- Volume 70, Issue 2, 2020
Volume 70, Issue 2, 2020
- New Taxa
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- Proteobacteria
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Pseudidiomarina gelatinasegens sp. nov., isolated from surface sediment of the Terra Nova Bay, Antarctica
More LessPolyphasic taxonomic analysis was performed to characterize a novel bacterium, which was isolated from surface sediment of the Terra Nova Bay, Antarctica, and designated as R04H25T. The cells of the isolate were Gram-stain-negative, aerobic, non-motile, slightly curved rods. Growth occurred at 4–42 °C, pH 7.0–9.5, and in 1–15 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R04H25T formed an independent lineage within the genus Pseudidiomarina and its nearest neighbours were Pseudidiomarina donghaiensis 908033T (98.2 %), Pseudidiomarina marina PIM1T (98.1 %), Pseudidiomarina woesei W11T (97.8 %), Pseudidiomarina maritima 908087T (97.1 %) and Pseudidiomarina tainanensis PIN1T (97.0 %). The average nucleotide identities between strain R04H25T and the nearest neighbours were 76.2–77.7 %. The major fatty acids were iso-C17 : 0, summed feature 9, iso-C15 : 0, C16 : 0 and iso-C11 : 0 3-OH. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, three unidentified glycolipids and two unidentified lipids. The predominant respiratory quinone was ubiquinone 8. The genomic DNA G+C content was 48.2 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic results, we propose a novel species named as Pseudidiomarina gelatinasegens sp. nov. in the genus Pseudidiomarina , with the type strain R04H25T (=GDMCC 1.1503T=KCTC 62911T).
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Paracoccus liaowanqingii sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii)
Two strains, designated 2251T and 3058, that were aerobic, Gram-stain-negative, non-motile, coccoid or short rod-shaped bacilli, have recently been isolated from Tibetan antelopes on the Qinghai-Tibet Plateau. The results of phylogenetic analyses of 16S rRNA gene sequences indicated that strains 2251T and 3058 represent a new species within the genus Paracoccus and are most similar to ‘ Paracoccus gahaiensis ’ CUG00006T (98.9 and 99.3 %), Paracoccus nototheniae I-41R45T (98.3 and 98.7 %) and Paracoccus hibiscisoli THG-T2.31T (97.6 and 97.8 %). Results of genomic sequence-based phylogenomic analysis agreed with those from 16S rRNA gene sequence analysis. Optimal growth was achieved at pH 7.0–7.5 and 28 °C with marine medium. Cells contained C18 : 1 ω7c as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. The polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phospholipid, glycolipid and an unidentified lipid. The cell-wall peptidoglycan amino acids were meso-2,6-diaminopimelic acid, alanine and glutamic acid; the major cell-wall sugar was galactose. The G+C content of strain 2251T was 66.5 mol%. Both strains (2251T and 3058) had DNA–DNA relatedness values less than 50 % with all available genomes of the genus Paracoccus in the ncbi database. Differential genotypic inferences, together with phenotypic and biochemical characteristics, demonstrated that strains 2251T and 3058 should be classified as a novel species of the genus Paracoccus , for which the name Paracoccus liaowanqingii sp. nov. is suggested. The type strain is 2251T (=CGMCC 1.16490T=DSM 106269T).
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Nioella ostreopsis sp. nov., isolated from toxic dinoflagellate, Ostreopsis lenticularis
A novel short-rod-shaped bacterial strain with poly-β-hydroxybutyric acid granules inside, designated as Z7-4T, was isolated from a culture of a marine dinoflagellate with palytoxin-producing capacity, Ostreopsis lenticularis OS06, collected from the East China Sea. Cells of Z7-4T were Gram-stain-negative, non-motile, strictly aerobic, 0.9–1.2 µm wide and 2.0–3.9 µm long. Growth occurred in 1–4 % (w/v) NaCl, at 15–37 °C and at pH 5.0–10.0, with optimum growth in 3.5 % (w/v) NaCl, at 30 °C and at pH 7.0. Analysis of 16S rRNA gene sequence revealed that Z7-4T shared the highest 16S rRNA gene sequence similarities with Nioella aestuarii JCM 30752T (98.8 %), followed by Nioella sediminis KCTC 42144T (98.6 %) and Nioella nitratireducens KCTC 32417T (96.9 %). Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that Z7-4T clearly represented a member of the genus Nioella within the family Rhodobacteraceae . The respiratory quinone of Z7-4T was identified as Q-10. Polar lipids of Z7-4T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C content of Z7-4T was 63.0 mol%. DNA–DNA hybridization values of the isolate against the closely related type strains were far below the 70 % limit for species delineation. The average nucleotide identity and in silico DNA–DNA genome hybridization relatedness between Z7-4T and the closely related members of the genus Nioella , N. sediminis KCTC 42144T and N. nitratireducens KCTC 32417T, were 91.1 and 46.3 %, and 79.3 and 19.4 %, respectively. On the basis of the results of polyphasic analysis, Z7-4T is proposed to represent a novel species of the genus Nioella , for which the name Nioella ostreopsis sp. nov. is proposed. The type strain of Nioella ostreopsis is Z7-4T (=KCTC 62459T=CCTCC AB 2017231T)
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Croceicoccus sediminis sp. nov., isolated from coastal sediment
More LessA Gram-stain-negative, cocci or short rod-shaped, yellow-pigmented bacterium, designated strain S2-4-2T, was isolated from coastal sediment of Spartina alterniflora in Quanzhou Bay, PR China. Growth was observed at 15–40 °C (optimum, 30 °C) and pH 6.0–8.0 (optimum, pH 7.0). Strain S2-4-2T tolerated 0–10 % NaCl (optimum, 1 %). The 16S rRNA gene of strain S2-4-2T showed highest sequence similarity to Croceicoccus pelagius Ery9T (98.2 %), followed by Croceicoccus naphthovorans PQ-2T, Croceicoccus marinus E4A9T and Croceicoccus mobilis Ery22T (97.6%, 96.3 and 96.3 %, respectively). Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on 92 up-to-date bacterial core gene sets indicated that strain S2-4-2T forms a distinct monophyletic branch affiliated to the genus Croceicoccus . The average nucleotide identity value between strain S2-4-2T and its close relatives were estimated to be 74.8–85.7 %. The respiratory quinone was found to be Q-10. The predominant fatty acids (>10 %) were identified as summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and C16 : 1ω6c). The polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified phospholipid. The draft genome size of strain S2-4-2T was 3.5 Mb with a genomic G+C content of 63.0 mol%. Based on these results, strain S2-4-2T is concluded to represent a novel species within the genus Croceicoccus , for which the name Croceicoccus sediminis sp. nov. is proposed with the type strain S2-4-2T (=MCCC 1K03706T=KCTC 72146T).
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Mixta tenebrionis sp. nov., isolated from the gut of the plastic-eating mealworm Tenebrio molitor L.
More LessA bacterial strain, BIT-26T, was isolated from the gut of plastic-eating mealworm Tenebrio molitor L. The taxonomic position of this new isolate was investigated by using a polyphasic approach. Cells of the strain were Gram-stain-negative, facultatively anaerobic, motile rods with peritrichous flagella. The 16S rRNA gene sequence (1412 bp) of strain BIT-26T showed the highest similarity (97.4 %) to Erwinia piriflorinigrans CFBP 5888T, followed by Citrobacter sedlakii NBRC 105722T (97.3 %), Mixta calida LMG 25383T (97.3 %), Cronobacter muytjensii ATCC 51329T (97.2 %) and Mixta theicola QC88-366 T (97.2 %). The results of phylogenetic analyses, based on the 16S rRNA gene and concatenated sequences of four housekeeping genes (atpD, gyrB, infB and rpoB), placed strain BIT-26T within the genus Mixta of the family Erwiniaceae . This affiliation was also supported by the chemotaxonomic data. Strain BIT-26T had similar predominant fatty acids, including C12 : 0, C14 : 0, C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c, to species of the genus Mixta . In silico DNA–DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain BIT-26T from other species of the genus Mixta with validly published names. Therefore, strain BIT-26T is considered to represent a novel species, for which the name Mixta tenebrionis sp. nov is proposed. The type strain is BIT-26T (=CGMCC 1.17041T=KCTC 72449T).
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Rubrivivax albus sp. nov., isolated from a freshwater pond
More LessStrain ICH-3T, isolated from a freshwater pond in Taiwan 9ROC), was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that ICH-3T is affiliated with the species in the genus Rubrivivax . ICH-3T was most closely related to Rubrivivax benzoatilyticus JA2T and Rubrivivax gelatinosus NCIB 8290T with 97.5 and 97.4 % 16S rRNA gene sequence similarity. The average nucleotide identity and digital DNA–DNA hybridization identity between ICH-3T and the two closely related strains were 77.3 and 20.9–21.0 %, respectively, indicating that ICH-3T represents a novel species of the genus Rubrivivax . Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed white colonies. Optimal growth occurred at 30 °C, pH 7.5–8.0 and with 0.5 % NaCl. The major fatty acids (>20 %) of ICH-3T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of ICH-3T was 70.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain ICH-3T should be classified as representing a novel species of the genus Rubrivivax , for which the name Rubrivivax albus sp. nov. is proposed. The type strain is ICH-3T (=BCRC 81155T=LMG 30930T=KCTC 62866T).
