International journal of systematic and evolutionary microbiology最新文献

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.

Four aerobic, Gram-stain-negative, non-motile, rod-shaped, psychrophilic and yellow to light orange-pigmented bacterial strains, designated 7A^T, 14A^T, 28A^T and 7E, were isolated from air samples collected at Fildes Peninsula, King George Island, Antarctica. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel strains were related to members of the genus Flavobacterium and revealed that strain 7A^T shared 98.40% similarity to Flavobacterium faecale WV33^T, while strains 14A^T, 28A^T and 7E showed 98.88%, 98.74% and 98.61% similarity, respectively, to Flavobacterium frigidarium A2i^T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between these novel isolates and their closest relatives were below the cut-off values used for species delineation of 95-96% and 70%, respectively. Moreover, the ANI and dDDH values between strains 28A^T and 7E were 97.62% and 78.30%, respectively, indicating that these strains represented the same species. All four strains contained menaquinone-6 as the sole respiratory quinone. The DNA G+C content of all strains ranged from 32.8 to 34.5 mol %. Based on phylogenetic, genomic and phenotypic data, we propose that strains 7A^T, 14A^T and 28A^T represent three novel species of the genus Flavobacterium, for which the names Flavobacterium psychraerolatum (7A^T=CCM 8976^T=DSM 111734^T), Flavobacterium aeripolare (14A^T=CCM 8972^T=CGMCC 1.18502^T) and Flavobacterium gelidicaeli (28A^T=CCM 8973^T=CGMCC 1.18503^T) are proposed.

A yellow, Gram-stain-negative, facultatively anaerobic and rod-shaped strain, designated as HB62^T, was isolated from seawater in the tidal region of Danzhou, Hainan Island, People's Republic of China. Growth of strain HB62^T occurs at 16-40 °C, 0.5-10.0% (w/v) and pH 6.0-9.5 with the optima of 37 °C, 1.5-2.0% (w/v) and pH 6.5-7.0. Strain HB62^T could grow anaerobically by using nitrate and sulphate as electron acceptors. The 16S rRNA gene sequence identity analysis showed that strain HB62^T shared the highest sequence identity of 98.0% with Salinimicrobium soli CAU 1287^T and those of ≤97.9% and ≤94.6% with the rest of Salinimicrobium type strains and other genera type strains, respectively. Phylogenetic trees based on 16S rRNA genes and single-copy orthologous clusters revealed that strain HB62^T was stably clustered into the genus Salinimicrobium. Average nucleotide identity and digital DNA-DNA hybridization values of strain HB62^T and Salinimicrobium type strains were 72.1-78.2% and 17.8-21.2%, respectively, which were lower than the species delineation thresholds. The sole respiratory quinone was identified as menaquinone-6. Major fatty acids (>10%) are iso-C_15:0, iso-C_16:0 and summed feature 9 (iso-C_17:1  ω9c and/or C_16:0 10-methyl). Polar lipids included phosphatidylethanolamine, two unidentified glycolipids, three unidentified lipids and two unidentified aminolipids. Based on the genetic, chemotaxonomic and phenotypic results, strain HB62^T is concluded to represent a novel Salinimicrobium species, for which the name Salinimicrobium aquimaris sp. nov. is proposed. The type strain is HB62^T (=KCTC 102226^T=MCCC 1K08856^T).

Bradyrhizobial strains nodulate the native legume Cytisus supranubius (Genisteae) in its natural habitat: the high-mountain ecosystem of Tenerife (Canary Islands), where nitrogen fixation is an essential activity in its N-poor soils. Three of these strains, SSUT18^T, SSUT77 and SSUT112, are representative of a major phylotype within the genus Bradyrhizobium, and the phylogenetic analysis of their 16S rRNA gene sequences showed that Bradyrhizobium canariense is their closest relative. Nevertheless, the multilocus sequence analysis and the genome analysis distinguished these strains from the type strain of B. canariense and from the remaining species of the genus Bradyrhizobium. The calculated Average Nucleotide Identity (blast) (ANIb) and digital DNA-DNA hybridization values between the genomes of the strains from the new species and B. canariense were also lower than the threshold values proposed for species differentiation. These data, together with differences observed in chemotaxonomic and phenotypic characteristics, support the classification of the strains SSUT18^T, SSUT77 and SSUT112 into a new species of Bradyrhizobium, for which we propose the name Bradyrhizobium nivariense sp. nov. (type strain SSUT18^T=CECT 30998^T=LMG 33353^T).

