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Volume 71,
Issue 9,
2021
Volume 71, Issue 9, 2021
- New Taxa
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- Firmicutes and Related Organisms
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Characterization of Staphylococcus roterodami sp. nov., a new species within the Staphylococcus aureus complex isolated from a human foot infection
This article introduces a new Staphylococcus species cultivated from a human foot wound infection in a Dutch traveller returning from the island of Bali, Indonesia: Staphylococcus roterodami sp. nov. Based on the genomic sequence, there is strong molecular evidence for assigning the strain to a novel species within the S. aureus complex. Differences in cellular fatty acid spectrum and biochemical tests underline these findings. Its ecological niche and pathogenicity require further study. The type strain is DSM111914T (JCM34415T).
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Anaerocolumna chitinilytica sp. nov., a chitin-decomposing anaerobic bacterium isolated from anoxic soil subjected to biological soil disinfestation
More LessAn obligately anaerobic bacterial strain (CTTWT) belonging to the family Lachnospiraceae within the class Clostridia was isolated from an anoxic soil sample subjected to biological or reductive soil disinfestation. Cells of the strain were Gram-stain-positive, short rods with peritrichous flagella. The strain was saccharolytic and decomposed polysaccharides, chitin, xylan and β-1,3-glucan. Strain CTTWT decomposed cell biomass and cell-wall preparations of an ascomycete plant pathogen, Fusarium oxysporum f. sp. spinaciae. The strain produced acetate, ethanol, H2 and CO2 as fermentation products from the utilized substrates. The major cellular fatty acids of the strain were C16 : 1 ω7c dimethylacetal (DMA), C16 : 0 DMA and C18 : 1 ω7c DMA. The closely related species of strain CTTWT based on the 16S rRNA gene sequences were species in the genus Anaerocolumna with sequence similarities of 95.2–97.6 %. Results of genome analyses of strain CTTWT indicated that the genome size of the strain was 5.62 Mb and the genomic DNA G+C content was 38.3 mol%. Six 16S rRNA genes with five different sequences from each other were found in the genome. Strain CTTWT had genes encoding chitinase, xylanase, cellulase, β-glucosidase and nitrogenase as characteristic genes in the genome. Homologous genes encoding these proteins were found in the genomes of the related Anaerocolumna species, but the genomic and phenotypic properties of strain CTTWT were distinct from them. Based on the phylogenetic, genomic and phenotypic analyses, the name Anaerocolumna chitinilytica sp. nov., in the family Lachnospiraceae is proposed for strain CTTWT (=NBRC 112102T=DSM 110036T).
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Blautia intestinalis sp. nov., isolated from human feces
More LessA strictly anaerobic bacterial strain (27-44T) was isolated from a stool specimen from an autistic child collected in PR China. The strain was Gram-stain-positive, non-motile, non-pigmented, non-spore-forming, and cells were oval to rod-shaped. Strain 27-44T grew at 20–40 °C (optimal at 37 °C) and at pH 6.0–10 (optimal at 6.0–8.0). The major polar lipids were one phospholipid, two glycolipids, two aminophospholipids and one unidentified lipid. The major cellular fatty acids of strain 27-44T were C16 : 0 and C17 : 0 2-OH. The end product of glucose fermentation was mainly butyric acid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 27-44T was a member of the genus Blautia and phylogenetically closely related to Blautia obeum ATCC 29174T (with 97.8 % seque nce similarity). The genome of strain 27-44T was 3.5 Mbp with a DNA G+C content of 42.36 mol%. A total of 3436 genes were predicted and, of these, 3133 genes were annotated by KEGG. On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons, strain 27-44T represents a novel species within the genus Blautia , for which the name Blautia intestinalis sp. nov. is proposed. The type strain is 27-44T= CGMCC 1.5285T=NBRC 113774T.