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Glycocaulis profundi sp. nov., a marine bacterium isolated from seawater of the Mariana Trench
More LessA Gram-stain-negative, strictly aerobic, rod-shaped bacterium, without flagellum and designated ZYF765T, was isolated from seawater sampled at a depth of 4000 m in the Mariana Trench. Strain ZYF765T grew with 1–15 % (w/v) NaCl (optimum, 4 %), at 16–37 °C (28 °C) and at pH 6.0–10.0 (pH 7.0–8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYF765T formed a lineage within the family Hyphomonadaceae , and was distinct from the most closely related species Glycocaulis abyssi , Glycocaulis albus and Glycocaulis alkaliphilus with 16S rRNA gene sequences similarities ranging from 98.42 to 98.63 %. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipids comprised three unidentified glycolipids, one unidentified aminophospholipid, one unidentified phospholipid and one unidentified aminolipid. The predominant fatty acids (more than 10 % of total fatty acids) were C18 : 1ω7c (46.2 %) and C18 : 0 (14.1 %). The DNA G+C content was 67.7 mol%. On the basis of the results of polyphasic taxonomic analysis, strain ZYF765T is considered to represent a novel species within the genus Glycocaulis , for which the name Glycocaulis profundi sp. nov. is proposed. The type strain is ZYF765T (=JCM 33028T=MCCC 1K03554T).
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Saccharospirillum alexandrii sp. nov., isolated from the toxigenic marine dinoflagellate Alexandrium catenella LZT09
A Gram-stain-negative, strictly aerobic, non-motile and non-pigmented spirillum, designated strain LZ-5T, was isolated from cultures of the paralytic shellfish poisoning (PSP) toxin-producing marine dinoflagellate Alexandrium catenella LZT09 collected from the Zhoushan sea area in the East China Sea during an algal bloom. The isolate grew at 4–40 °C (optimum, 25–33 °C) and pH 5.0–9.0 (optimum, 7.5) in the presence of 0.5–10 % (w/v) NaCl (optimum, 4.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LZ-5T clearly belonged to the genus Saccharospirillum of the family Saccharospirillaceae . Strain LZ-5T shared highest 16S rRNA gene sequence similarity with Saccharospirillum impatiens EL-105T (98.9 %), Saccharospirillum mangrovi HK-33T (97.2 %), Saccharospirillum correiae CPA1T (96.8 %), Saccharospirillum salsuginis YIM-Y25T (96.8 %) and Saccharospirillum aestuarii IMCC 4453T (95.1 %). The average nucleotide identity and in silico DNA–DNA hybridization between strain LZ-5T and the two most closely related Saccharospirillum strains, S. impatiens EL-105T and S. mangrovi HK-33T, were 82.2 and 19.3 %, and 72.2 and 13.2 %, respectively. The predominant respiratory quinone of strain LZ-5T was Q-8, and the major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipids of strain LZ-5T were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), glycolipid (GL), two unidentified glycophospholipids (GPLs), three unidentified aminophospholipids (APLs) and two unidentified lipids. The genomic DNA G+C content was 57.2 mol%. On the basis of this polyphasic characterization, strain LZ-5T represents a novel species of the genus Saccharospirillum , for which the name Saccharospirillum alexandrii sp. nov. is proposed. The type strain is LZ-5T (=KCTC 62460T=CCTCC AB2017232T).
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Sphingobium fluviale sp. nov., isolated from a river
More LessA Gram-stain-negative, rod-shaped, non-motile, poly-β-hydroxybutyrate-accumulating and aerobic bacterial strain, designated CHR27T, was isolated and characterized by using the polyphasic taxonomy approach. The results of phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CHR27T is affiliated with species in the genus Sphingobium . 16S rRNA gene sequence similarity results indicated that strain CHR27T was closely related to species of the genus Sphingobium (94.3–97.0 %), and had the highest sequence similarity to Sphingobium qiguonii X23T (97.0 %). Strain CHR27T showed 19.4–22.1 % digital DNA–DNA hybridization values and 73.2–74.8 % average nucleotide identity values with the strains of other Sphingobium species. Optimal growth occurred at 25 °C, pH 7.5 and in the absence of NaCl. The major fatty acids of strain CHR27T were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The predominant hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two unidentified sphingoglycolipids and an unidentified aminophospholipid. Strain CHR27T contained spermidine as the major polyamine and putrescine as a minor component. The only isoprenoid quinone was ubiquinone-10. The genomic DNA G+C content of strain CHR27Twas 61.8 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CHR27T was considered a representative of a novel species within the genus Sphingobium . The name Sphingobium fluviale sp. nov. is proposed, with strain CHR27T (=BCRC 81121T=LMG 30596T=KCTC 62510T) as the type strain.
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Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.)
A novel strain S29T with high nitrogen fixing ability was isolated from surface-sterilized leaf tissues of oil palm (Elaeis guineensis) growing in Science Park II, Singapore. On the basis of 16S rRNA gene analysis and multilocus sequence typing with the rpoB, gyrB, infB and atpD genes, strain S29T was a member of the genus Phytobacter , with Phytobacter ursingii ATCC 27989T and Phytobacter diazotrophicus LS 8T as its closest relatives. Unique biochemical features that differentiated strain S29T from its closest relatives were the ability to utilize melibiose, α-cyclodextrin, glycogen, adonital, d-arabitol, m-inositol and xylitol. The major fatty acids were C14 : 0, C16 : 0, C17 : 0, C16 : 1 ω5c and summed feature 2 containing C16 : 1 ω7c and/or C16 : 1 ω6c. The polar fatty acid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid and aminolipids. The draft genome of strain S29T comprised 5, 284, 330 bp with a G + C content of 52.6 %. The average nucleotide identity and digital DNA–DNA hybridization values between strain S29T and the phylogenetically related Enterobacterales species were lower than 95 % and 70 %, respectively. Thus, the polyphasic evidences generated through the phenotypic, chemotaxonomic and genomic methods confirmed that strain S29T represents a novel species of the genus Phytobacter , for which we propose the name Phytobacter palmae sp. nov. with the type strain of S29T (=DSM 27342T=KACC 17598T).
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Enterobacter wuhouensis sp. nov. and Enterobacter quasihormaechei sp. nov. recovered from human sputum
More LessTwo novel strains of members of the genus Enterobacter , WCHEs120002T and WCHEs120003T, were recovered from the sputum of two patients at a hospital in PR China in 2017. The strains were Gram-stain-negative, facultatively anaerobic, motile and non-spore-forming. The two strains were subjected to whole-genome sequencing. Phylogenetic analysis based on core genes of type strains of species of the family Enterobacteriaceae revealed that the two strains belonged to the genus Enterobacte r but were distinct from any previously known species of the genus. Both average nucleotide identity and in silico DNA–DNA hybridization values between strains WCHEs120002T and WCHEs120003T and type strains of all known species of the genus Enterobacter were lower than the recommended thresholds of 95 and 70 %, respectively, for species delineation. The major fatty acids of the two strains were C16 : 0, C17 : 0 cyclo and C18:1ω7c, which are similar to those of other species of the genus Enterobacter . Genomic DNA G+C contents of strains WCHEs120002T and WCHEs120003T were 56.09 and 55.91 mol%, respectively. WCHEs120002T ferments melibiose and sucrose but is negative for d-sorbitol and methyl-α-d-mannopyranoside reactions, which distinguish it from all other species of the genus Enterobacter . WCHEs120003T can be differentiated from other species of the genus Enterobacter by its ability to ferment potassium gluconate and its negative reactions for d-sorbitol and l-fucose. Genotypic and phenotypic characteristics indicate that strains WCHEs120002T and WCHEs120003T represent two novel species of the genus Enterobacter , for which the names Enterobacter wuhouensis sp. nov. and Enterobacter quasihormaechei sp. nov. are proposed, respectively. The type strain of E. wuhouensis sp. nov. is WCHEs120002T (=GDMCC1.1569T=NCTC 14273T) and the type strain of E. quasihormaechei sp. nov. is WCHEs120003T (=GDMCC1.1568T=NCTC 14274T).