An anaerobic, salt-tolerant, rod-shaped bacterium, strain JL216-2^T, was isolated from the shell of the hydrothermal gastropod Alviniconcha marisindica in the Tianxiu hydrothermal field on the Carlsberg Ridge, Indian Ocean. Cells of strain JL216-2^T were motile and 0.5×3-6 µm in size. Strain JL216-2^T grew at 10-32 °C (optimal 28 °C), pH 6.0-9.0 (optimal pH 7.0) and 0.5-12.0% (w/v) sodium chloride(NaCl, optimal 2.5%). Strain JL216-2^T exhibited metabolic versatility, being capable of heterotrophic growth on complex organic compounds. It also performed autotrophic growth by utilizing carbon dioxide (CO₂) fixation or sodium bicarbonate (NaHCO₃) as the sole carbon source, driven by hydrogen oxidation coupled with Fe(III) reduction. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to Helicovermis profundi S502^T (90.43% sequence similarity). The genome size of strain JL216-2^T was 4.91 Mb, with a G+C content of 39.54 mol%. Phylogenomic analysis and overall genome relatedness indices values indicated a close relatedness of strain JL216-2^T to H. profundi S502^T and Fusibacter spp. The combined genotypic and phenotypic data showed that strain JL216-2^T represents a novel genus within the order Eubacteriales. The type strain is JL216-2^T (=MCCC M30262^T=KACC 23553^T).

Four novel strains, designated p1-h21^T/p2-l61 and p3-h83^T/p4-l81, characterized as Gram-stain-negative, oxidase-positive, catalase-positive, obligately aerobic, non-motile and rod-shaped, isolated from blowhole swab samples of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis), collected from Hubei Province, China. Pairwise sequence comparisons of the 16S rRNA genes showed that these isolates were separated into two species. Strains p1-h21^T and p2-l61 were most closely related to Paracoccus endophyticus SYSUP0003^T (97.18% similarity) and Paracoccus aurantiacus TK008^T (97.03% similarity), whereas strains p3-h83^T and p4-l81 exhibited 96.89% similarity to Paracoccus kondratievae GB^T, and 96.53% similarity to Phaeovulum vinaykumarii DSM 18714^T. The DNA G+C contents of type strains p1-h21^T and p3-h83^T are 65.7 mol% and 66.9 mol%, respectively. These strains had summed feature 8 (comprising C_18 : 1  ω6c and/or C_18 : 1  ω7c) as major cellular fatty acids, ubiquinone 10 as the sole respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as major polar lipids, which are typical for members of the genus Paracoccus. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the four novel strains and their reference strains (ANI <75.3%, dDDH <20.5%) are lower than the species delineation thresholds, along with distinct phenotypic and biochemical characteristics, distinguishing them from their closest relatives and other recognized Paracoccus species. Therefore, strains p1-h21^T/p2-l61 and p3-h83^T/p4-l81 represent two novel species in the genus Paracoccus, for which the names Paracoccus jiaweipingae sp. nov. and Paracoccus zhouxuedongae sp. nov. are proposed, with p1-h21^T (=GDMCC 1.4971^T=JCM 37697^T) and p3-h83^T (=GDMCC 1.4972^T=JCM 37698^T) as type strains.

