimum, 0–1 %, w/v). The major cellular fatty acids in strain CBA3103T were anteiso-C15 : 0, anteiso-C15 : 1 A and iso-C14 : 0. The major respiratory quinone was menaquinone-9(H4). The polar lipids of strain CBA3103T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified glycolipids and three unidentified phospholipids. Based on the genotypic, phenotypic and chemotaxonomic analyses, strain CBA3103T represents a novel species of the genus Raineyella , for which the name Raineyella fluvialis sp. nov. (type strain CBA3103T=KACC 21446T=DSM 110288T) is proposed.
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Polaribacter septentrionalilitoris sp. nov., isolated from the biofilm of a stone from the North Sea
A new member of the family Flavobacteriaceae was isolated from the biofilm of a stone at Nordstrand, a peninsula at the German North Sea shore. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain ANORD1T was most closely related to the validly described type strains Polaribacter porphyrae LNM-20T (97.0 %) and Polaribacter reichenbachii KMM 6386T (96.9 % 16S rRNA gene sequence similarity) and clustered with Polaribacter gangjinensis K17-16T (96.0 %). Strain ANORD1T was determined to be mesophilic, Gram-negative, non-motile and strictly aerobic. Optimal growth was observed at 20–30 °C, within a salinity range of 2–7 % sea salt and from pH 7–10. Like other type strains of the genus Polaribacter , ANORD1T was tested negative for flexirubin-type pigments, while carotenoid-type pigments were detected. The DNA G+C content of strain ANORD1T was 30.6 mol%. The sole respiratory quinone detected was menaquinone 6 (MK-6). The major fatty acids identified were C15 : 0, iso-C15 : 0, C15 : 1 ω6c and iso-C15 : 0 3-OH. Based on the polyphasic approach, strain ANORD1T represents a novel species in the genus Polaribacter , with the name Polaribacter septentrionalilitoris sp. nov. being proposed. The type strain is ANORD1T (=DSM 110039T=NCIMB 15081T=MTCC 12685T).
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Muricauda hadalis sp. nov., a novel piezophile isolated from hadopelagic water of the Mariana Trench and reclassification of Muricauda antarctica as a later heterotypic synonym of Muricauda teanensis
A novel marine Gram-stain-negative, non-motile, aerobic and rod-shaped bacterium, designated as strain MT-229T, was isolated from the deep seawater in the Mariana Trench and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 30 °C (ranging 10–40 °C), pH 6 (ranging 3–11) and with 11 % (w/v) NaCl (ranging 0–17 %). Strain MT-229T was a piezophile, growing optimally at 20 MPa (range 0.1–70 MPa). The nearest phylogenetic neighbours were Muricauda antarctica CGMCC 1.2174T and Muricauda taeanensis JCM 17757T with 16S rRNA gene similarity of 98.7 %. The sole respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine (PE), two unidentified aminolipids (AL) and ten unidentified lipids. The major fatty acids of strain MT-229T were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The G+C content of the genomic DNA was 45.6 mol%. The combined genotypic and phenotypic data indicated that strain MT-229T represents a novel species of the genus Muricauda , for which the name Muricauda hadalis sp. nov. is proposed, with the type strain MT-229T (=DSM 109894T=MCCC 1K04201T). In addition, the whole-genome-based comparisons revealed that the type strains of Muricauda antarctica and Muricauda teanensis belong to a single species. It is, therefore, proposed that M. antarctica be recognized as a heterotypic synonym of M. teanensis.
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Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters
Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1–15 % NaCl) and mesophilic (4–37 °C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15 : 0, iso-C15 : 0 2-OH, and iso-C17 : 0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2 %), Salegentibacter mishustinae (93.1 %) and Mesonia mobilis (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81 % AAI; 78.9 % ANI), M. phycicola (76 % AAI; 76.3 % ANI), Mesonia maritima (72 % AAI, 74.9 % ANI), Mesonia hippocampi (64 % AAI, 70.8 % ANI) and Mesonia algae (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653T in a clade with species of the genus Mesonia . We conclude that strain ISS653T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653T (=CECT 9532T=LMG 31236T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.
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- Firmicutes and Related Organisms
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Streptococcus downii sp. nov., isolated from the oral cavity of a teenager with Down syndrome
More LessA new α-haemolytic streptococcal strain has been isolated from the dental plaque of a teenager with Down syndrome. Genetic and taxonomic analyses place this Streptococcus within the oralis group. It is a Gram-stain-positive, non-motile, non-spore-forming spherical alpha-haemolytic coccus arranged in chains, and it ferments a large number of monosaccharides and disaccharides, as well as polymeric carbohydrates. It differs biochemically from closely related species of Streptococcus due to its production of α-galactosidase, β-galactosidase and N-acetyl-β-d-glucosaminidase and by the absence of arginine dihydrolase deiminase and IgA1-protease. It grows in a temperature range of 25 to 40 °C (optimal growth temperature at 37 °C) and in a pH range of 4.5 to 8 (optimal pH at 7.0). A phylogenetic analysis based on its 16S and 23S rRNA gene sequences placed it close to Streptococcus dentisani CECT 7747T. The ANIb and ANIm values were 93.19 and 93.61 %, respectively, both below the accepted threshold to designate it as a new species of bacteria. A phylogenetic tree based on its core genome placed it close to Streptococcus oralis subsp. dentisani strain CECT 7747T with a distance in the expanded core phylogeny of 0.1298. The in silico DNA–DNA hybridization value was 52.2 % with respect to the closest species, S. oralis subsp. dentisani CECT 7747T. Based on these data, a new species of bacteria within the genus Streptococcus , family Streptococcaceae and order Lactobacillales is described, for which the name of Streptococcus downii sp. nov. is proposed (type strain CECT 9732T=CCUG 73139T).
