International journal of systematic and evolutionary microbiology最新文献

Two halophilic archaeal strains, AD34^T and PAK95, were isolated from a salt mine in Yunnan and rock salt in Jiangsu, two provinces in China that are 2,000 km apart, respectively. Cells of strain AD34^T were spherical while those of PAK95 were rod-shaped. Strains AD34^T and PAK95 were Gram-stain-negative, aerobic and able to grow at 1.4-4.8 M NaCl (with optimum at 3.1 M NaCl), pH 5.0-9.0 (optimum, pH 7.5) and 20-60 °C (optimum, 37 °C and 40 °C, respectively). Their 16S rRNA gene sequences showed the closest similarity to Haloparvum sedimenti DYS4^T, with similarities of 95.11% (AD34^T) and 95.46% (PAK95). The rpoB' gene sequences of strains AD34^T and PAK95 showed the highest similarity to species of Haloparvum alkalitolerans MK62-1^T with 91.40% (PAK95) and 91.53% (AD34^T) identity. Comprehensive phylogenetic analyses revealed that strains AD34^T and PAK95 form a robust, monophyletic clade with 100% bootstrap support, clearly distinct from related genera, particularly from the genus Haloparvum. From whole-genome sequencing, the DNA G+C content of AD34^T and PAK95 is 66.5 and 66.4 mol%, respectively, while that of DYS4^T and MK62-1^T is 68.3 and 69.1 mol%, respectively. The average nucleotide identity between AD34^T, PAK95 and the family Haloferacaceae ranged from 66.5 to 79.2%. The digital DNA-DNA hybridization values ranged from 19.6 to 32.8%, while the average amino acid identity (AAI) values were between 58.0 and 72.0%. Strains AD34^T and PAK95 may represent a novel species of a novel genus within the family Haloferacaceae, as judged by the AAI cutoff value (≤72.1%) proposed for differentiating genera within this family. The major polar lipids of strain AD34^T were phosphatidylglycerol (PG), PG phosphate methyl ester, PG sulphate and sulphated mannosyl glucosyl diether. Based on the phenotypic and phylogenetic analyses, it is proposed that strains AD34^T (=MCCC 4K00176^T=KCTC 4324^T) and PAK95 (=MCCC 4K00231=CGMCC 1.62791=KCTC 4376) represent a novel genus and species within the family Haloferacaceae, for which the name Halosubterraneus shenae gen. nov., sp. nov. is proposed. The type strain is AD34^T.

A phylogenetically distinct bacterial strain, designated as DFM-14^T, was isolated in 2022 from marine mud collected in Gochang, Jeollabuk-do, South Korea, and characterized using a polyphasic taxonomic approach. The isolate is Gram-stain-negative, motile, pale white and coccoid-shaped, typically forming clusters. It is facultatively aerobic, and phylogenetic analysis of the 16S rRNA gene placed it within the genus Thaumasiovibrio (family Vibrionaceae, phylum Pseudomonadota). Strain DFM-14^T formed a distinct clade with Thaumasiovibrio subtropicus C4V358^T and Thaumasiovibrio occultus C4II189ᵀ, sharing 16S rRNA gene sequence similarities of 95.6% and 95.2%, respectively. The major fatty acids are C_12 : 0, C_12 : 0 3-OH, C_16 : 0, C_16 : 1  ω9c and C_18 : 1  ω9c, while the predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The draft genome is 4.4 Mb in size, assembled into 56 contigs, and contains 4,445 coding sequences and 110 RNAs (8 rRNAs and 102 tRNAs), with a G+C content of 45.4 mol%. Optimal growth occurs at 25 °C, pH 7.0 and 2% (w/v) NaCl. Based on phenotypic, phylogenetic, chemotaxonomic and genomic evidence, strain DFM-14ᵀ represents a novel species of the genus Thaumasiovibrio, for which the name Thaumasiovibrio clandestinus sp. nov. is proposed. The type strain is DFM-14^T (=KEMB 24352^T=JCM 37837^T=KCTC 8887^T).

