International journal of systematic and evolutionary microbiology最新文献

Two Gram-stain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacteria, designated strains WXL103 and WXL210^T, were isolated from surface seawater which was collected from the South China Sea. Strain WXL103 was most closely related to Vibrio astriarenae JCM 19233^T with 97.8% sequence similarity, and WXL210^T was also most closely related to V. astriarenae JCM 19233^T (97.7% sequence similarity). Phylogenetic analysis based on 16S rRNA genes, phylogenomic analysis of single-copy gene families and whole-genome data placed WXL103 and WXL210^T within the genus Vibrio, and they formed a close branch with Vibrio agarivorans CECT 5085^T and V. astriarenae JCM 19233^T. The growth of strains WXL103 and WXL210^T occurred at 10-42 °C (optimum 28 °C), at pH 7.0-9.0 (optimum 7.0-8.0) and in the presence of 2.5-8% (w/v) NaCl (optimum 3-4%). The predominant fatty acids (>10%) were C_16 : 0, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c) and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). The DNA G+C contents of WXL103 and WXL210^T were 48.61 and 48.54 mol%, respectively. These two strains demonstrated average nucleotide identity values of 97.9% with each other, confirming that they were the same species. On the basis of the polyphasic evidence, strains WXL103 and WXL210^T are proposed to represent a novel species of the genus Vibrio, for which the name Vibrio glycogenivorans sp. nov. is proposed. The type strain is WXL210^T (KCTC 8711^T=MCCC 1K09445^T), and strain WXL103 is deposited in the culture collection centre with numbers KCTC 8767 and MCCC 1K09443.

Two species have been named in the provisional genus 'Candidatus Nostocoides': 'Ca. Nostocoides limicola' corrig. Blackall et al. 2000 and 'Ca. Nostocoides acidiphilum' corrig. Kulichevskaya et al. 2012. The type species of the genus, 'Ca. Nostocoides limicola' has since been transferred to Tetrasphaera Maszenan et al. 2000, which was later renamed Nostocoides Deshmukh and Oren 2024. This leaves 'Ca. Nostocoides acidiphilum' as an orphan species. Furthermore, Kulichevskaya et al. did not assign 'Ca. Nostocoides acidiphilum' to 'Ca. Nostocoides' corrig. Blackall et al. 2000. Instead, they proposed a new genus, 'Ca. Nostocoides' corrig. Kulichevskaya et al. 2012, in the phylum Planctomycetota. This is in violation of Rule 51b (4) of the International Code of Nomenclature of Prokaryotes, making 'Ca. Nostocoides' corrig. Kulichevskaya et al. 2012 and 'Ca. Nostocoides acidiphilum' corrig. Kulichevskaya et al. 2012 pro-illegitimate names. To resolve this situation, I propose the replacement names 'Ca. Nostocimimus' gen. nov. and 'Ca. Nostocimimus acidiphilus' comb. nov., respectively.

Two novel bacterial strains, designated YIM 135249^T and YIM 135347, were isolated from two distinct species of lichen samples collected from Shangri-La, Southwest of China. The strains were Gram-stain-positive, catalase-positive, oxidase-negative, aerobic, yellow-pigmented, non-motile and short rod-shaped. Growth occurred at 10-35 °C (optimum 28 °C), pH 4.0-9.0 (optimum pH 7.0) and with 0-9.0% sodium chloride (NaCl, w/v, optimum 0%). Menaquinone (MK)-10 and MK-11 were the predominant respiratory quinones, while polar lipids included phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Major fatty acids included iso-C_16:0, anteiso-C_15:0 and anteiso-C_17:0. The 16S rRNA gene sequences of strains YIM 135249ᵀ and YIM 135347 showed the highest similarity (98.6%) to those of the type strains Plantibacter flavus NBRC 103081ᵀ and Plantibacter auratus NBRC 15702ᵀ. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences revealed that the two strains formed a distinct clade within the genus Plantibacter. Genome-based comparisons further supported their taxonomic distinctiveness, with average nucleotide identity (ANI) values ≤78.8% and digital DNA-DNA hybridization (dDDH) values ≤23.1% between strain YIM 135249ᵀ and the type strains of recognized Plantibacter species. The dDDH and ANI values between strains YIM 135249ᵀ and YIM 135347 were 82.0% and 97.9%, respectively. The genomic G+C contents were 67.3 and 67.5 mol%. On the basis of phenotypic and genotypic data, strains YIM 135249ᵀ and YIM 135347 represent a novel species of the genus Plantibacter, for which the name Plantibacter lichenum sp. nov. is proposed, with YIM 135249ᵀ as the type strain (=MCCC 1K09942^T=NBRC 117222^T).