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Salinicoccus cyprini sp. nov., isolated from the gut of mirror carp, Cyprinus carpio var. specularis
More LessA novel orange to pink coloured bacterial strain designated as CT19T was isolated from the gastrointestinal tract of mirror carp, Cyprinus carpio var. specularis (Lacepède, 1803) collected from the Gobind Sagar reservoir at village Lathiani, Una, Himachal Pradesh, India. Cells of the strain were found to be aerobic, Gram-stain-positive, non-motile and non-spore-forming coccoids. Based on the 16S rRNA gene sequence, the strain was closely related to Salinicoccus hispanicus J-82T (=DSM 5352T; 97.4 %), followed by S. sesuvii CC-SPL15-2T (=DSM 23267T; 96.4 %), S. amylolyticus JC304T (=KCTC 33661T; 95.6 %) and S. roseus DSM 5351T (95.4 %). Identity with all other members of the genus were <94.5 %. The draft genome of strain CT19T was assembled to 2.4 Mbp with a G+C content of 47.9 mol%. Average nucleotide identity and digital DNA–DNA hybridization values between strain CT19T and S. hispanicus J-82T were found to be 85.9 and 31.3% respectively which is far below the threshold for species delineation. Iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, C16 : 0 and anteiso-C17 : 0 were the major cellular fatty acids of strain CT19T. Major polar lipids were diphosphatidylglycerol, phosphatidylgylcerol and an unidentified glycolipid. Respiratory quinone system was composed of menaquinone-6 and major cell wall amino acid was l-lysine. Based on phylogenomic, physiological and biochemical characteristics, strain CT19T represents a novel species of the genus Salinicoccus for which the name Salinicoccus cyprini sp. nov. is proposed. The type strain is CT19T (=KCTC 43022T =CCM 8886T=MCC 3834T).
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Terrilactibacillus tamarindi sp. nov., isolated from bark of Tamarindus indica
A Gram-stain-positive, catalase-positive, facultatively anaerobic, terminal-spore-forming rod, designated strain BCM23-1T, was isolated from bark of Tamarindus indica collected from Chiang Mai Province, Thailand. This strain produced d-lactic acid from glucose. It grew at 20–45 °C (optimum, 30 °C), pH 3.5–9 (optimum, pH 7.0) and in the presence of 1–4 % (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid (A1γ). The major isoprenoid quinone was menaquinone 7 (MK-7). Polar lipids analysis revealed the presence of diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified phospholipid and an unidentified lipid. The predominant cellular fatty acids were anteiso-C17 : 0, anteiso-C15:0, and iso-C16 : 0 when cultivated on GYP agar plates. The 16S rRNA gene sequence similarity between strain BCM23-1T and Terrilactibacillus laevilacticus NK26-11T was 98.3 %. The draft genome of BCM23-1T was 3.24 Mb in size and contained 3088 coding sequences with an in silico DNA G+C content of 37.1 mol%. The values of ANIb, ANIm and digital DNA–DNA hybridization between strain BCM23-1T and T. laevilacticus NK26-11T were 89.9, 90.8 and 40.4 %, respectively. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain BCM23-1T as representing a novel species of Terrilactibacillus for which the name Terrilactibacillus tamarindi sp. nov. is proposed. The type strain is BCM23-1T (=LMG 31662T=JCM 33748T=TISTR 2841T).
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Caproicibacter fermentans gen. nov., sp. nov., a new caproate-producing bacterium and emended description of the genus Caproiciproducens
More LessA strictly anaerobic bacterial strain designated EA1T was isolated from an enrichment culture inoculated with biogas reactor content. Cells of strain EA1T are spore-forming rods (1–3×0.4–0.8 µm) and stain Gram-negative, albeit they possess a Gram-positive type of cell-wall ultrastructure. Growth of strain EA1T was observed at 30 and 37 °C and within a pH range of pH 5–9. The major components recovered in the fatty acid fraction were C14:0, C16:0, C16:0 DMA (dimethyl acetal) and C16:1 ω7c. Strain EA1T fermented several mono- and disaccharides. Metabolic end products from fructose were acetate, butyrate, caproate and lactate. Furthermore, ethanol, CO2 and H2 were identified as products. The genome consists of a chromosome (3.9 Mbp) with 3797 predicted protein-encoding genes and a G+C content of 51.25 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EA1T represents a novel taxon within the family Oscillospiraceae . The most closely related type strains of EA1T, based on 16S rRNA gene sequence identity, are Caproiciproducens galactitolivorans BS-1T (94.9 %), [ Clostridium ] leptum DSM 753T (93.8 %), [ Clostridium ] sporosphaeroides DSM 1294T (91.7 %) and Ruminococcus bromii ATCC 27255T (91.0 %). Further phenotypic characteristics of strain EA1T differentiate it from related, validly described bacterial species. Strain EA1T represents a novel genus and novel species within the family Oscillospiraceae . The proposed name is Caproicibacter fermentans gen. nov., sp. nov. The type strain is EA1T (DSM 107079T=JCM 33110T).