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Caldicellulosiruptor diazotrophicus sp. nov., a thermophilic, nitrogen-fixing fermentative bacterium isolated from a terrestrial hot spring in Japan
More LessA novel nitrogen-fixing fermentative bacterium, designated as YA01T, was isolated from Nakabusa hot springs in Japan. The short-rod cells of strain YA01T were Gram-positive and non-sporulating. Phylogenetic trees of the 16S rRNA gene sequence and concatenated sequences of 40 single-copy ribosomal genes revealed that strain YA01T belonged to the genus Caldicellulosiruptor and was closely related to Caldicellulosiruptor hydrothermalis 108T, Caldicellulosiruptor bescii DSM 6725T and Caldicellulosiruptor kronotskyensis 2002T. The 16S rRNA gene sequence of strain YA01T shares less than 98.1 % identity to the known Caldicellulosiruptor species. The G+C content of the genomic DNA was 34.8 mol%. Strain YA01T shares low genome-wide average nucleotide identity (90.31–91.10 %), average amino acid identity (91.45–92.10 %) and <70 % digital DNA–DNA hybridization value (41.8–44.2 %) with the three related species of the genus Caldicellulosiruptor . Strain YA01T grew at 50–78 °C (optimum, 70 °C) and at pH 5.0–9.5 (optimum, pH 6.5). Strain YA01T mainly produced acetate by consuming d(+)-glucose as a carbon source. The main cellular fatty acids were iso-C17 : 0 (35.7 %), C16 : 0 (33.3 %), DMA16 : 0 (6.6 %) and iso-C15 : 0 (5.9 %). Based on its distinct phylogenetic position, biochemical and physiological characteristics, and the major cellular fatty acids, strain YA01T is considered to represent a novel species of the genus Caldicellulosiruptor for which the name Caldicellulosiruptor diazotrophicus sp. nov. is proposed (type strain YA01T=DSM 112098T=JCM 34253T).
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Alicyclobacillus mali sp. nov., Alicyclobacillus suci sp. nov. and Alicyclobacillus fructus sp. nov., thermoacidophilic sporeforming bacteria isolated from fruit beverages
Six thermo-acidophilic, spore-forming strains were isolated from a variety of juice products and were characterized genetically and phenotypically. According to 16S rRNA and rpoB gene phylogenetic analyses and average nucleotide identity comparisons against the species demarcation cutoff at <95 %, these six strains were determined to represent three novel species of Alicyclobacillus . The isolates were designated FSL-W10-0018T, FSL-W10-0037, FSL-W10-0048, VF-FSL-W10-0049T, FSL-W10-0057 and FSL-W10-0059T. All six isolates were Gram-positive, motile, rod shaped, contained menaquinone 7 as the major respiratory quinone and had ω-cyclohexane C17 : 0 as a major fatty acid. They were all able to grow aerobically in a range of acidic and moderate thermal conditions. Only isolates FSL-W10-0048 and VF-FSL-W10-0049T were able to produce guaiacol. The following names are proposed for the three new species: Alicyclobacillus mali sp. nov. (type strain FSL-W10-0018T =DSM 112016T=NCIMB 15266T); Alicyclobacillus suci sp. nov (VF-FSL-W10-0049T=DSM 112017T=NCIMB 15265T); and Alicyclobacillus fructus sp. nov. (FSL-W10-0059T=DSM 112018T=NCIMB 15264T).
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Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle
More LessA strict anaerobic, Gram-stain-positive rod-shaped bacterium, designated PTT, was isolated from the faecal material of a painted turtle (Chrysemys picta). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to Clostridium sensu stricto with the highest sequence similarities to Clostridium moniliforme (97.4 %), Clostridium sardiniense (97.2 %) and the misclassified organism Eubacterium multiforme (97.1 %). The predominant cellular fatty acids of strain PTT were C14 : 0, C16 : 0 and an unidentified product with an equivalent chain length of 14.969. The G+C content determined from the genome was 28.8 mol%. The fermentation end products from glucose were acetate and butyrate with no alcohols detected and trace amounts of CO2 and H2 also detected; no respiratory quinones were detected. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Clostridium for which the name Clostridium chrysemydis sp. nov. is proposed. The type strain is strain PTT (=CCUG 74180T=ATCC TSD-219T).