Low-temperature (34 °C) hydrothermal fluid was collected from Axial Seamount along the Juan de Fuca Ridge in the northeast Pacific Ocean. A thermophilic methanogen, designated strain Ax23^T, was isolated from this fluid. The archaeon was anaerobic, autotrophic and coccoidal and grew separately on H₂/CO₂ and formate. Ax23^T grew on NH₄ ⁺ and by fixing N₂, but did not grow on NO₃ ^-. The isolate grew at temperatures ranging from 33 to 75 °C (optimum 73 °C) and a minimum doubling time of 32 min, in the presence of 3-6% NaCl (optimum 3-4.5%) and pH 4.0-9.0 (optimum 6.0-8.0). It increased its growth yield (cells produced per mole of CH₄ produced) when grown on 10 kPa H₂ relative to 160 kPa H₂, suggesting that it is capable of a metabolic trade-off with varying H₂ availability. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain was 95.6-99.7% identical to other thermophilic species of the family Methanococcaceae in the kingdom Methanobacteriati. The complete genome of Ax23^T was sequenced, which yielded a 1,662,948 bp chromosome with 1,663 protein-coding sequences and a 7,732 bp plasmid. Based on genome-relatedness index analyses and its phenotypic characteristics, strain Ax23^T represents a novel species, for which the name Methanothermococcus jasoni is proposed. The type strain is Ax23^T (=DSM 118471^T=JCM39656^T).

Strain G4-2^T was isolated from the rhizosphere soil of alfalfa (*Medicago sativa* L.) in Dongying City, Eastern China. The isolate was rod-shaped, flagellate, motile and Gram-negative, and the colonies were flat, circular, beige and opaque. Strain G4-2^T grew at salinities of 0-1% (w/v) NaCl (optimum, 0.5%), pH 6.0-9.0 (optimum, 8.0) and 20-50 °C (optimum, 37 °C). Phylogenetic and phylogenomic analyses based on the 16S rRNA gene sequence suggest that G4-2^T belongs to the genus Microvirga and is most closely related to Microvirga vignae BR3299^T. Its major fatty acid was C_18 : 1  ω7c (68.3%). The polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol and partially unidentified phosphoglycolipid. The sole respiratory quinone detected was ubiquinone 10. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain G4-2^T and members of the Microvirga genus ranged from 74.0 to 90.3% and 20.3 to 42.0%, respectively. Both values are below the species delineation thresholds for species identification. Based on the result of the polyphasic characterization, we proposed a novel species in the genus Microvirga, Microvirga medicaginis sp. nov., the type strain of which was G4-2T (= ACCC 6437T = KCTC 18095T).

Streptosporangium is the second largest genus within the family Streptosporangiaceae, comprising 34 species with validly published names. One of the most recently described members of the genus is Streptosporangium soli, assigned on the basis of chemotaxonomic and morphological features and a limited phylogenetic analysis. Here, we reinvestigate the taxonomic assignment of S. soli KLBMP 9127^T using a polyphasic approach. We show that despite possessing chemotaxonomic and morphological features characteristic of the genus Streptosporangium, S. soli does not cluster with other members of the genus Streptosporangium in a 16S rRNA gene-based phylogeny of the entire family Streptosporangiaceae nor within a whole-genome-based phylogenomic tree. S. soli can be distinguished from its closest relatives within the phylogenomic tree using spore morphology and chemotaxonomic markers. Overall genome relatedness indices further suggest that S. soli represents a novel lineage within the family Streptosporangiaceae, sharing less than 71% average amino acid identity with the type strain of the type species of every genus with a validly published name within the family. Accordingly, we propose reassigning S. soli as the type species of a novel genus within the family Streptosporangiaceae, Dolomitihabitans soli gen. nov., comb. nov. We also revisit the 1987 proposal made by Kudo and Seino for Streptosporangium indianense to be reclassified as a member of the genus Streptomyces. On the basis of a wealth of morphological, chemotaxonomic and phylogenetic data, we show that S. indianense is not a member of the genus Streptosporangium, or even the family Streptosporangiaceae. Rather, S. indianense is most closely associated with the genus Streptomyces, family Streptomycetaceae.