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- Other Bacteria
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Gimesia benthica sp. nov., a planctomycete isolated from a deep-sea water sample of the Northwest Indian Ocean
A Gram-stain-negative, stalked, oval-shaped and budding bacterial strain, designated E7T, was isolated from a deep-sea water sample collected from the Northwest Indian Ocean. The novel strain was strictly aerobic, and catalase- and oxidase-positive. It grew at 6–40 °C (optimum 30 °C) and pH 5.5–8.0 (optimum pH 7.0–7.5). The strain required 0.5–9.0 % (w/v) NaCl (optimum 3.0–5.0 %) for growth. Aesculin, starch, pectin and Tween 20 were hydrolysed. Based on 16S rRNA gene sequence analysis, strain E7T showed the highest similarity with Gimesia maris DSM 8797T (97.5 %). The average nucleotide identity and in silico DNA–DNA hybridization values between strain E7T and G. maris DSM 8797T were 78.0 and 19.3 %, respectively. The predominant cellular fatty acids of strain E7T were C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major respiratory quinone was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), phosphatidyldimethylethanolamine (PDME), phosphatidylcholine (PC) and diphosphatidylglycerol (DPG). The genomic DNA G+C content of strain E7T was 52.8 mol%. On the basis of phylogenetic inference and phenotypic characteristics, it is proposed that strain E7T represents a novel species of the genus Gimesia , for which the name Gimesia benthica sp. nov. is proposed. The type strain is E7T (=CGMCC 1.16119T=KCTC 72737T).
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- Proteobacteria
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Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf
Strain B66T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15–45 °C (optimum, 30 °C), at pH 5–11 (optimum, pH 6.5–8) and with 0–6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66T was affiliated with the family Alteromonadaceae , sharing the highest sequence similarities to the genera Alteromonas (93.7–95.4 %), Aestuariibacter (94.0–95.1 %), Agaribacter (93.3–93.7 %), Glaciecola (92.0–93.7 %), Marisendiminitalea (93.2–93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium . Major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c/iso-C15 : 0 2-OH and iso-C15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66T (=QCC B003/17T=LMG 30288 T=CCUG 70703T).
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Sphingomonas chungangi sp. nov., a bacterium isolated from garden soil sample
More LessA novel bacterial strain, designated MAH-6T, was isolated from a garden soil sample. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. The colonies were light yellow, smooth, circular and 0.6–1.2 mm in diameter when grown on nutrient agar for 3 days. Strain MAH-6T grew at 15–35 °C, at pH 5.0–7.0 and with 0–0.5 % NaCl. Cell growth occurred on nutrient agar and Reasoner's 2A (R2A) agar. The strain was positive for both catalase and oxidase tests. Cells were able to hydrolyse starch, aesculin, Tween 20 and Tween 80. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingomonas and was most closely related to Sphingomonas polyaromaticivorans B2-7T (98.2 % sequence similarity), Sphingomonas oligoaromativorans SY-6T (96.9 %) and Sphingomonas morindae NBD5T (96.6 %). The novel strain MAH-6T has a draft genome size of 4 370 740 bp (28 contigs), annotated with 4199 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content of the strain was determined to be 66.2 mol% and the predominant isoprenoid quinone is Q-10. The major fatty acids were identified as summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c), C14 : 0 2OH and C16 : 0. The main polar lipids were phosphatidylcholine, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the results of phenotypic, genotypic, chemotaxonomic and DNA–DNA hybridization studies, strain MAH-6T represents a novel species, for which the name Sphingomonas chungangi sp. nov. is proposed, with MAH-6T as the type strain (=KACC 19292T=CGMCC1.13654T).
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Caulobacter soli sp. nov., isolated from soil sampled at Jiri Mountain, Republic of Korea
A Gram-stain-negative, yellow-pigmented, aerobic, non-spore-forming, motile with a single polar flagellum and rod-shaped bacterium, Ji-3-8T, was isolated from a soil sample taken from Jiri Mountain, Republic of Korea. Comparative 16S rRNA gene sequence studies showed the isolate had clear affiliation with Alphaproteobacteria and the closest relatedness to Caulobacter rhizosphaerae KCTC 52515T, Caulobacter henricii ATCC 15253T, Caulobacter segnis ATCC 21756T, Caulobacter hibisci THG-AG3.4T, Caulobacter flavus RHGG3T and Caulobacter vibrioides CB51T showing 99.1, 98.9, 97.7, 97.6, 97.5 and 97.4 % 16S rRNA gene sequence similarity, respectively, and 94.7–96.5 % to the remaining species of genus Caulobacter . The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1 ω7c 11-methyl, C16 : 0, summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The major polar lipids were found to be phosphatidylglycerol, two unidentified phosphoglycolipid and two unidentified glycolipids. The G+C content of the genomic DNA of strain Ji-3-8T was 68.1 mol%. Average nucleotide identity and digital DNA–DNA hybridization values of strain Ji-3-8T with C. rhizosphaerae KCTC 52515T, C. henricii ATCC 15253T, C. segnis ATCC 21756T, C. flavus RHGG3T and C. vibrioides were 79.7–87.7% and 23.0–34.3%, respectively. Based on the polyphasic evidence, it is proposed that strain Ji-3-8T forms a novel species in the genus Caulobacter , for which the name Caulobacter soli sp. nov. is proposed. The type strain is Ji-3-8T (=CCTCC AB 2019389T=KCTC 72990T).
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Cupriavidus agavae sp. nov., a species isolated from Agave L. rhizosphere in northeast Mexico
During the isolation of bacteria from the Agave L. rhizosphere in northeast Mexico, four strains with similar BOX-PCR patterns were collected. The 16S rRNA gene sequences of all four strains were very similar to each other and that of the type strains of Cupriavidus metallidurans CH34T (98.49 % sequence similarity) and Cupriavidus necator N-1T (98.35 %). The genome of strain ASC-9842T was sequenced and compared to those of other Cupriavidus species. ANIb and ANIm values with the most closely related species were lower than 95%, while the in silico DNA–DNA hybridization values were also much lower than 70 %, consistent with the proposal that they represent a novel species. This conclusion was supported by additional phenotypic and chemotaxonomic analyses. Therefore, the name Cupriavidus agavae sp. nov. is proposed with the type strain ASC-9842T (=LMG 26414T=CIP 110327T).
