International journal of systematic and evolutionary microbiology最新文献

Twenty-three novel psychrophilic bacteria, represented by the type strains LB2P44^T, LB2P6^T, LB1P62^T, LB3P6^T, LS1P3^T, XS2P39^T, XS1P32^T, ZB4P13^T, ZS1P14^T and GT2P42^T, were isolated from ice, cryoconite and meltwater of five Tibetan Plateau glaciers. All strains were Gram-stain-negative, aerobic, rod-shaped and psychrophilic, with optimal growth at 14-20 °C and pH 7.0. 16S rRNA gene sequence similarities to validly named Flavobacterium species ranged from 98.12% to 99.56%. Phylogenomic analysis of 81 concatenated core genes positioned the 23 strains (comprising the ten novel species) within a robust monophyletic clade - the 'Cryospheric Lineage' - together with 31 other psychrophilic type strains predominantly from glaciers, permafrost and polar regions. Average nucleotide identity (ANI) values of ≤94.4% and digital DNA-DNA hybridization (dDDH) values of ≤57.3% against closest relatives were below species thresholds (95-96% ANI, 70% dDDH). Major fatty acids were iso-C_15:0 (8.1-16.8%), iso-C_15:0 3-OH (3-hydroxy, 5.2-16.0%) and summed feature 3 (C_16:1  ω7c and/or C_16:1  ω6c, 10.1-27.6%), with elevated branched-chain and unsaturated components typical of cold adaptation. Polyphasic taxonomic evidence supports the description of ten novel species within the genus Flavobacterium: Flavobacterium amylolyticum sp. nov. (LB2P44^T=CGMCC 1.11256^T=NBRC 114815^T), Flavobacterium glucosi sp. nov. (LB2P6^T=CGMCC 1.11263^T=NBRC 114816^T), Flavobacterium esculini sp. nov. (LB1P62^T=CGMCC 1.11346^T=NBRC 114817^T), Flavobacterium labens sp. nov. (LB3P6^T=CGMCC 1.11428^T=NBRC 114818^T), Flavobacterium pasteuri sp. nov. (LS1P3^T=CGMCC 1.11474^T=NBRC 114821^T), Flavobacterium rhamnosi sp. nov. (XS2P39^T=CGMCC 1.23204^T=NBRC 115054^T), Flavobacterium frigidum sp. nov. (XS1P32^T=CGMCC 1.23370^T=NBRC 115055^T), Flavobacterium glycogeni sp. nov. (ZB4P13^T=CGMCC 1.24050^T=NBRC 115056^T), Flavobacterium kochi sp. nov. (ZS1P14^T=CGMCC 1.24093^T=NBRC 114828^T) and Flavobacterium cryophilum sp. nov. (GT2P42^T=CGMCC 1.24821^T=NBRC 114831^T).

An aerobic, Gram-stain-positive and non-motile actinobacterial strain, designated SALV-R1^T, was isolated from flower of Salvia splendens in Muan, Republic of Korea. Growth was observed at 10-30 °C (optimum, 28 °C) and pH 7.0-9.0 (optimum, pH 8.0) with up to 3% (w/v) NaCl (optimum, 1%). blast analysis of 16S rRNA gene sequences revealed the highest sequence similarity of strain SALV-R1^T to Herbiconiux oxytropis CPCC 203406^T (98.76%) followed by Herbiconiux flava VKM Ac-2058 (98.69%) and 'Herbiconiux gentiana' CPCC 205716^T (98.69%). According to the 16S rRNA gene-based phylogenetic tree, strain SALV-R1^T formed a clade with H. flava NBRC 164003^T and 'H. gentiana' CPCC 205716^T, which subsequently clustered with H. oxytropis CPCC 203406^T. Strain SALV-R1^T was closely related to Herbiconiux moechotypicola KCTC 19653^T as well as H. flava NBRC 164003^T and 'H. gentiana' CPCC 205716^T based on phylogenomic tree. OrthoANI and digital DNA-DNA hybridization values of strain SALV-R1^T with the closely related strains were lower than 81.2 and 24.8%, respectively. The major respiratory menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipid. The major fatty acids (>10%) of strain SALV-R1^T were anteiso-C_15:0, iso-C_16:0 and anteiso-C_17:0. The cell wall peptidoglycan contained cross-linked l-diaminobutyric acid (type B2γ). The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that strain SALV-R1^T represents a novel species of the genus Herbiconiux, for which the name Herbiconiux salviae sp. nov. (type strain SALV-R1^T=KACC 21604^T=NBRC 116987^T) is proposed.