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Paenibacillus oceani sp. nov., isolated from surface seawater
More LessA Gram-stain-positive and motile bacterial strain, designated IB182363T, was isolated from surface seawater of the South China Sea. Cells grew at pH 5.0–9.5 (optimum, pH 7.0–8.0), 20–40 °C (optimum, 30 °C) and with 1–8 % (w/v) NaCl (optimum, 2–4 %). On the basis of 16S rRNA gene sequence analysis, strain IB182363T was affiliated to the genus Paenibacillus and the closest phylogenetically related species was Paenibacillus ginsengarvi DSM18677T with 96.9 % sequence similarity. The values of whole genome average nucleotide identity analysis and digital DNA–DNA hybridization between the isolate and the closely related type strains were less than 86.3 and 25.6 %, respectively. Chemotaxonomic analysis revealed that strain IB182363T possessed meso-diaminopimelic acid in the cell-wall peptidoglycan and contained menaquinone MK-7 as the predominant isoprenoid quinone. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid, two unidentified aminolipids, two unidentified phospholipids and four unidentified aminophospholipids. The genomic DNA G+C content was 54.5 mol%. On the basis of the above results, strain IB182363T represents a novel species of the genus Paenibacillus , for which we propose the name Paenibacillus oceani sp. nov. with the type strain IB182363T (=MCCC 1K04630T=JCM 34214T).
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Paradesulfitobacterium ferrireducens gen. nov., sp. nov., a Fe(III)-reducing bacterium from petroleum-contaminated soil and reclassification of Desulfitobacterium aromaticivorans as Paradesulfitobacterium aromaticivorans comb. nov.
More LessA strictly anaerobic bacterium, strain PLL0T, was isolated from petroleum-contaminated soil sampled in Gansu Province, PR China. Cells were rods, non-motile and Gram-stain-positive. The strain grew at 25–37 °C (optimum, 30 °C) in the presence of 0–3 % (w/v) NaCl (optimum, 2 %). Strain PLL0T was able to reduce ferrihydrite, Fe(III) citrate and thiosulphate. The 16S rRNA gene analysis revealed that this strain clustered with the genus Desulfitobacterium , and showed highest similarity to Desulfitobacterium aromaticivorans UKTLT (95.4 %) followed by Desulfitobacterium chlororespirans Co23T (93.9 %). However, strains PLL0T and UKTLT showed no more than 94.0 % similarity to other species of the genus Desulfitobacterium , and formed an independent group in the phylogenetic tree. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain PLL0T and Desulfitobacterium species (except for D. aromaticivorans ) were 67.4–68.5 % and 12.6–12.7 %, respectively, which are far below the threshold for delineation of a new species. Based on ANI, dDDH, average amino acid identity, phylogenetic analysis and physiologic differences from the previously described taxa, we suggest that strain PLL0T represents a novel species of a novel genus, for which the name Paradesulfitobacterium ferrireducens gen. nov. sp. nov. is proposed. The type strain is PLL0T (=MCCC 1K05549=KCTC 25248). We also propose the reclassification of D. aromaticivorans as Paradesulfitobacterium aromaticivorans comb. nov.