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Dickeya oryzae sp. nov., isolated from the roots of rice
A novel Gram-stain-negative strain, designated ZYY5T, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5T was a member of the genus Dickeya , with a highest similarity to Dickeya zeae DSM 18068T (98.5%). The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Multi-locus sequence analysis using five concatenated genes (16S rRNA, atpD, infB, recA and gyrB) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5T formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of D. zeae . The orthologous average nucleotide identity (ANI) and digital DNA–DNAhybridization (dDDH) values among these six strains ranged from 96.8–99.9% and 73.7–99.8%, which supported that they were belonged to the same species. However, strain ZYY5T shared 58.4 of dDDH and 94.5% of ANI values with type strain D. zeae DSM 18068T, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5T contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus Dickeya . Based on the results of the polyphasic approaches, we propose that strain ZYY5T represents a novel species in the genus Dickeya , for which the name Dickeya oryzae sp. nov. (=JCM 33020 T=ACCC 61554 T) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of D. oryzae same as ZYY5T.
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Pukyongiella litopenaei gen. nov., sp. nov., a novel bacterium isolated from the gut content of a whiteleg shrimp Litopenaeus vannamei
More LessA Gram-negative, aerobic bacterium, designated as SH-1T, was isolated from the gut content of a whiteleg shrimp, Litopenaeus vannamei collected in a shrimp farm in South Korea. The bacterial cells were ovoid rod-shaped, non-motile, oxidase-positive and catalase-negative. Growth was observed at 20–35 °C (optimum, 30 °C), pH 5.0–9.5 (pH 8.5) and in the presence of 0–6 % (w/v) NaCl (2–3 %). The major polar lipids were phosphatidylglycerol, phosphatidylinositolmannoside, unidentified aminolipid and two unidentified lipids. The G+C content was 66.1 mol% and the predominant respiratory quinone was Q-10. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SH-1T was placed in a distinct clade with Primorskyibacter marinus PX7T (96.97 % sequence similarity), Pontibaca methylaminivorans DSM 21219T (96.03 %) and Pelagivirga sediminicola BH-SD19T (95.02 %) in the family Rhodobacteraceae and distantly related with them to be a new genus. The digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) values calculated from whole-genome-sequence comparison between the SH-1T and the close species were in the ranges of 19.0–19.8, 73.8–74.9 and 64.1–65.9 %, respectively. Based on the polyphasic analysis presented in this study, we suggest that strain SH-1T represents a novel genus and species in the family Rhodobacteraceae , for which the name Pukyongiella litopenaei gen. nov., sp. nov. is proposed. The type strain of Pukyongiella litopenaei is SH-1T (=KCTC 62276T=MCCC 1K04072T).
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Pseudomonas defluvii sp. nov., isolated from hospital sewage
More LessA novel Gram-negative, obligate aerobic, mobile, rod-shaped and non-spore-forming bacterial strain, WCHP16T, was isolated from the wastewater treatment plant at West China Hospital in Chengdu, PR China. It was characterized using a polyphasic approach. Analysis of its 16S rRNA gene sequence showed that strain WCHP16T belonged to the genus Pseudomonas with the highest similarity to Pseudomonas qingdaonensis JJ3T (99.34 %), Pseudomonas shirazica VM14T (99.0 %), Pseudomonas plecoglossicida NBRC 103162T (99.0 %) and Pseudomonas asiatica RYU5T (99.0 %). Phylogenomic analysis based on 107 core gene sequences demonstrated that WCHP16T was a member of the Pseudomonas putida group but was distant from all closely related species. Whole-genome comparisons, using average nucleotide identity based on blast (ANIb) and in silico DNA–DNA hybridization (isDDH), confirmed low genome relatedness to all the known Pseudomonas species (below the recommended thresholds of 95 % [ANIb] and 70 % [isDDH] for species delineation). Phenotypic characterization tests showed that the utilization of phenylacetic acid and capric acid, but not d-arabitol, and inability to produce fluorescent (King B medium) in combination could distinguish this strain from other related species of the genus Pseudomonas . Therefore, based on genetic and phenotypic evidence, it is clear that strain WCHP16T represents a novel species, for which the name Pseudomonas defluvii sp. nov. is proposed. The type strain is WCHP16T (GDMCC1.1215T=CCTCC AB 2017103T=KCTC 52991T).