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Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov., two marine bacteria isolated from the East China Sea
Two Gram-staining-negative, facultatively anaerobic, motile, short clavate and flagellated marine bacteria, designated strains BEI233T and LJC006T, were isolated from the East China Sea. On the basis of the results of 16S rRNA gene sequencing and multilocus sequence analysis, BEI233T and LJC006T should be assigned to the genus Vibrio . The closest phylogenetic relatives of BEI233T are Vibrio scophthalmi LMG 19158T (98.7 % 16S rRNA gene sequence pairwise similarity), Vibrio ichthyoenteri DSM 14397T (98.5 %), Vibrio renipiscarius KCTC 42287T (97.7 %), Vibrio aestuarianus ATCC 35048T (97.3 %) and Vibrio thalassae MD16T (96.5 %), whereas for LJC006T they were Vibrio furnissii CAIM 518T (97.1 %), Vibrio fluvialis LMG 7894T (97.0%), Vibrio tritonius JCM 16456T (96.9 %) and Vibrio xuii LMG 21346T (96.1 %). The growth of BEI233T occurred at 10–37 °C, pH 5.0–8.0 and with 1–7 % (w/v) NaCl, while the growth of LJC006T occurred at 10–37 °C, pH 6.0–9.0, and 0–8 % (w/v) NaCl. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c or/and C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c or/and C18 : 1ω6c), with different proportions. The DNA G+C contents of BEI233T and LJC006T are 42.41 mol% and 41.88 mol%, respectively. On the basis of the results of polyphasic analysis, BEI233T and LJC006T are considered to represent novel species of the genus Vibrio, for which the names Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov. are proposed. The type strains are BEI233T (=JCM 32692T=KCTC 62618T) and LJC006T (=JCM 32693T=KCTC 62620T), respectively.
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Sphingomonas populi sp. nov., isolated from bark of Populus × euramericana
More LessOne Gram-stain-negative, aerobic, motile bacterial strain, 3-7T, was isolated from symptomatic canker bark tissue of Populus × euramericana. 16S rRNA gene sequence data revealed that the novel isolate shared highest similarity with Sphingomonas panacis DCY99T (98.8 %), and <96.5 % sequence similarity with all other species with validly published names. Growth occurred between 15 and 37 °C and at pH 6.0–9.0, and optimal growth occurred at 30 °C and pH 7.0–8.0. Nitrogen was produced from nitrates. The strain was positive for acetoin production and activity of catalase, oxidase, β-galactosidase, arginine dihydrolase and β-glucosidase. The major fatty acids were C16 : 0, C18 : 1ω7c and/or C18 : 1ω6c. The polar lipids of the novel isolate included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, glycolipid, two uncharacterized phospholipids and two uncharacterized lipids. The respiratory quinones detected in isolate 3-7T were Q-10 (96.9 %) and Q-9 (3.1 %). The DNA G+C content was 65.1 mol%. Based on phenotypic and genotypic characteristics, the isolate represents a novel species within the genus Sphingomonas , for which the name Sphingomonas populi is proposed. The type strain is 3-7T (=CFCC 11561T=LMG 30138T).
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Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate
More LessA polyphasic approach was used to investigate the taxonomic status of two bacterial strains, WS 5072T and WS 5092, isolated from skimmed milk concentrate and raw cow’s milk. The 16S rRNA and rpoD gene sequences affiliated the strains to the same, hitherto unknown, Pseudomonas species. Further examinations of the draft genomes based on multilocus sequence analysis and average nucleotide identity confirmed the presence of a novel Pseudomonas species. It was most closely related to Pseudomonas fragi DSM 3456T with 86.3 % ANIm. The DNA G+C content of strain WS 5072T was 56.3 mol%. Cells were aerobic, Gram-negative, catalase and oxidase positive, rod-shaped and motile. Growth occurred at 4–34 °C, pH 5.5–8.0 and with salt concentrations of up to 7 %. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The dominating quinone was Q-9 with 94 %, with noticeable amounts of Q-8 (5 %) and traces of Q-7 and Q-10. Fatty acid profiles showed a composition common for Pseudomonas with the major component C16 : 0. Based on these results, the novel species Pseudomonas saxonica sp. nov. is proposed, with the type strain WS 5072T (=DSM 108989T=LMG 31234T) and the additional strain WS 5092 (=DSM 108990=LMG 31235).
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Pseudomonas rhizoryzae sp. nov., isolated from rice
More LessTwo yellow-pigmented, Gram-stain-negative and rod-shaped bacterial strains, designated as RY24T and ZYY160, were isolated from rice. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strains RY24T and ZYY160 belonged to the genus Pseudomonas , and the 16S rRNA gene sequence similarity was 100 % The DNA homology between the two strains was 99.7 %. The 16S rRNA and rpoD gene sequences of the two strains showed highest similarity values to Pseudomonas oryzihabitans CGMCC 1.3392T and Pseudomonas psychrotolerans DSM 15758T (sharing 99.31 and 94.34 %, respectively). The major fatty acids of two strains were identified as summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16;0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c), and the major respiratory quinone was identified as ubiquinone Q-9, which are typical chemotaxonomic features of members of the genus Pseudomonas . The genomic DNA G+C contents of strains RY24T and ZYY160 were determined to be 64.25 and 64.21 mol%, respectively. The DNA–DNA relatedness and average nucleotide identity values between the two strains and their closely related type strains were below 36 and 90 %, which supported that RY24T and ZYY160 represent a novel species in the genus Pseudomonas . Phylogenetic and chemotaxonomic evidence, together with phenotypic characteristics, showed that the two isolates constitute a novel species of the genus Pseudomonas . The type strain is RY24T (JCM 33201T=ACCC 61555T), for which the name Pseudomonas rhizoryzae sp. nov. is proposed.
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Luteimonas yindakuii sp. nov. isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibetan Plateau
Two strains (S-1072T and 1626) of Gram-stain-negative, oxidase- and catalase-positive, aerobic, rod-shaped, motile bacteria with a single polar flagellum, were isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai–Tibet Plateau of China. The cells grew optimally at 28 °C, pH 7.0 and with 0.5 % (w/v) NaCl on brain–heart infusion agar. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains S-1072T and 1626 belong to the genus Luteimonas , sharing the highest similarity with Luteimonas arsenica CCTCC AB 2014326T (97.0 %), Luteimonas terricola CGMCC 1.8985T (96.9 %) and Luteimonas aestuarii KCTC 22048T (96.6 %). The phylogenomic tree indicated that strains S-1072T and 1626 were most closely related to Luteimonas abyssi CGMCC 1.12611T. The biochemical characteristics revealed that strains S-1072T and 1626 could neither produce trypsin nor produce acid from d-glucose, N-acetylglucosamine and maltose, distinguishing them from four closest relatives. The DNA G+C contents of strains S-1072T and 1626 were 69.2 and 69.3 mol% respectively. The digital DNA–DNA hybridization values of our isolates with their four closely related species were below the 70 % threshold. The predominant menaquinone was Q-8 (98.7 %) and the major polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1 ω9c). Based on the data obtained, strains S-1072T and 1626 should be classified as a novel species of the genus Luteimonas , for which the name Luteimonas yindakuii sp. nov. is proposed. The type strain is S-1072T (=CGMCC 1.13927T=JCM 33487T).
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Ferrovibrio terrae sp. nov., isolated from soil
Designated strain K5T was isolated from soil on Jeju Island. The bacterium was aerobic, Gram-stain-negative, oxidase-positive, catalase-low activity, motile, short-rod shaped, opaque and formed white colonies that were circular, raised and had entire margins. Strain K5T was able to grow at 15–40 °C, pH 4–9 and at 0–2 % (w/v) NaCl concentration. Phylogenetic analysis based on its 16S rRNA gene sequences indicated that strain K5T is closely related to Ferrovibrio soli A15T (98.9 % sequence similarity), Ferrovibrio denitrificans Sp-1T (98.7 %) and Ferrovibrio xuzhouensis LM-6T (97.4 %). The sole respiratory quinone was determined to be ubiquinone-10. The dominant fatty acids of strain K5T were summed feature 8 (C18 : 1 ω7c / C18 : 1ω6c, 29.8 %), C19 : 0 cyclo ω8c (20.2 %) and C16 : 0 (24.4 %). DNA G+C content was 63.6 % and DNA–DNA relatedness between strain K5T and other three members of the genus Ferrovibrio ranged from 24 to 28 %. The major polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine and aminolipids. Moreover, polyphasic characterization revealed that strain K5T represents a novel species in the genus Ferrovibrio, for which the name Ferrovibrio terrae sp. nov. is proposed. The type strain is K5T (=KCCM 43295T=LMG 30611T).