A novel strain, designated Mg75^T, was isolated from a vineyard soil sample collected in Mostaganem, Algeria. This Gram-positive, non-motile strain produces a branched, fragmented substrate mycelium with a yellowish-orange colour and a white aerial mycelium on International Streptomyces Project 2 (ISP2), ISP3 and ISP4. Mg75^T exhibited growth across a temperature range of 15-40 °C, with an optimal range of 28-30 °C. It thrived at pH levels between 5.0 and 10.0, with an optimum at pH 7.0, and tolerated NaCl concentrations ranging from 0% to 3% (w/v), with an optimal concentration range of 0-1% (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence indicated the highest similarity with Saccharothrix yanglingensis Hhs.015^T (98.95%). The G+C content of the genomic DNA of strain Mg75^T was 73.4 mol%. Digital DNA-DNA hybridization (dDDH) between strain Mg75^T and its neighbouring Saccharothrix species ranged from 23.2% to 39.9%. Average nucleotide identity (ANI) ranged from 82.08% to 90.91%, and average amino acid identity (AAI) ranged from 79.8% to 92.57%, way below the thresholds of 70% for dDDH and 95-96% for ANI and AAI used for species delimitation. Strain Mg75^T was found to share a similar chemotaxonomic profile based on genomic chemotaxonomic markers. The phylogenetic and phylogenomic analyses, together with the in silico chemotaxonomic and phenotypic data, indicated that strain Mg75^T (=DSM 118769^T=CECT 31160^T) represented a novel species of the genus Saccharothrix, for which the name Saccharothrix sabaoui sp. nov. is proposed.

Two novel Gram-stain-negative strains, designated as MAC3^T and MAC8^T, which produced brownish-yellow and bright-orange colonies, respectively, were isolated from seawater collected off Minmeoru Beach, Ganghwa Island, Republic of Korea. These strains were facultatively anaerobic, catalase- and oxidase-positive, rod-shaped and motile with flagella. Both strains grew at 4-40 °C and at pH 4.0-10.0. Strain MAC3^T grew in sodium chloride (NaCl) concentrations (w/v) of 0-15.0%, while strain MAC8^T tolerated 0-14.0%. Both strains contained ubiquinone-10 as the predominant respiratory quinone and C_18:1  ω7c (or summed feature 8, comprising C_18:1  ω6c and/or C_18:1  ω7c) as the major fatty acid. The major polar lipids of both strains included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified aminoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequences placed the two strains within the genus Fulvimarina. Strain MAC3^T shared the highest sequence similarity (97.7%) with Fulvimarina endophytica 85^T, while strain MAC8^T shared 97.9% sequence similarity with Fulvimarina pelagi HTCC2506^T. The DNA guanine and cytosine (G+C) content of both MAC3^T and MAC8^T was 61.5 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the novel strains and related type strains were 20.8-26.2% and 75.1-82.9%, respectively. Based on the results of the polyphasic analysis, strains MAC3^T and MAC8^T represent two novel species in the genus Fulvimarina, for which the names Fulvimarina fulva sp. nov. and Fulvimarina thalattae sp. nov. are proposed, respectively. The F. fulva and F. thalattae type strains are MAC3^T (=KACC 23727^T=TBRC 19011^T) and MAC8^T (=KACC 23726^T=TBRC 19010^T), respectively.

Three strains designated c1-l78^T, c2-A9 and c3-l95 were isolated from blowhole swab samples of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) in Hubei Province, China. The strains are Gram-stain-negative, oxidase-positive, catalase-positive, obligately aerobic, non-motile, non-haemolytic, proteolytic and short-rod-shaped bacteria. Based on 16S rRNA gene sequence analysis, strain c1-l78^T was assigned to the family Moraxellaceae (order Pseudomonadales), with the genus Acinetobacter being its closest relative (93.96 % similarity). Average nucleotide identity and digital DNA-DNA hybridization values between c1-l78^T and type strains of all validly published species of the genus Acinetobacter were very low, ranging from 71.2 to 73.2 % and 20.9 to 26.6 %, respectively. The average amino acid identity was 65.0-69.9 % with orthologous fraction (55.3-67.5 %), and the percentage of conserved proteins was 39.0-55.4 %. Phylogenomic analysis further confirmed a distinct lineage, supported by a high relative evolutionary divergence value of ~0.94. The DNA G+C content of strain c1-l78^T is 39.1 mol %. The major cellular fatty acids were 9-octadecenoic acid (C_18 : 1  ω9c), summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c) and hexadecanoic acid (C_16 : 0). The sole respiratory quinone was ubiquinone-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminophosphoglycolipid. Based on the polyphasic analysis, we propose that the three strains represent a novel genus and species, for which the name Hubeiibacter gen. nov., type species Hubeiibacter jixunmingi gen. nov., sp. nov. is proposed. The type strain is c1-l78^T (=GDMCC 1.4970^T=JCM 37696^T).