Seventeen bacterial strains were isolated from cryoconite and glacial ice samples collected from five glaciers in China. Phylogenetic analyses based on 16S rRNA gene sequences placed these strains within the genus Variovorax. Pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons among the 17 strains supported their assignment to 13 separate genomic species. The highest ANI (≤94.2%) and dDDH (≤60.5%) values between them and their closest type strains were below the accepted species thresholds, indicating that they cannot be assigned to any known Variovorax species. Consistently, the phylogenomic tree resolved 13 well-supported, independent lineages corresponding to these genomic species. The major cellular fatty acids in the majority of strains were C_{16 : 0}, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). Based on combined phenotypic, genotypic and phylogenetic evidence, the 17 strains represent 13 novel species of the genus Variovorax, for which the following names are proposed: Variovorax glucosi sp. nov. (RHLX14ᵀ=CGMCC 1.10104^T=NBRC 116946^T), Variovorax frigidus sp. nov. (LT1R16ᵀ=CGMCC 1.11618^T=NBRC 116947^T), Variovorax trehalosi sp. nov. (LT1R20ᵀ=CGMCC 1.11621^T=NBRC 116948^T), Variovorax restrictus sp. nov. (LT1P1ᵀ=CGMCC 1.11725^T=NBRC 116949^T), Variovorax cryoconiti sp. nov. (LT2P21^T=CGMCC 1.11737^T=NBRC 116950^T), Variovorax pasteuri sp. nov. (RB3P1^T=CGMCC 1.11853^T=NBRC 116951^T), Variovorax nivicola sp. nov. (ZT5P49^T=CGMCC 1.23581^T=NBRC 116952^T), Variovorax multivorans sp. nov. (ZT5R36^T=CGMCC 1.23587^T=NBRC 116953^T), Variovorax nitratireducens sp. nov. (RT4R15^T=CGMCC 1.24376^T=NBRC 116954^T), Variovorax monticola sp. nov. (GB4P3^T=CGMCC 1.24632^T=NBRC 116955^T), Variovorax raffinosi sp. nov. (GB1P17^T=CGMCC 1.24747^T=NBRC 116956^T), Variovorax glacialis sp. nov. (GT1P44^T=CGMCC 1.24874^T=NBRC 116957^T) and Variovorax sucrosi sp. nov. (ZT4R33^T=CGMCC 1.25067^T=NBRC 116958^T).

A strictly anaerobic bacterial strain, designated LBK-2^T, was isolated from the intestinal tract of a raccoon dog. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LBK-2^T shared the highest similarity (99.3 -95.0 %) with type strains in the genus Acidaminococcus. The cells were coccoid, Gram-negative, non-motile and non-haemolytic. They tested negative for oxidase and catalase but positive for alkaline phosphatase. Growth occurred at 20-50℃ (optimum: 37 ℃), pH 3.5-8.0 (optimum: pH 7.0) and 0-2 % NaCl. Major fatty acids include C_16 : 1  ω9c, C_18 : 1  ω9c, C_12 : 0 and C_12 : 0 aldehyde. The average nucleotide identity and digital DNA-DNA hybridization values between LBK-2^T and type strains of other Acidaminococcus species ranged from 64.83 to 88.25 % and 18.0 to 64.6 %, respectively, both below the species delineation thresholds. The genomic DNA G+C content was 53.6 %. Based on polyphasic taxonomic evidence, strain LBK-2^T (=CGMCC 1.18153^T=KCTC 25959^T) represents a novel species within the genus Acidaminococcus, for which the name Acidaminococcus nyctereutis sp. nov. is proposed.