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Genome analysis-based reclassification of Enterobacter tabaci Duan et al. 2016 as a later heterotypic synonym of Enterobacter mori Zhu et al. 2011
More LessWe performed a comparative genomic analysis to clarify the taxonomic relationship between the two Enterobacter species, Enterobacter tabaci and Enterobacter mori . Whole genome sequences of types strains of the two species became available recently. Average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) between the two type strains were determined. Type strains of the two species had a 97.25 % ANI and an 80.4 % isDDH value, which are above the well-recognized cutoffs (≥95–96 % ANI and ≥70 % isDDH) for bacterial species delineation. The two strains have similar overall phenotypic characteristics and are clustered together with high bootstrap values in the multi-locus sequence analysis on rpoB, gyrB, infB and atpD housekeeping genes. It therefore becomes evident that the two species actually belong to the same species. E. mori has priority over E. tabaci , therefore we proposed that E. tabaci Duan et al. 2016 is a later heterotypic synonym of E. mori [ 15 ]
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Pseudorivibacter rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere soil of Camellia sinensis (L.) O. Ktze and emended description of the genus Rivibacter
A Gram-stain-negative, facultative anaerobic, motile and straight rod-shaped bacterium, designated strain C1-9T, was isolated from rhizosphere soil of Camellia sinensis (L.) O. Ktze collected from a tea garden in Huize, south-western PR China. Cells were oxidase-positive and catalase-negative. Growth occurred at 20–40 °C and pH 6.0–10.0, with an optimal growth at 30 °C and pH 7.0. The respiratory quinone was detected as ubiquinone-8 (Q-8). The major fatty acids were identified as summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c or C18 : 1ω6c). The cellular polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, two unidentified lipids, one unidentified aminophospholipid and one unidentified aminolipid. The polyamine types were detected as 1,8-diaminooctane and 2-hydroxyputrescine. The genomic DNA G+C content was 68.6 mol%. Based on the results of 16S rRNA gene sequence analysis, strain C1-9T (MF687442) showed highest sequence similarity to Rivibacter subsaxonicus DSM 19570T (97.1 %). The phylogenetic tree based on 16S rRNA gene sequences showed that strain C1-9T clustered close to R. subsaxonicus DSM 19570T, Methylibium petroleiphilum CCTCC AB 2014193T and species belonging to the genera Rhizobacter and Piscinibacter . The phylogenomic tree indicated that strain C1-9T formed a clade with R. subsaxonicus . The average nucleotide identity value was 76.0 % between strain C1-9T and R. subsaxonicus DSM 19570T, which is lower than the prokaryotic species delineation threshold of 95.0–96.0 %. The polyphasic taxonomic characteristics indicated that strain C1-9T represents a novel species of a new genus within the order Burkholderiales , for which the name Pseudorivibacter rhizosphaerae gen. nov., sp. nov. (type strain C1-9T = KCTC 62325T=CGMCC 1.13864T) is proposed.
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Salinibius halmophilus gen. nov., sp. nov., isolated from a marine solar saltern
More LessA novel Gram-stain-negative, facultatively anaerobic, flagellated and spiral-shaped bacterium, designated WDS2A16AT was isolated from a marine solar saltern in Weihai, PR China. Growth was observed at 20–40 °C (optimal 33–37 °C), 1–15 % (w/v) NaCl (optimal 3–4 %) and pH 6.0–9.0 (optimal pH 7.5). Major cellular fatty acids (>10 %) were C18 : 1ω7c and C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid were detected as the predominant polar lipids. The sole respiratory quinone was Q-8. The DNA G+C content of strain WDS2A16AT was 48.5 mol%. The 16S rRNA gene sequence similarities of WDS2A16AT with other species were less than 91 %. The average nucleotide identity, in silico DNA–DNA hybridization and amino acid identity of strain WDS2A16AT with the most related strain Gynuella sunshinyii YC6258 T were 66.1, 19.3 and 48.1 %, respectively. Comparative analysis of 16S rRNA gene sequences and phenotypic characterization indicated that strain WDS2A16AT represents a novel species in a new genus, for which the name Salinibius halmophilus gen. nov., sp. nov. is proposed. The type strain is WDS2A16AT (=KCTC 52225T=MCCC 1H00139T).
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Polymorphobacter arshaanensis sp. nov., containing the photosynthetic gene pufML, isolated from a volcanic lake
More LessAn aerobic, Gram-stain-negative, yellowish, rod-shaped bacterium, designated DJ1R-1T, was isolated from water sample from a volcanic lake, located on Da Hinggan Ling Mountain, PR China. Growth of DJ1R-1T optimally occurred at pH 7.0, at 22–25 °C and with 0–0.5 % (w/v) NaCl concentration. Phylogenetic analysis of 16S rRNA gene sequences indicated that DJ1R-1T was clustered into the genus Polymorphobacter, and showed 96.5 %, 95.9 % and 95.6 % similarities to Polymorphobacter fuscus D40PT, Polymorphobacter multimanifer 262-7T and Polymorphobacter glacialis B555-2T, respectively. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, three unidentified aminolipids and one unidentified phospholipid. The major fatty acids were summed feature 8 (C18 : 1ω7c / C18 : 1ω6c, 40.0 %), summed feature 3 (C16 : 1ω7c / C16 : 1ω6c, 25.6 %) and C16 : 0 (13.7 %). The respiratory quinone was ubiquinone-10. The DNA G+C content was 65.0 % according to the genomic sequencing results. On the basis of the results of the phylogenetic analysis, physiological and biochemical properties comparisons, DJ1R-1T was proposed to represent a novel species of the genus Polymorphobacter , with the name Polymorphobacter arshaanensis. The type strain is DJ1R-1T (=CGMCC 1.13788T=KCTC 72014T).
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Nitrincola tapanii sp. nov., a novel alkaliphilic bacterium from An Indian Soda Lake
A novel Gram-stain-negative bacterial strain designated as MEB193T was isolated from a sediment sample collected from Lonar Lake, India. The cells were motile, non-spore-forming and rod-shaped. The strain was oxidase- and catalase-positive. It grew optimally at pH 9.0 and at 1 % (w/v) NaCl concentration at 30 °C. Based on 16S rRNA gene sequence similarity, MEB193T belongs to genus Nitrincola , with Nitrincola alkalilacustris ZV-19T (95.89 %) and Nitrincola lacisaponensis 4CAT (95.87 %) as its closest neighbours. The major fatty acid was summed feature 8 comprising C18:1ω7c/C18:1ω6c (52 %) followed by C16 : 0 (25 %). Phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG) were present as the major polar lipids. The draft genome obtained in this study was 2 793 747 bp and the G+C content was 50.79 mol%. Average nucleotide identity (71.76 %) and DNA–DNA hybridization (<20 %) values between strain MEB193T and Nitrincola lacisaponensis 4CAT confirmed the novelty of this new species. Based on phenotypic including chemotaxonomic and genotypic characterization data, strain MEB193T represents a new species of the genus Nitrincola for which the name Nitrincola tapanii sp. nov. is proposed. The type strain is MEB193T (=MCC 2863T=JCM 31570 T=KCTC 52390 T).
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Novosphingobium umbonatum sp. nov., isolated from a freshwater mesocosm
More LessA bacterial strain designated FSY-9T was isolated from a freshwater mesocosm in Taiwan and characterized to determine its taxonomic affiliation. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-9T formed a phylogenetic lineage in the genus Novosphingobium . Strain FSY-9T was most closely related to Novosphingobium humi R1-4T with a 97.2 % 16S rRNA gene sequence similarity. Strain FSY-9T showed 71.3–72.6 % average nucleotide identity and 17.7–23.0 % digital DNA–DNA hybridization identity with the strains of other Novosphingobium species. Cells of strain FSY-9T were facultatively anaerobic, Gram-negative, rod-shaped, non-motile and formed light yellow coloured colonies. Growth occurred at 15–37 °C and pH 5.5–7, and in the presence of 0–0.5 % NaCl. The major fatty acids (>10 %) of strain FSY-9T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c and C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, sphingoglycolipid, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 61.5 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-9T should be classified as a novel species of the genus Novosphingobium , for which the name Novosphingobium umbonatum sp. nov. is proposed. The type strain is FSY-9T (=BCRC 81052T=LMG 30054T=KCTC 52813T).
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Haliea alexandrii sp. nov., isolated from phycosphere microbiota of the toxin-producing dinoflagellate Alexandrium catenella
A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, named strain LZ-16-2T, was isolated from the phycosphere microbiota of the paralytic shellfish poisoning toxin-producing marine dinoflagellate Alexandrium catenella LZT09. Strain LZ-16-2T grew optimally at 28 °C at pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain LZ-16-2T fell within the genus Haliea and was most closely related to Haliea salexigens DSM 19537T, with which the new isolate exhibited 98.5 % 16S rRNA gene sequence similarity. The major respiratory quinone was Q-8. The predominant cellular fatty acids were C17 : 1 ω8c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C17 : 1 ω6c, C11 : 0 3-OH and C17 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The average nucleotide identity and in silico DNA–DNA genome hybridization relatedness values between strain LZ-16-2T and its closest relative, H. salexigens DSM 19537T, were 92.8 and 55.1 %, respectively. The DNA G+C content was 61.3 mol%. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain LZ-16-2T from all other members of the genus Haliea . On the basis of the polyphasic characterization, strain LZ-16-2T represents a novel species of the genus Haliea , for which the name Haliea alexandrii sp. nov. is proposed. The type strain is LZ-16-2T (=KCTC 62344T=CCTCC AB2017229T).