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- Other Bacteria
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Thermosynergistes pyruvativorans gen. nov., sp. nov., an anaerobic, pyruvate-degrading bacterium from Shengli oilfield, and proposal of Thermosynergistaceae fam. nov. in the phylum Synergistetes
A strictly anaerobic, thermophilic, Gram-stain-negative bacterium, named as strain S15T, was isolated from oily sludge of Shengli oilfield in PR China. Cells of strain S15T were straight or slightly curved rods with 0.4–0.8 µm width × 1.4–3 µm length and occurred mostly in pairs or short chains. Endospore-formation was not observed. The strain grew optimally at 55 °C (range from 30–65 °C), pH 6.5 (pH 6.0–8.5) and 0–30 g l−1 NaCl (optimum with 10 g l−1 NaCl). Yeast extract was an essential growth factor for strain S15T. The major cellular fatty acid was iso-C15 : 0 (58.2 %), and the main polar lipids were amino phospholipid (APL), glycolipids (GLs) and phosphatidylethanolamine (PE). The G+C content of DNA of strain S15T was 52.2 mol%. Strain S15T shared 89.8 % 16S rRNA gene similarity with the most related organism Acetomicrobium hydrogeniformans DSM 22491T in the phylum Synergistetes . The paired genomic average amino acid identity (AAI) and percentage of conserved proteins (POCP) values showed relatedness of less than 58.0 and 39.7 % with type strains of the species in the phylum Synergistetes . On the basis of phenotypic, phylogenetic and phylogenomic evidences, strain S15T constitutes a novel species in a novel genus, for the name Thermosynergistes pyruvativorans gen. nov., sp. nov. is proposed. The type strain is S15T (=CCAM 583T=JCM 33159T). Thermosynergistaceae fam. nov. is also proposed.
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- Proteobacteria
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Aquabacterium soli sp. nov., a novel bacterium isolated from soil under the long-term application of bifenthrin
More LessStrain SJQ9T, an aerobic bacterium isolated from a soil sample collected in Shanghai, PR China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, 30–35 °C and in the presence of 1 % (w/v) NaCl. A comparative analysis of 16S rRNA gene sequences showed that strain SJQ9T fell within the genus Aquabacterium . The closest phylogenetic relatives of strain SJQ9T were Aquabacterium citratiphilum DSM 11900T (98.6 % sequence similarity) and Aquabacterium commune DSM 11901T (96.4 %). Cells of the strain were Gram-stain-negative, motile, non-spore-forming, rod-shaped and positive for oxidase activity and negative for catalase. The chemotaxonomic properties of strain SJQ9T were consistent with those of the genus Aquabacterium : the major fatty acid was summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 65.7 mol%. Strain SH9T exhibited a DNA–DNA relatedness level of 34±2 % with A. citratiphilum DSM 11900T and 28±3 % with A. commune DSM 11901T. Based on the obtained data, strain SJQ9T represents a novel species of the genus Aquabacterium , for which the name Aquabacterium soli sp. nov. is proposed. The type strain is SJQ9T (=JCM 33106T=CCTCC AB 2018284T).
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Pontivivens ytuae sp. nov., isolated from deep sea sediment of the Mariana Trench
More LessA Gram-stain-negative, light pink-coloured, rod-shaped, flagellated and facultative anaerobic bacterial strain, designated MT2928T, was isolated from deep-sea sediment collected from the Mariana Trench. Growth of strain MT2928T occurred optimally at 28 °C, pH 8.0–9.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT2928T belongs to the genus Pontivivens and has the highest sequence similarity to Pontivivens insulae GYSW-23T (96.6 %). Genomic analysis indicated that strain MT2928T contains a circular chromosome of 4 199 362 bp with G+C content of 67.2 mol%. The strain did not produce bacteriochlorophyll a, but produced carotenoid. The predominant respiratory quinone of MT2928T was ubiquinone-10. The polar lipids of MT2928T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and two unidentified phospholipids. The major fatty acids of strain MT2928T contained summed feature 8 (C18 : 1 ω7c or/and C18 : 1 ω6c), C18 : 0 and summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH). On the basis of phylogenetic, physiological, biochemical and other phenotypic properties, strain MT2928T represents a novel species of the genus Pontivivens , and the name Pontivivens ytuae sp. nov. is proposed with the type species MT2928T (=MCCC 1K05575T=JCM 34320T).