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Serratia inhibens sp. nov., a new antifungal species isolated from potato (Solanum tuberosum)
More LessA novel bacterial strain, S40T, with strong antifungal activity was isolated from the rhizosphere of green potato collected from Zealand, Denmark. Polyphasic analysis with a combined phenotypic, phylogenetic and genomic approach was used to characterize S40T. Phylogenetic analysis based on the 16S rRNA gene and MLSA (concatenated gyrB, rpoD, infB and atpD sequences) showed that strain S40T was affiliated with the genus Serratia and with Serratia plymuthica PRI-2C as the closest related strain [average nucleotide identity (ANI), 99.26 %; DNA–DNA hybridization (dDDH), 99.20%]. However, whole genome sequence analyses revealed that S40T and S. plymuthica PRI-2C genomes displayed lower similarities when compared to all other S. plymuthica strains (ANI ≤94.34 %; dDDH ≤57.6 % relatedness). The DNA G+C content of strain S40T was determined to be 55.9 mol%. Cells of the strain were Gram-negative, rod-shaped, facultative anaerobic and displayed growth at 10–37 °C (optimum, 25–30 °C) and at pH 6–9 (optimum, pH 6–7). Major fatty acids were C16 : 0 (27.9 %), summed feature (C16 : 1 ω6c/C16 : 1 ω7c; 18.0 %) and C17 : 0 cyclo (15.1 %). The respiratory quinone was determined to be Q8 (94 %) and MK8 (95 %) and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The results of phenotypic, phylogenetic and genomic analyses support the hypothesis that strain S40T represents a novel species of the genus Serratia , for which the name Serratia inhibens sp. nov. is proposed. The type strain is S40T (=LMG 31467T=NCIMB 15235T). In addition, we propose that S. plymuthica PRI-2C is reclassified and transferred to the species S. inhibens as S. inhibens PRI-2C.
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Pseudomonas izuensis sp. nov., a novel species isolated from Izu Oshima, Japan
An aerobic, Gram-stain-negative, rod-shaped bacterial strain, IzPS43_3003T, was isolated from Izu Oshima, an active volcanic island located 22 km east of the Izu Peninsula, Japan. The sequence of its 16S rRNA gene indicated that IzPS43_3003T belongs to the Pseudomonas fluorescens lineage, with its sequence being most similar to that of Pseudomonas vancouverensis DhA-51T (99.79 %). Phylogenetic analysis based on whole genome sequences showed that IzPS43_3003T was a member of the Pseudomonas jessenii subgroup. The average nucleotide identity values and genome-to genome distances between the whole genome sequences of IzPS43_3003T and other type strains showed that the highest correlations were with Pseudomonas moorei DSM 12647T (87.3 and 33.5% respectively). These genotypic and phenotypic analyses indicated that IzPS43_3003T belongs to a novel species, Pseudomonas izuensis sp. nov. Its type strain is IzPS43_3003T (=LMG 31527T,=CECT 9963T).
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Gemmobacter serpentinus sp. nov., isolated from conserved forages
More LessA Gram-stain-negative, long-rod-shaped and facultative aerobic bacterium, designated HB-1T, was isolated from a round hay bale at the Kansas State University Beef Stocker Unit. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that strain HB-1T clustered within the genus Gemmobacter and its closest relatives were Gemmobacter aquaticus A1-9T (98.0 %), Gemmobacter lutimaris YJ-T1-11T (98.0 %), Gemmobacter fontiphilus JS43T (97.8 %), Gemmobacter aquatilis DSM 3857T (97.5 %) and Gemmobacter lanyuensis Orc-4T (96.9 %). Additional phylogenomic analysis also indicated that strain HB-1T belongs to the genus Gemmobacter . The draft genome of strain HB-1T had a total length of 4.23 Mbp and contained 4071 protein-coding genes. The average nucleotide identity values between the genomes of strain HB-1T and the three most-related type strains ranged from 77.5 to 78.1 %. The DNA G+C content of strain HB-1T was 63.7 mol%. The novel strain grew at 10–37 °C, pH 5–10 and with 0–2 % NaCl. Oxidase and catalase activities were positive. Cells were 0.3–0.4 µm wide, 3.0–7.0 µm long and usually found in pairs or chains of cells. The major respiratory quinone of strain HB-1T was Q-10 (90 %), with a minor amount of Q-9 (10 %). The major fatty acids were C18 : 1 ω7c (54.6 %) and C16 : 0 (18.2 %). On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain HB-1T (=DSM 109828T=ATCC TSD-211T) is considered to represent a novel species of the genus Gemmobacter , for which the name Gemmobacter serpentinus sp. nov. is proposed.
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Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov.
Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium , but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense , Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA–DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.
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Alcanivorax sediminis sp. nov., isolated from deep-sea sediment of the Pacific Ocean
More LessA taxonomic study was carried out on strain PA15-N-34T, which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0–15.0% NaCl and at temperatures of 10–45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34T belonged to the genus Alcanivorax , with the highest sequence similarity to Alcanivorax profundi MTEO17T (97.7 %), followed by Alcanivorax nanhaiticus 19 m-6T (97.3 %) and 12 other species of the genus Alcanivorax (93.4 %–97.0 %). The average nucleotide identity and DNA–DNA hybridization values between strain PA15-N-34T and type strains of the genus Alcanivorax were 71.46–81.78% and 18.7–25.2 %, respectively. The principal fatty acids (>10 %) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 31.2 %), C16 : 0 (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34T represents a novel species within the genus Alcanivorax , for which the name Alcanivorax sediminis sp. nov. is proposed, with the type strain PA15-N-34T (=MCCC 1A14738T=KCTC 72163T).