A novel Gram-stain-negative, rod-shaped, non-spore-forming, non-flagellated, strictly aerobic strain, designated as R2331^T, was isolated from coastal seawater of Yantai, P.R. China (127.59° E, 37.46° N). The organism grew optimally at 28-32 °C, at pH 7.0 and in the presence of 3.0% (w/v) NaCl. Strain R2331^T contained ubiquinone-10 as the predominant respiratory quinone and C_18 : 1  ω7c and/or C_18 : 1  ω6c as the major fatty acids. The predominant polar lipids of strain R2331^T were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and two unidentified aminolipids. The DNA G+C content of strain R2331^T was 59.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Yoonia ponticola KCTC 42133^T with 96.3% sequence similarity. Calculated ANI values, dDDH values and AAI values between strain R2331^T and the phylogenetically related species were in the range 71.4-73.7 %, 18.0-19.4 % and 67.2-71.1 %, respectively. Strain R2331^T fell within the cluster of the genus Cognatiyoonia in the phylogenomic tree. Based on polyphasic analyses, strain R2331^T represents a novel species of the genus Cognatiyoonia, for which the name Cognatiyoonia denitrificans sp. nov. is proposed. The type strain is R2331^T (=KCTC 8319^T=MCCC 1K04209^T).

A novel chlorophototrophic bacterium, strain BV2-C^T, was isolated from a microbial mat (~40 °C) at Rupite hot springs, Bulgaria. Cells were rod-shaped, Gram-negative, with numerous fimbriae/pili, but non-motile. Optimal growth occurred under micro-oxic conditions in the light (20-50 µmol photons m^-2 s^-1) at 45 °C (range 35-50 °C) and pH 7.2 (range pH 5.5-9.0). Bacteriochlorophyll c, bacteriochlorophyll a _P, echinenone and γ-carotene were the major pigments in cells capable of producing chlorosomes and type-1 homodimeric reaction centres. Dense liquid culture appeared greenish-brown, with cells forming small clumps and aggregates. Strain BV2-C^T grows photoheterotrophically using organic compounds as carbon source (i.e. a mixture of 20 proteinogenic amino acids or peptone) and thioglycolate as reduced sulphur source. Strain BV2-C^T obligately required branched-chain amino acids (l-isoleucine, l-leucine and l-valine) and l-lysine for growth. It is closely related to Chloracidobacterium thermophilum and 'Candidatus Chloracidobacterium aggregatum' with 16S rRNA gene sequence identities of 96.97 and 97.78%, respectively. The genome of strain BV2-C^T comprises two circular chromosomes of 2,659,040 and 1,000,103 bp (total genome, 3.65 Mb) and G+C content of 59.9 mol%. Phenotypic, phylogenetic and genomic analyses demonstrated that Chloracidobacterium validum strain BV2-C^T (=DSM 113832^T=JCM 39534^T) represents a novel species of the genus 'Candidatus Chloracidobacterium', which we hereby propose as Chloracidobacterium gen. nov. with Chloracidobacterium validum sp. nov. as the type species. Based on phylogenomic analyses, we also propose a new family, Chloroacidobacteriaceae fam. nov., and a new order, Chloracidobacteriales ord. nov., within the class Blastocatellia. We further propose the name 'Ca. C. aggregatum' for pro-valid publication with the genome sequence of strain E as nomenclatural type.

A Gram-negative bacillus isolated from human clinical cases in Aotearoa | New Zealand (NZ) and Australia was identified as a new species within the genus Yersinia based on genetic and phenotypic characteristics. This species demonstrated distinct biochemical differences in comparison to those typically reported for Yersinia enterocolitica (biotypes 1A, 1B, 2, 3, 4 and 5), including the ability to utilise raffinose and melibiose. Whole-genome sequencing data identified a total of 11 strains as a novel multi locus sequence type 598 (using the seven-gene McNally scheme). A closed genome for this species was obtained using Oxford Nanopore long-read sequencing, polished with high-accuracy Illumina short-read sequence data. Analysis of the 16S rRNA showed the closest similarity (98.36%) to Yersinia hibernica and Yersinia artesiana. Average nucleotide identity (ANI) values were below the threshold of ≤95% ANI when compared to the type strains of other Yersinia species, with Y. enterocolitica subsp. enterocolitica (94.1%) identified as the closest relative, thereby providing evidence that these strains should be considered as a novel species. The type strain is NZRM 4767^T =DSM 120367^T.