Two potential novel plant-beneficial bacteria, designated CR1201^T and CR3202^T, were isolated from the rhizosphere soil of citrus in Deqing county, located in Zhaoqing, Guangdong Province, PR China. They could produce indole-3-acetic acid and siderophores. Cells of the two novel strains were Gram-stain-negative, motile with polar flagella, aerobic and non-spore-forming rods. Strain CR1201^T showed high antagonistic activity against the citrus canker pathogen Xanthomonas citri subsp. citri. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that strains CR1201^T and CR3202^T belonged to the genus Metapseudomonas and were most closely related to the four validly published species Metapseudomonas lalkuanensis PE08^T, Metapseudomonas boanensis DB1^T, Metapseudomonas furukawaii KF707^T and Metapseudomonas resinovorans LMG 2274^T. The average nucleotide identity and digital DNA-DNA hybridization values between the two isolates and their most closely related type strains were 80.06-92.76% and 19.2-49.8%, respectively, which were well below the threshold values for species delimitation. The genomic DNA G+C content of strains CR1201^T and CR3202^T was 64.5 mol% for both strains. The major fatty acids of strain CR1201^T were identified as summed feature 8 (C_18:1  ω7c and/or C_18:1  ω6c), C_16:0 and C_17:0 cyclo, whereas those of strain CR3202^T were identified as summed feature 8 (C_18:1  ω7c), summed feature 3 (C_16:1  ω7c and/or C_16:1  ω6c) and C_16:0. The predominant quinone for both strains was ubiquinone 10. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid and an unidentified phospholipid. Based on the phenotypic, genotypic, chemotaxonomic analyses and genome comparison, strains CR1201^T and CR3202^T were identified as two novel species within the genus Metapseudomonas, for which the names Metapseudomonas phytobenefica sp. nov. and Metapseudomonas cellulosilytica sp. nov. are proposed, with CR1201^T (=GDMCC 1.4560^T=JCM 37070^T) and CR3202^T (=GDMCC 1.4918^T=CCM 9447^T) as the type strains, respectively.

Three bacterial strains, AG2a^T, AX9b^T and BK9b, were isolated from symptomatic onion bulbs (Allium cepa) collected in the USA between 2013 and 2016. Phylogenomic analyses based on whole-genome sequencing, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) revealed that strain AG2a^T belongs to a novel species within the genus Phytobacter, and strains AX9b^T and BK9b represent a novel species within the genus Kosakonia. ANI and isDDH values between these strains and their closest relatives were well below the species delineation thresholds (ANI <85.3%, isDDH <27.9%), and they were phenotypically different from their closest phylogenomic neighbours. Genomic assemblies yielded complete circular chromosomes and plasmids, with G+C contents ranging from 53.48% to 53.70%. Despite nitrogen fixation being a characteristic trait of both genera, none of the strains harboured the nif operon. Based on these results, we propose the establishment of the two novel species Phytobacter cepae sp. nov., with strain AG2a^T as the designated type strain (= CCOS 2093^T = CFBP 9466^T) and Kosakonia beeri sp. nov., with strain AX9b^T as the designated type strain (= CCOS 2091^T = CFBP 9467^T).

A facultative anaerobic, catalase-negative, lactic acid-producing, non-endospore-forming, Gram-positive coccoid bacterium, strain MT/JULY 2010^T, was isolated from the stomach of a Helicobacter pylori-positive Japanese female patient with pre-neoplastic gastric mucosa. This bacterium can form clusters, chains or pairs or occurs singly in liquid media. The growth ranges for temperature, pH and NaCl concentration were 20-45 °C, pH 5.0-7.0 and 1-4%, respectively. Cells exhibited an unusual tumbling motion when observed under the microscope using a hanging drop assay. Observation under an electron microscope showed some unidentified structures and numerous fimbriae-like appendages. The combined results of 16S rRNA gene sequence analysis and the overall genome-related index [average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH)] classified the bacterium as a novel species of the genus Streptococcus. It forms a monophyletic cluster with Streptococcus parasanguinis ATCC 15912^T in the phylogenetic tree with 94.4% ANI. Furthermore, the conventional DNA-DNA hybridization assay and dDDH of the two strains identified their relatedness as 62.5% and 58.7% (both below the 70% threshold), respectively. The DNA G+C content, determined by nuclease P1-digested genomic DNA, was 42.6 mol%, while the digital G+C content calculated in silico was 41.8 mol%. Based on the phenotypic and genotypic results, strain MT/JULY 2010^T represents a novel species within the genus. The name Streptococcus mobilis sp. nov. is proposed. The type strain is MT/JULY 2010^T (=ATCC BAA-2258^T=NBRC 107862^T=NCBI 948105^T=V10/022878^T).