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Paracoccus xiamenensis sp. nov., isolated from seawater on the Xiamen
More LessStrain 12-3T was isolated from seawater of the Guanyinshan Coast, Xiamen, Fujian Province, PR China. The bacterium was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-negative. Growth of strain 12-3T occurred at 10–37 °C (optimum, 20–30 °C), at pH 5.0–11.0 (optimum, pH 7.0–8.0) and at a salinity range of 0–10 % (optimum, 3–5 %). The results of phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain 12-3T belonged to the genus Paracoccus and had the highest sequence similarity to Paracoccus lutimaris HDM-25T (97.4 %), followed by Paracoccus isoporae SW-3T (96.9 %), Paracoccus caeni MJ17T (96.9 %), Paracoccus pacificus F14T (96.8 %) and other species in the genus Paracoccus (95.3–96.5 %). The average nucleotide identity (ANI) and DNA–DNA hybridization (DDH) values between strain 12-3T and P. lutimaris HDM-25T were 76.1 and 17.0 %, respectively. ANI and DDH values between strain 12-3T and P. isoporae SW-3T were 78.9 and 18.2 %, respectively. The principal fatty acid of strain 12-3T was summed feature 8 (C18 : 1 ω6c/ω7c) and C18 : 0. The respiratory quinone of strain 12-3T was Q10. The polar lipids included phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The G+C content of the chromosomal DNA was 63.9 mol%. The combination of the results of the phylogenetic, phenotypic and chemotaxonomic analyses, and its low ANI and DDH values indicate that strain 12-3T represents a novel species of the genus Paracoccus , for which the name Paracoccus xiamenensis sp. nov. is proposed. The type strain is 12-3T (=MCCC 1A16381T=KCTC 72687T).
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Frigidibacter oleivorans sp. nov., isolated from a deep well with oil reservoir water
More LessA Gram-stain-negative, rod-shaped bacterium, designated XJ4T, was isolated from oil-contaminated water, collected from Xinjiang Province, north-west PR China (45° 1′ 27″ N, 85° 6′ 14″ E). Growth occurred at 20–45 °C (optimum, 30 °C) and pH 6.0–10.0 (optimum, pH 6.0–7.0). Strain XJ4T could tolerate up to 7 % (w/v) NaCl and grow optimally in the absence of NaCl. Phylogenetic analysis based on comparative sequence analysis of 16S rRNA gene sequences indicated that strain XJ4T belonged to the genus Frigidibacter , and that was closely related to Frigidibacter mobilis cai42T (97.2 %), Frigidibacter albus SP32T (97.0 %) and Rhodobacter aestuarii JA296T (97.0 %). The average nucleotide identity values between XJ4T and three type strains were 77.9, 77.6 and 71.9 %, respectively. The DNA G+C content of strain XJ4T was 69.5 mol%. The sole respiratory quinone was Q-10. The major cellular fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C18 : 0 and 11-methyl C18 : 1 ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, an unidentified aminolipid and unidentified lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain XJ4T represents a novel species of the genus Frigidibacter , for which the name Frigidibacter oleivorans sp. nov. is proposed. The type strain is XJ4T (=CGMCC 1.13778T=LMG 30952T).
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Jiella pacifica sp. nov., isolated from the West Pacific Ocean
A Gram-stain-negative bacterium, designated strain 40Bstr34T, isolated from a sediment sample from the West Pacific Ocean, was taxonomically characterized by using a polyphasic approach. The strain was phylogenetically close to Jiella aquimaris LZB041T and Jiella endophytica CBS5Q-3T, with 16S rRNA gene sequence similarities of 98.5 and 97.1 %, respectively. The genome of strain 40Bstr34T featured a G+C content of 65.7 % for a 5.8 Mb chromosome. Up-to-date bacterial core gene set analysis revealed that strain 40Bstr34T represents one independent lineage with J.aquimaris LZB041T. In silico DNA–DNA hybridization values between strain 40Bstr34T and its phylogenetic neighbours ranged from 30.3–34.2 %, below the cutoff of 70 %. In addition, the corresponding average nucleotide identity values were between 81.8–83.7 %, which are lower than 95 % threshold. The predominant cellular fatty acids of strain 40Bstr34T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), cyclo-C19 : 0 ω8c and iso-C17 : 0 3-OH, and ubiquinone-10 as the predominant respiratory quinone. The major polar lipids included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and two unidentified lipids. Based on the results of phenotypic, chemotaxonomic and genetic analyses, strain 40Bstr34T is identified as representing a novel species of the genus Jiella for which the name Jiella pacifica sp. nov. is proposed. The type strain is 40Bstr34T (=JCM 33903T=MCCC 1K04569T).
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Gluconobacter aidae sp. nov., an acetic acid bacteria isolated from tropical fruits in Thailand
Two bacterial strains, isolates AC10T and AC20, which were reported in a previous study on the diversity of acetic acid bacteria in Thailand, were subjected to a taxonomic study. The phylogenetic analysis based on the 16S rRNA gene sequences showed that the two isolates were located closely to the type strains of Gluconobacter oxydans and Gluconobacter roseus . However, the two isolates formed a separate cluster from the type strains of the two species. The genomic DNA of isolate AC10T was sequenced. The assembled genomes of the isolate were analysed for average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH). The results showed that the highest ANI and dDDH values between isolate AC10T and G. oxydans DSM 3503T were 91.15 and 68.2 %, which are lower than the suggested values for species delineation. The genome-based tree was reconstructed and the phylogenetic lineage based on genome sequences showed that the lineage of isolate AC10T was distinct from G. oxydans DSM 3503T and its related species. The two isolates were distinguished from G. oxydans and their relatives by their phenotypic characteristics and MALDI-TOF profiles. Therefore, the two isolates, AC10T (=BCC 15749T=TBRC 11329T=NBRC 103576T) and AC20 (=BCC 15759=TBRC 11330=NBRC 103579), can be assigned to an independent species within the genus Gluconobacter , and the name Gluconobacter aidae sp. nov. is proposed for the two isolates.