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Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor
A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA–DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).
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Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
More LessA novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.
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Dyella telluris sp. nov. and Dyella acidiphila sp. nov., isolated from forest soil of Dinghushan Biosphere Reserve, China
More LessCells of bacterial strains G9T and 7MK23T, isolated from forest soil samples collected from the Dinghushan Biosphere Reserve, Guangdong Province, PR China, were Gram-stain-negative, aerobic and rod-shaped. Strain G9T was motile with single polar flagellum and grew at 12–37 °C (optimum, 28 °C), pH 4.5–8.0 (optimum, pH 6.0–7.5) and in the presence of 0–3.5 % NaCl (optimum, 1.5%, w/v); while strain 7MK23T was non-motile and grew at 12–42 °C (optimum, 28–33 °C), pH 2.5–8.5 (optimum, pH 4.5–6.5) and NaCl levels of 0–1.0 % (optimum, 0–0.5 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates fell within the cluster of the genus Dyella . The closely related species (with a 16S rRNA gene sequence similarity >98.65%) of strain G9T were Dyella terrae JS14-6T (99.0 %), D . kyungheensis THG-B117T (98.8 %) and D . amyloliquefaciens DHC06T (98.7 %) while that of strain 7MK23T were D . mobilis DHON07T (99.2 %) and D . flava DHOC52T (99.1 %), but the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strains G9T, 7MK23T and the closely related Dyella species listed above were in the ranges of 77.5–83.8 % and 22.0–27.0 %, much lower than the species demarcation lines of 95.5 and 70 %, respectively. Phylogenomic analyses using UBCG and Phylophlan also supported that these two strains represent two novel species of Dyella . The major fatty acids of strain G9T were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 while that of strain 7MK23T were iso-C15 : 0 and anteiso-C15 : 0. Ubiquinone-8 was the only respiratory quinone detected in both strains. The polar lipids of strain G9T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and several unknown phospholipids, aminophospholipids, aminolipids and lipid while strain 7MK23T contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and several unknown phospholipids and aminophospholipids. The DNA G+C contents of strains G9T and 7MK23T were 64.7 and 63.4 mol%, respectively. On the basis of 16S rRNA gene sequence phylogenetic and phylogenomic analyses as well as phenotypic data obtained, we propose that strains G9T and 7MK23T represent two novel species of the genus Dyella , for which the names Dyella telluris sp. nov. (type strain G9T=KACC 21725T=GDMCC 1.2132T) and Dyella acidiphila sp. nov. (type strain 7MK23T=KCTC 62739T=GDMCC 1.1446T) are proposed.
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Massilia puerhi sp. nov., isolated from soil of Pu-erh tea cellar
A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3T, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Massilia . The closest phylogenetic relative was Massilia arenae CICC 24458T (99.5 %), followed by M. timonae CCUG45783T (97.9 %), M. oculi CCUG43427AT (97.8 %), and M. aurea DSM 18055T (97.8 %). The major fatty acids were C16 : 0 and C16 : 1 ω7c and/or C16 : 1 ω6c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA–DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3T and Massilia arenae CICC 24458T was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3T represents a new species, for which we propose the name Massilia puerhi sp. nov. with the type strain SJY3T (=CGMCC 1.17158T=KCTC 82193T).