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Francisella opportunistica sp. nov., isolated from human blood and cerebrospinal fluid
Two isolates of a Gram-negative, non-spore-forming coccobacillus cultured from the blood and cerebrospinal fluid of immunocompromised patients in the United States were described previously. Biochemical and phylogenetic analyses revealed that they belong to a novel species within the Francisella genus. Here we describe a third isolate of this species, recovered from blood of a febrile patient with renal failure, and formally name the Francisella species. Whole genome comparisons indicated the three isolates display greater than 99.9 % average nucleotide identity (ANI) to each other and are most closely related to the tick endosymbiont F. persica , with only 88.6–88.8 % ANI to the type strain of F. persica . Based on biochemical, metabolic and genomic comparisons, we propose that these three isolates should be recognized as Francisella opportunistica sp. nov, with the type strain of the species, PA05-1188T, available through the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSM 107100) and the American Type Culture Collection (ATCC BAA-2974).
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Marinobacter fonticola sp. nov., isolated from deep sea cold seep sediment
More LessIn this study, we report a novel Gram-negative bacterium, designated as strain CS412T, isolated from deep-sea sediment collected in a cold seep area of the South China Sea. Growth of strain CS412T occurred at 4–40 °C (optimum, 28 °C), pH 5.0–11.0 (optimum, pH 6.0) and with 0–19 % (w/v) NaCl (optimum, 1–2 %). Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain CS412T belonged to the genus Marinobacter . The closest phylogenetic neighbours of strain CS412T were Marinobacter pelagius HS225T (96.9 %), Marinobacter szutsaonensis NTU-104T (96.8%), Marinobacter santoriniensis NKSG1T (96.4%) and Marinobacter koreensis dd-M3T (96.3 %). The genomic DNA G+C content of strain CS412T was 58.0 mol%. The principal respiratory quinone was ubiquinone-9 (Q-9). The polar lipids of CS412T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipidand and four glycolipids. The major fatty acids of CS412T contained cyclo-C19 : 0ω8c, C16 : 0, C18 : 1ω7c and C18 : 1ω7c 11-methyl. The results of phylogenetic, physiological, biochemical and morphological analyses suggested that strain CS412T represents a novel species of the genus Marinobacter , and the name Marinobacter fonticola sp. nov. is proposed with the type species CS412T (=CCTCC AB 2019197T=KCTC 72475T).
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Roseomonas vastitatis sp. nov. isolated from Badain Jaran desert in China
More LessA Gram-stain-negative, non-motile, coccobacillus-shaped bacterium, designated CPCC 101021T, was isolated from a sandy soil sample collected from Badain Jaran desert, China. Its 16S rRNA gene sequence was closely related to those of members of the genus Roseomonas, showing high similarities with Roseomonas hibiscisoli THG-N2.22T (98.0 %), Roseomonas oryzae KCTC 42542T (97.9 %), Roseomonas rhizosphaerae YW11T (97.9 %) and Roseomonas suffusca S1T (97.8 %). In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 101021T formed a distinct subclade with R. oryzae KCTC 42542T within the genus Roseomonas . Growth of the isolate occurred at 15–37 °C and pH 6.0–8.5, with optimal growth at 30 °C and pH 7.0. The major cellular fatty acids were C18 : 1ω7c, summed feature 8 (C16 : 1ω7c/C16 : 1ω6c), summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C16 : 0ω6c. Q-10 was detected as the main component in the respiratory quinone system, with Q-9 as a minor component. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and an unidentified glycolipid were found in the polar lipid profile. The genomic DNA G+C content was 68.7 mol%. The average nucleotide identity was 84.6 % when comparing the draft genome sequences of strain CPCC 101021T with R. oryzae KCTC 42542T. On the basis of genotypic, chemotaxonomic and phenotypic characteristics, strain CPCC 101021T is proposed to represent a novel species of the genus Roseomonas with the name Roseomonas vastitatis sp. nov. Strain CPCC 101021T (=J1A743T=KCTC 62043T) is the type strain of the species.
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Pseudooceanicola onchidii sp. nov., isolated from a marine invertebrate from the South China Sea
More LessA novel bacterial strain, XY-99T, was isolated from the epidermis of a marine invertebrate of the genus Onchidium from seawater of the South China Sea. The cells of the strain were aerobic, Gram-stain-negative, non-motile, and oval-shaped (0.8–1.0 µm wide and 1.0–1.5 µm long) without a flagellum. The strain grew at temperatures of 15–37 °C (optimum, 35–37 °C), at pH 5.5–9.5 (optimum 7.5), and at NaCl concentrations of 0–12.0 % (w/v) (optimum 1.5–3.0 %). The major fatty acids (>10 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and 11-methyl C18 : 1ω7c. The predominant polar lipid was diphosphatidylglycerol. The respiratory quinone was Q-10. The closet phylogenetic neighbours were Pseudooceanicola flagellatus DY470T and Pseudooceanicola nitratireducens JLT1210T, showing 97.5 and 97.3 % of 16 s rRNA gene sequence similarity. The genome size of XY-99T was 3 673 499 bp, with 64.5 % DNA G+C content. The average nucleotide identity and digital DNA–DNA hybridization values between XY-99T and Pseudooceanicola flagellatus DY470T were 72.8 and 14.0 %, respectively, while they were 79.3 and 22.3 % between XY-99T and Pseudooceanicola nitratireducens JLT1210T. Characterization based on phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that XY-99T represents a novel species of the genus Pseudooceanicola , for which the name Pseudooceanicola onchidii sp. nov. is proposed. The type strain is XY-99T (=KCTC 72211T=MCCC 1K03607T).
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Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae
Strain ISS155T, isolated from surface Mediterranean seawater, has cells that are Gram-reaction-negative, motile, strictly aerobic chemoorganotrophic, oxidase-positive, unable to reduce nitrate to nitrite, and able to grow with cellulose as the sole carbon and energy source. It is mesophilic, neutrophilic, slightly halophilic and has a requirement for sodium and magnesium ions. Its 16S rRNA gene sequence places the strain among members of Cellvibrionaceae , in the Gammaproteobacteria , with Agarilytica rhodophyticola 017T as closest relative (94.3 % similarity). Its major cellular fatty acids are C18 : 1, C16 : 0 and C16 : 1; major phospholipids are phosphatidyl glycerol, phosphatidyl ethanolamine and an unidentified lipid, and the major respiratory quinone is Q8. The genome size is 6.09 Mbp and G+C content is 45.2 mol%. A phylogenomic analysis using UBCG merges strain ISS155T in a clade with A. rhodophyticola , Teredinibacter turnerae , Saccharophagus degradans and Agaribacterium haliotis type strain genomes, all of them possessing a varied array of carbohydrate-active enzymes and the potential for polysaccharide degradation. Average amino acid identity indexes determined against available Cellvibrionaceae type strain genomes show that strain ISS155T is related to them by values lower than 60 %, with a maximum of 58 % to A. rhodophyticola 017T and 57 % to T. turnerae T7902T and S. degradans 2-40T. These results, together with the low 16S rRNA gene sequence similarities and differences in phenotypic profiles, indicate that strain ISS155T represents a new genus and species in Cellvibrionaceae , for which we propose the name Thalassocella blandensis gen. nov., sp. nov., and strain ISS155T (=CECT 9533T=LMG 31237T) as the type strain.
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Rheinheimera sediminis sp. nov., a marine bacterium isolated from coastal sediment
More LessA Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-1T, was isolated from coastal sediment in Jiangsu Province (PR China) and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 28 °C (range 4–40 °C) and pH 7 (range pH 6–11). Phylogenetic analysis based on 16S rRNA gene sequence indicated that YQF-1T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera mesophila DSM 29723T (98.5 %), followed by Rheinheimera tangshanensis DSM 19460T (98.4 %), Rheinheimera tilapiae Ruye-90T (97.9 %), Rheinheimera soli BD-d46T (97.9 %), Rheinheimera aquatica GR5T (97.4 %), Rheinheimera coerulea TAPG2T (97.3 %) and Rheinheimera texasensis A62-14BT (97.1 %). The 16S rRNA gene sequence identities between YQF-1T and other members of the genus Rheinheimera were below 97.0 %. The digital DNA–DNA hybridization value between YQF-1T and Rheinheimera mesophila DSM 29723T was 25.1±2.3 %. The average nucleotide identity (ANI) value between YQF-1T and Rheinheimera mesophila DSM 29723T was 81.4 %. The major respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, two unidentified aminolipids and three unidentified lipids. The strain had summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0, and anteiso-C17 : 1 ω9c as the major fatty acids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-1T represents a novel species of the genus Rheinheimera , for which the name Rheinheimera sediminis sp. nov. is proposed, with the type strain YQF-1T (=KCTC 72183T=MCCC 1K03646T).