During a screening of sulphur-oxidizing bacteria from different Spanish soils, a strain designated AFSI2.2^T was isolated from the rhizosphere soil of a mulberry plant thriving in a sulphur-rich environment. Cells of this strain were Gram-stain-negative motile rods with flagella. Its taxonomic classification was determined through a polyphasic approach. Phylogenetic analysis of the 16S rRNA gene revealed that strain AFSI2.2^T shares high similarity (99.64%) with certain Variovorax species, suggesting that the isolate belongs to this genus. Whole-genome phylogeny showed that the novel strain forms a distinct lineage within the genus Variovorax. Whole-genome analysis of AFSI2.2^T exhibited average nucleotide identity values of 78.37-89.63% and digital DNA-DNA hybridization values of 21.90-38.90% with closely related Variovorax species, both below the established thresholds for species delineation. The predominant cellular fatty acids of strain AFSI2.2^T were C_16 : 0, Summed Feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c) and Summed Feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). Apart from the ability of oxidizing inorganic sulphur compounds, AFSI2.2^T presented further in vitro plant growth-promoting (PGP) activities such as production of indole-3-acetic acid and siderophores and 1-aminocyclopropane-1-carboxylate deaminase activity. Genes associated with these PGP traits, as well as with cytokinin and gamma-aminobutyric acid biosynthesis, were identified in the AFSI2.2^T genome, supporting its potential as a PGP bacterium. In conclusion, phylogenetic, genomic, phenotypic and chemotaxonomic analyses support the classification of the isolate as a novel species within the genus Variovorax, for which the name Variovorax palleresanus sp. nov. is proposed. The type strain is AFSI2.2^T (=CECT 31217^T=CIP 112526^T).

A Gram-stain-positive, rod-shaped, motile bacterium, strain REN36^T, was isolated from fermented grains of baijiu. The optimal growth conditions for this organism were observed at a salt concentration of 0% (with a tolerance range of Sodium chloride (NaCl) from 0% to 2%), a temperature of 37 °C (with a tolerance range from 20 to 45 °C) and a pH of 6.0 (with a tolerance range from pH 4.0 to 8.0). The 16S rRNA gene sequence of the isolate showed 98.04% similarity to Cohnella nanjingensis D45^T. The predominant respiratory quinone identified was menaquinone 7, while anteiso-C_15:0 and C_16:0 were the major fatty acids. The polar lipid profile of strain REN36^T included diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, four aminophospholipids, two phospholipids, one glycolipid, one aminoglycolipid, one aminolipid and seven lipids. The DNA G+C content was 58.8 mol%. Notably, strain REN36^T exhibited cellulolytic activity: it utilizes sodium carboxymethyl cellulose as the sole carbon source and encoded three endoglucanases [glycoside hydrolase family 5 (GH5)/GH9] that synergistically degrade cellulose. Digital DNA-DNA hybridization of the isolate with two reference strains showed relatedness values of 29.2% with C. nanjingensis DSM 28246^T and 21.6% with Cohnella ginsengisoli DSM 18997^T. The phylogenetic, chemotaxonomic and phenotypic data supported the classification of strain REN36^T as a representative of a novel species within the genus Cohnella, for which the name Cohnella baijiui sp. nov. is proposed. The type strain is REN36^T (=GDMCC 1.2866^T=JCM 35185^T).

As part of a broader effort to survey and characterize the diversity of pectolytic bacteria affecting potato crops in Mexico, phytopathogenic strains were isolated from soft-rot symptoms on potato plants in Sinaloa. Among them, an atypical Pectobacterium-like strain, LFLA-215^T, could not be confidently assigned to any known species through biochemical or molecular methods. To clarify its taxonomic position and explore its genomic and functional features, whole-genome sequencing and comparative analyses were conducted, along with biochemical, morphological and pathogenicity evaluations. The strain LFLA-215^T is Gram-stain-negative, with peritrichous flagella, catalase-positive and oxidase-negative. Phylogenetic analyses based on the 16S rRNA operon, dnaJ and 923 core genes confirmed that strain LFLA-215^T and three additional strains (CFBP8739, CSR2 and CSR3) are members of the genus Pectobacterium. Although genomic similarity values between LFLA-215^T and other Pectobacterium species ranged from 87.73 to 93.53% (OrthoANI blast-based), 87.63-93.46% (OrthoANI USEARCH) and 34.0-52.1% (digital DNA-DNA hybridization), falling below species delineation thresholds, phylogenomic reconstructions consistently positioned all four strains within a coherent clade. This clade showed the closest relationship to 'Pectobacterium colocasium' LJ1, whereas Pectobacterium parmentieri RNS 08-42-1A^T was the most distantly related. Although LFLA-215^T fulfilled Koch's postulates and demonstrated pathogenicity in potato plants, its virulence on tubers was comparatively lower than that of other known Pectobacterium strains, which could be related to the size and the reduction in the total number of genes when its complete genome is reported here. Our findings support the classification of the strains LFLA-215^T, CFBP8739, CSR2 and CSR3 as a novel species within the genus Pectobacterium, for which the name Pectobacterium sinaloense sp. nov. is proposed, with LFLA-215^T (=NCCB 101086=CM CNRG 1201=ATCC TSD-577) designated as the type strain.