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Entomomonas asaccharolytica sp. nov., isolated from Acheta domesticus
More LessStrain F2AT, isolated from the cricket Acheta domesticus, was subjected to a polyphasic taxonomic characterization. Cells of the strain were rod-shaped, Gram-stain-negative and catalase- and oxidase-positive. It did not assimilate any carbohydrates. The strain's 16S rRNA gene sequence showed highest similarity to Entomomonas moraniae QZS01T (96.4 %). The next highest similarity values were found to representatives of related genera (<93 %). The genome size of strain F2AT was 3.2 Mbp and the G+C content was 36.4 mol%. Average nucleotide identity values based on blast and MUMmer and average amino acid identity values between strain F2AT and E. moraniae QZS01T were 74.29/74.43, 83.88 and 74.70 %, respectively. The quinone system predominantly contained ubiquinone Q-8. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid were detected. The polyamine pattern consisted of the major compounds putrescine and spermidine. Major fatty acids were C18 : 1 ω7c and C16 : 0 and the hydroxyl acids were C12 : 0 3-OH, C14 : 0 2-OH and C14 : 0 3-OH. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Due to its association with the only species of the genus Entomomonas but its distinctness from E. moraniae we here propose the novel species Entomomonas asaccharolytica sp. nov. F2AT (=CCM 9136T=LMG 32211T).
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Photorhabdus hindustanensis sp. nov., Photorhabdus akhurstii subsp. akhurstii subsp. nov., and Photorhabdus akhurstii subsp. bharatensis subsp. nov., isolated from Heterorhabditis entomopathogenic nematodes
More LessTwo Gram-negative, rod-shaped bacteria, H1T and H3T, isolated from the digestive tract of Heterorhabditis entomopathogenic nematodes were biochemically and molecularly characterized to determine their taxonomic positions. The 16S rRNA gene sequences of these strains indicate that they belong to the Gammaproteobacteria, to the family Morganellaceae , and to the Photorhabdus genus. Deeper analyses using whole genome-based phylogenetic reconstructions show that strains H1T and H3T are closely related to P. akhurstii DSM 15138T, to P. hainanensis DSM 22397T, and to P. namnaonensis PB45.5T. In silico genomic comparisons confirm these observations and show that strain H1T shares 70.6, 66.8, and 63.5 % digital DNA–DNA hybridization (dDDH) with P. akhurstii DSM 15138T, P. hainanensis DSM 22397T, and P. namnaonensis PB45.5T, respectively, and that strain H3T shares 76.6, 69.4, and 59.2 % dDDH with P. akhurstii DSM 15138T, P. hainanensis DSM 22397T, and P. namnaonensis PB45.5T, respectively. Physiological and biochemical characterization reveals that these two strains differ from most of the validly described Photorhabdus species and from their more closely related taxa. Given the clear phylogenetic separations, that the threshold to discriminate species and subspecies is 70 and 79% dDDH, respectively, and that strains H1T and H3T differ physiologically and biochemically from their more closely related taxa, we propose to classify H1T and H3T into new taxa as follows: H3T as a new subspecies within the species P. akhurstii , and H1T as a new species within the Photorhabdus genus, in spite that H1T shares 70.6 % dDDH with P. akhurstii DSM 15138T, score that is slightly higher than the 70 % threshold that delimits species boundaries. The reason for this is that H1T and P. akhurstii DSM 15138T cluster apart in the phylogenetic trees and that dDDH scores between strain H1T and other P. akhurstii strains are lower than 70 %. Hence, the following names are proposed: Photorhabdus hindustanensis sp. nov. with the type strain H1T (=IARI-SGMG3T,=KCTC 82683T=CCM 9150T=CCOS 1975T) and P. akhurstii subsp. bharatensis subsp. nov. with the type strain H3T (=IARI-SGHR2T=KCTC 82684T=CCM 9149T=CCOS 1976T). These propositions automatically create P. akhurstii subsp. akhurstii subsp. nov. with DSM 15138T as the type strain (currently classified as P. akhurstii ).