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Shewanella maritima sp. nov., a facultative anaerobic marine bacterium isolated from seawater, and emended description of Shewanella intestini
More LessA Gram-stain-negative, motile, facultative anaerobic rod-shaped marine bacterium, designated strain D4-2T, was isolated from a sample of seawater collected at Dong-do marina, Dokdo Island, in the East Sea of the Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain D4-2T was affiliated with members of genus Shewanella and closely related to Shewanella intestini XMDDZSB0408T (97.4%), followed by Shewanella gelidii RZB5-4T (96.7 %) and Shewanella inventionis KX27T (96.1 %). D4-2T has a single circular chromosome of 4.72 Mbp with a DNA G+C content of 44.5 mol%. Average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) values between strain D4-2T and the previously mentioned type strains of species of the genus Shewanella were in range of 69–83.8 % and 20.5–21.7 %, respectively. Growth was observed at 10–36 °C (optimum 29–32 °C), at pH 6–9 (optimum pH 7), and with 1–6% NaCl (optimum 2%). The predominant fatty acids (>10 %) of D4-2T were iso-C15:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The respiratory quinones were Q-7, Q-8, MK-7 and MMK-7. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified aminolipid and four unidentified lipids were detected in D4-2T. On the basis of phenotypic, chemotaxonomic and molecular properties, D4-2T represents a novel species of the genus Shewanella , for which the name Shewanella maritima sp. nov. is proposed with D4-2T as the type strain (=KCTC 72040T=JCM 33294T).
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Rhodobacter sediminicola sp. nov., isolated from a fresh water pond
More LessA phototrophic bacterium, designated as strain JA983T, was isolated from a freshwater pond in Gujarat, India. The strain was yellowish brown, catalase- and oxidase-positive, rod-to-oval shaped, Gram-stain-negative and motile. Growth was observed at 20–35 °C. NaCl was not required for optimum growth and up to 5 % was tolerated. Growth was observed at pH 6.0–8.0, with an optimum at pH 7.0. An unidentified glycolipid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminolipids (AL1, AL2) and two unidentified lipids (L1 and L2) are the polar lipids of JA983T. Q10 is the only quinone. C18 : 1 ω7c/C18 : 1 ω6c is the major fatty acid. JA983T showed highest 16S rRNA gene sequence similarity with the type strains of Rhodobacter sphaeroides (98.99%), Rhodobacter megalophilus (98.99 %), Rhodobacter johrii (98.99 %) and other members of the genus Rhodobacter with less than 98.7 % similarity. In a 16S rRNA gene sequence-based phylogenetic tree, JA983T formed a different sub-clade with its nearest phylogenetic members of genus Rhodobacter . Phenotypic, chemotaxonomic, phylogenetic and genomic [average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) differences indicated that JA983T is significantly different from other species of the genus Rhodobacter and thus represents a novel species of the genus for which the name Rhodobacter sediminicola sp. nov. is proposed. The type strain is JA983T (=KCTC 15782T=NBRC 113843T).
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Elioraea thermophila sp. nov., a thermophilic bacterium from hot spring of the class Alphaproteobacteria, emended description of the genus Elioraea and proposal of Elioraeaceae fam. nov.
A Gram-staining-negative, aerobic, curved rod-shaped and thermophilic bacterial strain, designated YIM 72297T, was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth was observed at pH 5.0–9.0 with an optimum of pH 7.0–7.5, and at 45–60 °C with an optimum of 55 °C. Positive for catalase and oxidase. The 16S rRNA gene sequence comparison indicated that strain YIM 72297T was most closely related to Elioraea tepidiphila DSM 17972T (96.9 %) and showed <91 % sequence similarities to members of the order Rhodospirillales . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 72297T formed a distinct lineage within the genus Elioraea , and revealed that the genus Elioraea formed a novel family-level clade in the order Rhodospirillales . The ANI and the dDNA-DNA hybridization estimate values between strains YIM 72297T and Elioraea tepidiphila DSM 17972T were 70.8 and 20.1 %, respectively. Strain YIM 72297T contained Q-10 as the predominant ubiquinone. The major fatty acids (>5 %) were summed C18 : 0 (35.8 %), summed feature 8 (30.1 %), C16 : 0 (12.6 %), C18 : 1 2OH (5.6 %) and C16 : 0 2OH (5.4 %). The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, diphosphosphatidylglycerol and phosphatidylglycerol in addition to two unidentified aminolipids. The DNA G+C content of YIM 72297T was 70.8 mol% (draft genome). On the basis of the polyphasic taxonomic evidence presented in this study, strain YIM 72297T should be classified as representing a novel species of the genus Elioraea , for which the name Elioraea thermophila sp. nov. is proposed, with the type strain YIM 72297T (=CCTCC AB 2017169T=KCTC 62323T). In addition, a novel family, Elioraeaceae fam. nov., is proposed to accommodate the genus Elioraea .
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Taxonomic reassessment of the genus Pseudocitrobacter using whole genome sequencing: Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis and description of Pseudocitrobacter vendiensis sp. nov.
The taxonomic status of all Pseudocitrobacter species was re-evaluated by comparative genomics based on whole genome sequencing. As a result, it is obvious that Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis . In addition, genome-based analysis of strain CPO20170097T, isolated from a patient in northern Denmark was allocated to the genus Pseudocitrobacter . This strain showed significant genotypic and phenotypic differences from P. faecalis and it is proposed that this strain represents a novel species of the genus, for which the name Pseudocitrobacter vendiensis sp. nov. is proposed with the type strain CPO20170097T (=CCUG 73096T=LMG 31042T).
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Pararobbsia silviterrae gen. nov., sp. nov., isolated from forest soil and reclassification of Burkholderia alpina as Pararobbsia alpina comb. nov.
More LessA novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterial strain, DHC34T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China (112° 31′ E 23° 10′ N). It grew optimally on R2A medium at 28 °C, at pH 6.0–7.0 and in the presence of 0–1 % (w/v) NaCl. Strain DHC34T was closely related to Burkholderia alpina LMG 28138T (98.5 % 16S rRNA gene sequence similarity). 16S rRNA gene sequence analysis showed that strain DHC34T formed a clade with B. alpina LMG 28138T, which is next to but branched deeply with Robbsia andropogonis ICMP 2807T. The phylogenetic relationships among these three strains were also supported with the phylogram based on concatenated partial gyrB, recA and trpB gene sequences. The phylogenomic tree generated with the UBCG tool showed that strains DHC34T and R. andropogonis ICMP 2807T were in a different clade. The DNA–DNA relatedness values between strain DHC34T and B. alpina LMG 28138T and R. andropogonis ICMP 2807T were much lower than 70 %. Strain DHC34T contained ubiquinone 8 as the major respiratory quinone. Its major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The DNA G+C content of strain DHC34T was 64.2 mol%. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, three unidentified aminophospholipids, four unidentified phospholipids, one unidentified aminolipid and a polar lipid. The phenotypic, phylogenetic, genotypic and chemotaxonomic data showed that strain DHC34T represents a novel species of a new genus in the family Burkholderiaceae , for which the name Pararobbsia silviterrae gen. nov., sp. nov. is proposed. The type strain of Pararobbsia silviterrae is DHC34T (=KCTC 42628T=LMG 28845T). On the basis of the current data, Burkholderia alpina is renamed as Pararobbsia alpina comb. nov.
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Bradyrhizobium ivorense sp. nov. as a potential local bioinoculant for Cajanus cajan cultures in Côte d’Ivoire
More LessFor many smallholder farmers of Sub-Saharan Africa, pigeonpea (Cajanus cajan) is an important crop to make ends meet. To ascertain the taxonomic status of pigeonpea isolates of Côte d’Ivoire previously identified as bradyrhizobia, a polyphasic approach was applied to strains CI-1BT, CI-14A, CI-19D and CI-41S. Phylogeny of 16S ribosomal RNA (rRNA) genes placed these nodule isolates in a separate lineage from current species of the B. elkanii super clade. In phylogenetic analyses of single and concatenated partial dnaK, glnII, gyrB, recA and rpoB sequences, the C. cajan isolates again formed a separate lineage, with strain CI-1BT sharing the highest sequence similarity (95.2 %) with B. tropiciagri SEMIA 6148T. Comparative genomic analyses corroborated the novel species status, with 86 % ANIb and 89 % ANIm as the highest average nucleotide identity (ANI) values with B. elkanii USDA 76T. Although CI-1BT, CI-14A, CI-19D and CI-41S shared similar phenotypic and metabolic properties, growth of CI-41S was slower in/on various media. Symbiotic efficacy varied significantly between isolates, with CI-1BT and CI-41S scoring on the C. cajan ‘Light-Brown’ landrace as the most and least proficient bacteria, respectively. Also proficient on Vigna radiata (mung bean), Vigna unguiculata (cowpea, niébé) and additional C. cajan cultivars, CI-1BT represents a potential bioinoculant adapted to local soil conditions and capable of fostering the growth of diverse legume crops in Côte d'Ivoire. Given the data presented here, we propose the 19 C. cajan isolates to belong to a novel species called Bradyrhizobium ivorense sp. nov., with CI-1BT (=CCOS 1862T=CCMM B1296T) as a type strain.