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Tepidiphilus olei sp. nov., isolated from the production water of a water-flooded oil reservoir in PR China
A novel, moderately thermophilic, Gram-stain-negative bacterium, designated strain J18T, was isolated from a water-flooded oil reservoir. Cells were aerobic, oxidase- and catalase-positive, with a polar flagellum. Growth occurred at 35–60 °C and at pH 6–8.5. The respiratory quinones were ubiquinone 8 and ubiquinone 9. The dominant cellular fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and an unidentified aminophospholipid. The strain showed the highest 16S rRNA gene sequence similarities to Tepidiphilus margaritifer DSM 15129T (98.6 %), Tepidiphilus succinatimandens DSM 15512T (98.4 %) and Tepidiphilus thermophilus DSM 27220T (98.1 %), respectively, and the similarity to other species was lower than 93 %. In the phylogenetic trees, it constituted a unique sub-cluster within the genus Tepidiphilus . The DNA G+C content of strain J18T was 64.44 mol%. As compared with the type strains, the genome-to-genome distances of strain J18T were 34.7–40 %. These results confirmed the separate species status of J18T with its close relatives. On the basis of physiological, chemotaxonomic and phylogenetic analyses along with the low levels of identity at the whole-genome level, it can be concluded that strain J18T represents a new species of the genus Tepidiphilus , for which the name Tepidiphilus olei sp. nov. is proposed. The type strain of T. olei is J18T (=CGMCC 1.16800T=LMG 31400T).
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Pseudooceanicola pacificus sp. nov., isolated from deep-sea sediment of the Pacific Ocean
More LessA Gram-strain-negative, rod-shaped, aerobic bacterium, designated 216_PA32_1T, was isolated from deep-sea sediment of the Pacific Ocean. Cells of strain 216_PA32_1T were non-motile, oxidase-positive and catalase-negative. The strain could grow at temperatures of 10–45 °C (optimum, 32–35 °C), at pH 5.0–10.0 (optimum, 6.0–7.0) and at salinities of 0–10% (optimum, 2–8%). The principal fatty acid (>10 %) was summed feature 8 (C18:1 ω6c/ω7c). The sole respiratory quinone was Q10 (100 %). The polar lipids included phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, two unidentified phospholipids and five unidentified aminolipids. The G+C content of the chromosomal DNA was 66.3 mol%. According to the 16S rRNA gene similarity, strain 216_PA32_1T showed the highest sequence similarity to Pseudooceanicola nitratireducens JLT 1210T (97.3 %), followed by Pseudooceanicola nanhaiensis SS011B1-20T (97.1 %). Phylogenetic trees indicated that strain 216_PA32_1T clustered with strain P. nanhaiensis SS011B1-20T. The average nucleotide identity and the DNA–DNA hybridization values between strain 216_PA32_1T and all species of the genus Pseudooceanicola were below 79.5 and 20.6%, respectively. A combination of the phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that strain 216_PA32_1T represents a novel species of the genus Pseudooceanicola , for which the name Pseudooceanicola pacificus sp. nov. is proposed. The type strain is 216_PA32_1T (=MCCC 1A14128T=KCTC 72688T).
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Nitratireductor alexandrii sp. nov., from phycosphere microbiota of toxic marine dinoflagellate Alexandrium tamarense
A taxonomic study was carried out on a novel algae-associated bacterial strain Z3-1T, which was isolated from phycosphere microbiota of toxic marine dinoflagellate Alexandrium tamarense 880. Cells of strain Z3-1T were Gram-stain-negative, rod-shaped and strictly aerobic and were motile by means of flagella. Strain Z3-1T grew at 25–42 °C, pH 5.0–10.0 and 1.0–5.0 % (w/v) NaCl. Strain Z3-1T reduced nitrate to nitrite, but did not reduce nitrite to nitrogen gas. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Z3-1T belongs to the genus Nitratireductor showing the highest sequence similarity (97.0 %) to Nitratireductor basaltis JCM 14935T. The average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Z3-1T and type strains of genus Nitratireductor with available genome sequences were in the ranges of 72.4–74.4 % and 22.7–23.3 %, respectively. The major fatty acids were summed in feature 8 (C18:1 ω7c and/or C18:1 ω6c), C19:0 ω8c cyclo, C18:1 ω7c 11-metyl and iso-C17:0. The major polar lipids were determined as diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and four unidentified polar lipids. The genomic DNA G+C content calculated from genome sequence was 65.6 mol%. Based on genotypic, chemotaxonomic and phenotypic data obtained, strain Z3-1T represents a novel species of the genus Nitratireductor , for which the name Nitratireductor alexandrii sp. nov. is proposed with the type strain Z3-1T (=KCTC 62458T=CCTCC AB 2017227T).
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- Eukaryotic Micro-Organisms
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Blastobotrys baotianmanensis sp. nov. and Blastobotrys xishuangbannaensis f.a., sp. nov., two novel yeast species associated with insects and rotting wood
More LessFive yeast strains were isolated from the gut of the groundbeetle Pterostichus gebleri and rotting wood, which were collected from two different localities in China. These strains were identified as representing two novel species of the genus Blastobotrys through comparison of sequences in the D1/D2 domains of the LSU rRNA gene and other taxonomic characteristics. Blastobotrys baotianmanensis sp. nov. produces two to three spherical ascospores per ascus, and is most closely related to the type strains of B. elegans, B. capitulata, B. arbuscula, and an undescribed species represented by strain BG02-7-20-006A-3-1. Blastobotrys baotianmanensis sp. nov. differed from these strains by 3.6–8.4 % divergence (21–46 substitutions and 0–4 gaps) in the D1/D2 sequences. Blastobotrys xishuangbannaensis f.a., sp. nov. is closely related to B. nivea, B. elegans and B. aristata but the formation of ascospores was not observed on various sporulation media, and it differed from its relatives by 6.2–8.5 % divergence (34–43 substitutions and 2–6 gaps) in the D1/D2 sequences. The holotype of Blastobotrys baotianmanensis sp. nov. is NYNU 1581 and the holotype of Blastobotrys xishuangbannaensis f.a., sp. nov. is NYNU 181030.