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Novosphingobium decolorationis sp. nov., an aniline blue-decolourizing bacterium isolated from East Pacific sediment
Aniline blue-decolourizing bacterial strain 502str22T, isolated from sediment collected in the East Pacific, was subjected to characterization by a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 502str22T belongs to the genus Novosphingobium , with closely related type strains ‘ Novosphingobium profundi ’ F72T (97.6%), N. mathurense SM117T (97.1%) and N. arvoryzae Jyi-02T (97.0%). Digital DNA–DNA hybridization and average nucleotide identity values between strain 502str22T and closely related type strains were 20.3–24.8% and 74.1–81.9%, respectively. The major cellular fatty acid (>10%) was C18:1 ω7c. The polar lipid profile consisted of a mixture of phosphatidylcholine, one sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content of strain 502str22T was 65.5 mol%. The polyphasic taxonomic results indicated that strain 502str22T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium decolorationis sp. nov is proposed. The type strain is 502str22T (=KCTC 82134T= MCCC 1K04799 T).
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Massilia rhizosphaerae sp. nov., a rice-associated rhizobacterium with antibacterial activity against Ralstonia solanacearum
A novel rhizobacterium, designated strain NEAU-GH312T, with antibacterial activity against Ralstonia solanacearum was isolated from rhizosphere soil of rice (Heilongjiang Province, PR China) and characterized with a polyphasic approach. Cells of strain NEAU-GH312T were Gram-stain-negative, aerobic, non-spore-forming, motile with peritrichous flagella and rod-shaped. Colonies were light orange, convex and semi-translucent on Reasoner's 2A (R2A) agar after 2 days of incubation at 28 °C. Growth was observed on R2A agar at 10–40 °C, pH 4.0–8.0 and with 0–5 % (w/v) NaCl. The respiratory quinone was ubiquinone Q-8. The major cellular fatty acids of strain NEAU-GH312T were C16 : 1 ω7c and/or C16 : 1 ω6c, C16 : 0 and C18 : 1 ω7c and/or C18 : 1 ω6c. The main polar lipids were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Phylogenetic analyses confirmed the well-supported affiliation of strain NEAU-GH312T within the genus Massilia , close to the type strains of Massilia arvi THG-RS2OT (98.7 %), Massilia norwichensis NS9T (98.7 %) and Massilia kyonggiensis TSA1T (98.6 %). Strain NEAU-GH312T had a genome size of 6.68 Mb and an average DNA G+C content of 66.3 mol%. Based on the genotypic, phenotypic and chemotaxonomic data obtained in this study, strain NEAU-GH312T could be classified as representative of a novel species of the genus Massilia , for which the name Massilia rhizosphaerae sp. nov. is proposed, with strain NEAU-GH312T (=DSM 109722T=CCTCC AB 2019142T) as the type strain.
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Ramlibacter algicola sp. nov., isolated from a freshwater alga Cryptomonas obovoidea
More LessA Gram-stain-negative, strictly aerobic, catalase-negative, oxidase-positive and non-motile rod-shaped bacterium, designated strain CrO1T, was isolated from a freshwater alga Cryptomonas obovoidea in the Nakdong river of South Korea. Colonies of CrO1T were white, convex and circular and growth was observed at 25–40 °C (optimum, 37 °C) and pH 6.0–9.0 (optimum, pH 7) and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). CrO1T contained C16 : 0, summed feature 5 (comprising C18 : 0ante and/or C18 : 2ω6,9c), C18 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) as the major cellular fatty acids (>5 %) and ubiquinone-8 as the sole respiratory quinone. Phosphatidylethanolamine was detected as the major polar lipid. The DNA G+C content of CrO1T, calculated from the whole genome sequence was 69.6 mol%. CrO1T was most closely related to Ramlibacter humi 18x22-1T with a 97.6 % 16S rRNA sequence similarity and shared less than 97.4 % 16S rRNA sequence similarities with other type strains. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences revealed that CrO1T formed a distinct phyletic lineage within the genus Ramlibacter . On the basis of the results of phenotypic, chemotaxonomic and molecular analysis, CrO1T clearly represents a novel species of the genus Ramlibacter , for which the name Ramlibacter algicola sp. nov. is proposed. The type strain is CrO1T (=KACC 19926T=JCM 33302T).
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