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- Eukaryotic Micro-Organisms
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Saturnispora mangrovi f.a., sp. nov. from Syhat mangrove, Saudi Arabia
More LessStrain SY-07 was isolated from decaying leaves of Avicennia marina collected from Syhat mangroves, Dammam city, Arabian Gulf, Saudi Arabia. Phylogenetic analyses of three genes [D1/D2 region of the LSU and SSU rRNA genes and internal transcribed spacer (ITS) region] showed that strain SY-07 represents a novel species of the genus Saturnispora distinct from closely related species. Saturnispora mendoncae was the most closely related species with an LSU gene sequence similarity of 89.3 % (58 nucleotide substitutions and four indels out of 578 nt), 97 % similarity for the SSU gene (42 nucleotide substitutions and 10 indels out of 1614 nt) and 88 % similarity for the ITS region (15 nucleotide substitutions and eight indels out of 430 nt). In addition, strain SY-07 differed from S. mendoncae by its ability to assimilate d-galactose (weak), d-xylose (weak), meso-erythritol (delayed), glucono-δ-lactone, citrate (delayed) and ethylamine. S. mendoncae produced persistent asci that contain two to four spherical ascospores and lacked pseudohyphae, while sexual reproduction was not observed in strain SY-07 and extensive and pseudohyphae were present. Strain SY-07 was able to grow at between 25 and 40 °C, while S. mendoncae did not grow at 37 °C. The name Saturnispora mangrovi f.a., sp. nov. is proposed for strain SY-07. The holotype is CBS 15874, with the ex-type culture AUMC 12005. The MycoBank number for Saturnispora mangrovi f.a., sp. nov. is MB 827036.
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Saccharomycopsis oxydans sp. nov., a new non-fermentative member in the genus Saccharomycopsis isolated from a traditional dairy product of Iran
More LessA total of 21 yeast isolates were recovered as part of a research project on biodiversity of yeasts in traditional dairy products in Alborz province, Iran. Standard protocols were used to carry out phenotypic, biochemical, physiological characterization and the phylogenetic analysis of combined the D1/D2 domain of the large ribosomal subunit (26S or LSU) and ITS region sequences. Five strains represented a potential new ascomycetous yeast species. Ascospore formation was not observed in these strains, and they did not ferment the examined carbon sources. Phylogenetic analysis placed these isolates in a well-supported sub-clade in the genus Saccharomycopsis. Here, we describe this novel yeast as Saccharomycopsis oxydans sp. nov.
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Mycosarcoma aegyptiacum sp. nov., an antagonistic polymorphic basidiomycetous yeast related to smut fungi
More LessSix polymorphic yeast strains with strong antifungal activities isolated from dicot plants in an alkaline-lake desert region were subjected to taxonomic examination. The phylogenetic trees reconstructed by using neighbour-joining, maximum-likelihood and Bayesian methods from concatenated D1/D2 and ITS-5.8S-ITS2 sequences revealed phylogenetic affinity to Ustilaginaceae, but the large phylogenetic distance separating the isolates from the most closely related groups of species indicates that they represent a separate species. The sequences of the genes coding for the LSU rDNA, act1, rpb2 and a protein of unknown function corroborate this position. The isolates can easily be distinguished from their closest relatives by physiological tests (utilisation of carbon and nitrogen sources). Based on these results, a new species, Mycosarcoma aegyptiacum sp. nov., is proposed to accommodate the isolates. All isolates are polymorphic. Transitions between budding-yeast and pseudohyphal morphologies which take place during colony formation result in morphologically different colony sectors and invasive growth into the medium. Neither sexual mating nor sporulation was observed in cultures growing on laboratory media.
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Torulaspora nypae sp. nov., a novel yeast species isolated from nipa (Nypa fruticans Wurmb.) inflorescence sap in southern Thailand
More LessTwo strains (YSP-384 and YSP-399), representing a novel Torulaspora species, were isolated from two nipa inflorescence sap samples collected in Trang province in the southern part of Thailand. The two strains had identical sequences of the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions. The two strains were closest to Torulaspora maleeae CBS 10694T, but with 1.1 % nucleotide substitutions in the D1/D2 domains of the LSU rRNA gene and 5.2 % nucleotide substitutions in the ITS regions. Phylogenetic analysis based on the concatenated sequences of the ITS regions and the D1/D2 domains of the LSU rRNA gene supported that the two strains represented a distinct species in the genus Torulaspora. Some phenotypic characteristics of the two strains differed from T. maleeae including the two strains have ability to assimilate d-xylose, d-glucono-δ-lactone and melizitose, and inability to ferment maltose and raffinose, whereas T. maleeae has opposite results. Therefore, the two strains are described as representing a novel species, for which the name Torulaspora nypae sp. nov. was proposed.
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Wickerhamomyces psychrolipolyticus f.a., sp. nov., a novel yeast species producing two kinds of lipases with activity at different temperatures
More LessTwo yeast strains isolated from soil collected in Hokkaido, Japan, were found to secrete two extracellular lipases that exhibited activities at both 25 and 4 °C. Both strains could utilize olive oil, rapeseed oil, lard and fish oil as sole carbon sources. The similarity of the D1/D2 domain of the large subunit ribosomal RNA (LSU rRNA) sequence of these yeast strains to that of other yeasts in the GenBank database was very low (<96 %). The phylogenetic trees based on the LSU rRNA sequences and translation elongation factor-1-α (tef1-α) sequences indicated that both strains represented a member of the Wickerhamomyces /Candida clade. Sexual reproduction was not observed. The name Wickerhamomyces psychrolipolyticus f.a., sp. nov is proposed for this newly described yeast species producing cold-active lipases. This novel species is distinguishable from the type strains of other related species, Wickerhamomyces alni, Candida ulmi and Candida quercuum due to their abilities to grow at 4 to 30 °C, to produce lipase that is active also at 4 °C and to assimilate soluble starch.
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Beltrania sinensis sp. nov., an endophytic fungus from China and a key to species of the genus
More LessDuring a survey of endophytic fungi in plant roots in secondary forests in Yunnan, China, a novel ascomyceteous taxon, Beltrania sinensis, was isolated from Quercus cocciferoides Hand.-Mazz. and Fraxinus malacophylla Hemsl. This novel species is characterized by having oval or obovoid conidiogenous cells with several apical, flat-tipped denticles, and biconic, aseptate, smooth, pale brown conidia with a hyaline to subhyaline equatorial transverse band and apical tubular appendage. Phylogenetic analysis of the combined sequences of the internal transcribed spacer and the LSU rRNA gene confirmed its novel species status within the genus Beltrania. Here, the novel species is described and illustrated, and a taxonomic key to species in the genus Beltrania is provided.
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Fourteen novel lipomycetaceous yeast species isolated from soil in Japan and transfer of Dipodascopsis anomala to the genus Babjevia based on ascospore production phenotype
More LessFourteen novel lipomycetaceous yeasts species were isolated from soil samples collected from the Hokkaido, Chiba and Okinawa prefectures of Japan. Phylogenetic analyses of the D1/D2 domains of the large subunit rRNAs and translation elongation factor 1 alpha genes (TEF1-α) revealed that five strains of two species from the soil in Furano-shi, Hokkaido were related to Dipodascopsis anomala and 29 strains representing 12 species from soils in Kamogawa-shi, Chiba and Iriomote Island, Okinawa were in the Myxozyma clade. The two species of Dipodascopsis form globose or ellipsoid ascospores in their sac-like ascus and pseudohyphae. Furthermore, these species produce ascospores in their pseudohyphae and do not produce an acicular ascus, which is common among the three species including D. anomala. Therefore, we propose transferring D. anomala to the genus Babjevia and amending Babjevia. Two novel species were described and included in the genus Babjevia: Babjevia hyphoforaminiformans sp. nov. (holotype NBRC 111233; MycoBank no. MB 829051) and Babjevia hyphasca sp. nov. (holotype NBRC 112965; MycoBank no. MB 829053). The 12 species in the Myxozyma clade produce neither ascospores nor pseudohyphae and have different characteristics in assimilating several carbon sources from each other. Thus, we propose that the novel species of Lipomyces be classified as forma asexualis (f.a.). From Kamogawa-shi, Chiba (19 strains representing five species): Lipomyces melibiosiraffinosiphilus f.a., sp. nov. (holotype NBRC 111411; MycoBank no. MB 829034), Lipomyces kiyosumicus f.a., sp. nov. (holotype NBRC 111424; MycoBank no. MB 829035), Lipomyces chibensis f.a., sp. nov. (holotype NBRC 111413; MycoBank no. MB 829036), Lipomyces kamogawensis f.a., sp. nov. (holotype NBRC 112967; MycoBank no. MB 829037), Lipomyces amatsuensis f.a., sp. nov. (holotype NBRC 111420; MycoBank no. MB 829041). From Iriomote island, Okinawa (10 strains representing seven species): Lipomyces taketomicus f.a., sp. nov. (holotype NBRC 112966; MycoBank no. MB 829042), Lipomyces yaeyamensis f.a., sp. nov. (holotype NBRC 110433; MycoBank no. MB 829050), Lipomyces iriomotensis f.a., sp. nov. (holotype NBRC 110436; MycoBank no. MB 829045), Lipomyces haiminakanus f.a., sp. nov. (holotype NBRC 110435; MycoBank no. MB 829046), Lipomyces komiensis f.a., sp. nov. (holotype NBRC 110440; MycoBank no. MB 829047), Lipomyces nakamensis f.a., sp. nov. (holotype NBRC 110434; MycoBank no. MB 829048), Lipomyces sakishimensis f.a., sp. nov. (holotype NBRC 110439; MycoBank no. MB 829049).