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Clonostachys viticola sp. nov., a novel species isolated from Vitis vinifera
More LessA collection of fungal isolates obtained from crop plants, specifically grapevine and blueberry, in Peru were characterised through morphological and DNA sequence analyses of the nuclear ribosomal internal transcribed spacer (ITS), beta-tubulin (tub2) and translation elongation factor 1-alpha (tef-1α) regions. Isolates produced monomorphic and dimorphic conidiophores typical of members of the genus Clonostachys. Single- and multi-locus gene phylogenies confirmed the isolates as representing members of the genus Clonostachys, more closely related to species in the subgenus Bionectria. In phylogenetic analyses the isolates grouped in two separate clades, one corresponding to the species Clonostachys pseudochroleuca and the other one distinct from all known species of the genus Clonostachys. These isolates are recognized as representing a novel species species for which the name Clonostachys viticola is proposed.
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Starmera foglemanii sp. nov. and Starmera ilhagrandensis sp. nov., two novel yeast species isolated from ephemeral plant substrates
Four isolates of two novel ascosporogenous species belonging to the clade Starmera were obtained from cactus tissues and rotting wood in Brazil. Results of analyses of the sequences of the ITS and D1/D2 domains of the large subunit rRNA gene indicated that the two isolates of the cactophilic species are related to Starmera caribaea and Starmera pilosocereana, yeasts that are associated with cacti and require an organic source of sulfur for growth. We propose the novel species Starmera foglemanii sp. nov. (CBS 16113T; MycoBank number: MB 834400) to accommodate these isolates. The other two isolates are phylogenetically related to Candida dendrica, Candida laemsonensis and Candida berthetii, also in the Starmera clade. The novel species name Starmera ilhagrandensis sp. nov. (CBS 16316T; MycoBank number: MB 834402) is proposed for this species.
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- Taxonomic Note
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Reclassification of Streptomyces hygroscopicus subsp. glebosus and Streptomyces libani subsp. rufus as later heterotypic synonyms of Streptomyces platensis
More LessWe investigated the taxonomic relationships among Streptomyces hygroscopicus subsp. glebosus , Streptomyces libani subsp. rufus and Streptomyces platensis . The three species formed a single clade in the phylogenetic trees based on 16S rRNA gene sequence and multilocus sequence analyses. Digital DNA–DNA hybridization using whole genome sequences suggested that S. hygroscopicus subsp. glebosus , S. libani subsp. rufus and S. platensis belong to the same genomospecies. Previously reported phenotypic data also supported this synonymy. Therefore, S. hygroscopicus subsp. glebosus and S. libani subsp. rufus should be reclassified as later heterotypic synonyms of S. platensis .
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Three alternative proposals to emend the Rules of the International Code of Nomenclature of Prokaryotes to resolve the status of the Cyanobacteria in the prokaryotic nomenclature
More LessThree alternative proposals to emend the Rules of the International Code of Nomenclature of Prokaryotes are presented to resolve the status of the Cyanobacteria in the prokaryotic nomenclature. Two were earlier published (Oren and Garrity, Int J Syst Evol Microbiol 2014;64 : 309–310; Pinevich, Int J Syst Evol Microbiol 2015;65 : 1070–1074). The third proposal is based on reciprocation of Article 45.1 of the International Code of Nomenclature for algae, fungi, and plants. According to Article 13b of the Statutes of the International Committee on Systematics of Prokaryotes, a decision on these proposals must be reached within 11 months from the date of this publication.
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- Research Article
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Rhodococcus cavernicola sp. nov., isolated from a cave, and Rhodococcus degradans is a later heterosynonym of Rhodococcus qingshengii
More LessA Gram-reaction-positive, strictly aerobic, catalase-positive, oxidase-negative, non-motile actinobacterium, designated C1-24T, was isolated from a soil sample collected inside a natural cave. The organism exhibited a rod–coccus developmental cycle during its growth phase. Results of 16S rRNA gene-based phylogenetic analysis showed that the novel strain belonged to the genus Rhodococcus and formed a distinct sublineage at the base of the radiation including a Rhodococcus enclensis–Rhodococcus kroppenstedtii–Rhodococcus corynebacterioides–Rhodococcus trifoli cluster. In the results of phylogenomic analysis, the novel strain was loosely associated to Rhodococcus corynebacterioides . The closest relatives were Rhodococcus qingshengii (98.01 % 16S rRNA gene sequence similarity) and Rhodococcus degradans (98.01 %). The genome size was 5.66 Mbp and the DNA G+C content was 64.30 mol%. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H2) was the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid and three unidentified phospholipids. Mycolic acids were present. The major fatty acids were C16 : 0, C18 : 1 ω9c, C16 : 1 ω7c and/or C16 : 1 ω6c and 10-methyl C18 : 0. Digital DNA–DNA hybridization and average nucleotide identity values revealed that the novel strain should be assigned to a different species. Based on the combined data obtained here, strain C1-24T (=KACC 19964T=DSM 109484T) represents a new species of the genus Rhodococcus , for which Rhodococcus cavernicola sp. nov. is proposed. Also, it is proposed that R. degradans is a later heterosynonym of R. qingshengii based on analyses of 16S rRNA gene and whole-genome sequences.
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Volumes and issues
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