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- Letters
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Necessity and rationale for the proposed name changes in the classification of Mollicutes species. Reply to: ‘Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein’, by M. Balish et al. (Int J Syst Evol Microbiol, 2019;69:3650–3653)
More LessThis response summarizes the highly disordered state of the Mollicutes taxonomy that existed until recently, where most Mollicutes taxa lacked proper circumscriptions and their names were not in accordance with the International Code of Nomenclature of Prokaryotes and illegitimate. We also summarize the comprehensive phylogenomic and comparative genomic studies forming the basis for the proposed changes in the classification of Mollicultes species. Our responses to the concerns raised by Balish et al., show that the proposed taxonomic changes do not violate any essential point of the Code. Instead the proposed name changes rectify numerous taxonomic anomalies that have long plagued the classification of Mollicute s species, leading to a better understanding of their evolutionary relationships and bringing their nomenclature in conformity with the Code.
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- ICSP Matters
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Opinions 97, 98 and 99
More LessThe International Committee on Systematics of Prokaryotes has formally endorsed the conclusions of the Judicial Commission on three pending Requests for an Opinion, thereby allowing the corresponding Opinions to be issued. According to Opinion 97, the request for the conservation of the name Streptomyces scabies is denied, allowing the continued use of the correction Streptomyces scabiei . Opinions 98 and 99 conclude that in the absence of associated authentic type material, the names Bacillus aeolius and Pectinatus portalensis , respectively, are not validly published.
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- Erratum
- Taxonomic Description
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- New taxa
- Actinobacteria
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Cryptosporangium phraense sp. nov., isolated from plant litter
More LessA novel zoosporic actinomycete, designated strain A-T 5661T, was isolated from plant litter collected in Thailand. Strain A-T 5661T developed large multilocular sporangia containing motile sporangiospores at the ends of sporangiophores on substrate mycelium. The results of our polyphasic taxonomic study demonstrated that the strain had characteristics typical of members of the genus Cryptosporangium . The 16S rRNA gene sequence and phylogenetic analyses indicated that strain A-T 5661T shared the sequence similarity ≤98.5 % with all members of the genus Cryptosporangium . The values of DNA–DNA relatedness that distinguished this novel strain from its closest related species were below 70 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars were acofriose, arabinose, galactose, glucose, mannose, xylose and ribose. The predominant menaquinones were MK-9(H8) and MK-9(H6) with minor amounts of MK-9(H4) and MK-9(H2). The predominant fatty acids were iso-C16 : 0, C18 : 1ω9c and anteiso-C17 : 0. The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and unidentified polar lipids. The G+C content of the genomic DNA was 71.6 mol%. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, the novel zoosporic actinomycete A-T 5661T (=TBRC 8127T=NBRC 113237T) is proposed to be the type strain of a novel species, Cryptosporangium phraense sp. nov.
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- Firmicutes and related organisms
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Description of Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov., isolated from cave soil
Two Gram-positive, rod-shaped, motile, endospore-forming strains, SYSU K30003T and SYSU K30004T, were isolated from cave soil sampled in Xingyi County, Guizhou Province, south-west PR China. The 16S rRNA gene sequence results indicated that strains SYSU K30003T and SYSU K30004T had highest sequence similarities to Paenibacillus thermoaerophilus DSM 26310T (93.2 %) and Paenibacillus haemerocallicola KCTC 33185T (97.8 %), respectively. Optimum growth for both strains occurred at pH 7.0 and 37 °C. Both strains contained meso-2,6-diaminopimelic acid in their cell-wall peptidoglycan and MK-7 was the only isoprenoid quinone detected. The polar lipid profile of strain SYSU K30004T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, an unidentified glycolipid, unidentified phospholipids and two unidentified polar lipids. The polar lipid profile of strain SYSU K30003T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified glycolipid. The major fatty acids (>5 %) of strain SYSU K30003T were anteiso-C15:0, C16 : 0, anteiso-C17 : 0 and iso-C16 : 0, while those of strain SYSU K30004T were anteiso-C15:0, C16:0, anteiso-C17 : 0, iso-C15 : 0, iso-C16:0 and iso-C17 : 0. The genome G+C contents of strains SYSU K30003T and SYSU K30004T were 59.0 and 53.6 mol%, respectively. The average nucleotide identity values between strains SYSU K30003T and SYSU K30004T and other closely related Paenibacillus members were below the cut-off level (95–96 %) for species identification. Based on the results of phenotypic, chemotaxonomic and genome analyses, strains SYSU K30003T and SYSU K30004T represent two novel species of the genus Paenibacillus , for which the names Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov. are proposed. The type strains are SYSU K30003T (=KCTC 33956T=CGMCC 1.13505T) and SYSU K30004T (=KCTC 33957T=CGMCC 1.13872T).
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- Proteobacteria
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Segnochrobactrum spirostomi gen. nov., sp. nov., isolated from the ciliate Spirostomum yagiui and description of a novel family, Segnochrobactraceae fam. nov. within the order Rhizobiales of the class Alphaproteobacteria
More LessA bacterial strain, designated Sp-1T, was isolated from the heterotrich ciliate Spirostomum yagiui collected from a reservoir located in Ulsan, Republic of Korea. Cells of Sp-1T were Gram stain-negative, rod-shaped, non-spore-forming, non-motile and contained poly-β-hydroxybutyrate granules. Phylogenetic analyses based on 16S rRNA gene sequences indicated that Sp-1T constituted a distinct phylogenetic lineage within different families in the order Rhizobiales with a pairwise sequence similarity of 95 % to the species of the genus Ochrobactrum: Ochrobactrum anthropi ATCC 49188T and Ochrobactrum cytisi ESC1T (family Brucellaceae ). The major cellular fatty acids were C19 : 0 cyclo ω8c (44.4 %) and C16 : 0 (32.1 %). The identified sole isoprenoid quinone was ubiquinone-10 (Q-10). The major polar lipids produced were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, two unidentified phospholipids and three unidentified lipids. The genome size was about 5.4 Mbp and the DNA G+C content was 68.2 mol%. Sp-1T exhibited the highest average nucleotide identity value of 76.6 % and in silico DNA–DNA hybridization value of 22.1 % with Pseudoxanthobacter soli DSM 19599T (family Xanthobacteraeae). This strain is distinguishable from closely related members of the order Rhizobiales by its differential phenotypic, chemotaxonomic, genomic and phylogenetic characteristics. On the basis of evidence from polyphasic taxonomic analysis, we concluded that Sp-1T represents a novel species in a novel genus within the order Rhizobiales , for which the name Segnochrobactrum spirostomi gen. nov., sp. nov. is proposed. The type strain is Sp-1T (=KCTC 62036T=JCM 32162T). We also describe a novel family, Segnochrobactraceae fam. nov., to encompass the proposed novel genus and species.
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Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil
More LessStrains of Lysobacter , thought to play vital roles in the environment for their high enzyme production capacity, are ubiquitous in various ecosystems. During an analysis of bacterial diversity in saline soil, a Gram-stain-negative, aerobic, chitin-degrading bacterial strain, designated SJ-36T, was isolated from saline-alkaline soil sampled at Tumd Right Banner, Inner Mongolia, PR China. Strain SJ-36T grew at 4–40 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0–8.0) and 0–6 % NaCl (optimum, 1.0 %). Oxidase and catalase activities were positive. A phylogenetic tree based on 16S rRNA gene sequences and the phylogenomic tree both showed that strain SJ-36T formed a tight clade with Lysobacter maris KMU-14T (sharing 97.6 % 16S rRNA gene similarity) and Lysobacter aestuarii S2-CT (97.8 %). The major polar lipids of strain SJ-36T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified lipids and one unidentified phospholipid. The major fatty acids were iso-C15 : 0 (37.5 %), summed feature 9 (14.0 %; iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C11 : 0 (10.6 %). Q-8 was the predominant ubiquinone. Its genomic DNA G+C content was 66.6 mol%. The average nucleotide identity values of strain SJ-36T to L. maris KMU-14T, L. aestuarii S2-CT and other type strains were 81.5, 79.1 and <79.0 %, respectively. The results of physiological, phenotypic and phylogenetic characterizations allowed the discrimination of strain SJ-36T from its phylogenetic relatives. Lysobacter alkalisoli sp. nov. is therefore proposed with strain SJ-36T (=CGMCC 1.16756T=KCTC 43039T) as the type strain.
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Volumes and issues
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