Marine sponges host diverse microbial communities that play essential roles in nutrient cycling and host health. During a study of the microbiota of marine sponges from Taiwan, two Gram-stain-negative, motile and facultatively anaerobic strains, XeTr1^T and StTr2, were isolated from Xestospongia sp. and Stylissa carteri, respectively. Cells were rod-shaped and showed catalase and oxidase activities. Growth was observed at 15-37 °C, pH 6.0-9.0 and 1.0-3.0% (w/v) NaCl. Strains XeTr1^T and StTr2 contained ubiquinone-8 and ubiquinone-9 as major quinones and summed feature 3 (C_16:1  ω7c), summed features 8 (C_18:1  ω7c) and C_16:0 as major fatty acids. The major polar lipids identified in strains XeTr1^T and StTr2 were phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis based on the 16S rRNA gene sequence placed strains XeTr1^T and StTr2 within the family Endozoicomonadaceae, forming a distinct lineage that shared 94% or less sequence homology with its closest relatives, including Endozoicomonas lisbonensis NE40^T, Endozoicomonas arenosclerae CBAS 572^T and Endozoicomonas montiporae CL-33^T. The average amino acid identity values were below the cutoff range for species of the same genus, supporting the placement of strains XeTr1^T and StTr2 as representing a novel genus within the family Endozoicomonadaceae. Distinct phenotypic and chemotaxonomic characteristics, combined with low sequence similarity and a clear phylogenetic separation from known genera, support the proposal of a novel genus and species in the family Endozoicomonadeae, for which the name Spongorhabdus nitratireducens gen. nov., sp. nov. is proposed. The type strain is XeTr1^T (=JCM 37577^T=UCCCB 249^T).

A Gram-stain-negative, aerobic, oxidase- and catalase-positive, motile with a polar flagellum, rod-shaped bacterium designated as strain EMRT-3^T was isolated from sediment collected in a coal mine drainage treatment system in the Republic of Korea. Growth of strain EMRT-3^T was observed in Reasoner's 2A medium at 10-35 °C (optimum, 25-30 °C) and pH 4.5-8.0 (optimum, pH 6.5-7.5) and in the presence of 0-0.5% NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain EMRT-3^T belongs to the genus Asticcacaulis and was closely related to Asticcacaulis solisilvae CGM1-3EN^T, Asticcacaulis biprosthecium DSM 4723^T, Asticcacaulis benevestitus DSM 16100^T and Asticcacaulis taihuensis CGMCC 1.3431^T with 97.0, 96.3, 96.2 and 95.9% sequence similarities, respectively. A phylogenomic tree also showed that strain EMRT-3^T formed a distinct clade within genus Asticcacaulis and clustered with the four type species (CGM1-3EN^T, DSM 4723^T, DSM 16100^T and CGMCC 1.3431^T). The average nucleotide identity and digital DNA-DNA hybridization values between strain EMRT-3^T and closely related type strains were 72.8-75.6% and 20.0-20.7%, respectively. The genomic DNA G+C content of EMRT-3^T was 60.0 mol%. Genome annotation for strain EMRT-3^T indicated broad metabolic capacity, encompassing complete pathways for central carbohydrate and amino acid metabolism as well as the biosynthesis of essential cofactors and vitamins. Importantly, the detection of genes associated with copper, nickel/cobalt and iron homeostasis, along with acid tolerance, highlights its adaptation to metal-rich and acidic environments. The major fatty acids of EMRT-3^T were C_12:0, C_16:0, C_12:0 3-OH, C_15:0 2-OH, C_16:0 2-OH, C_16:1 2-OH, 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 major polar lipids were phosphatidylglycerol, aminophospholipids and glycolipids. Based on the polyphasic taxonomic evidence, strain EMRT-3^T represents a novel species within the genus Asticcacaulis, for which the name Asticcacaulis carbonis sp. nov. is proposed. The type strain is EMRT-3^T (=KACC 22206^T=JCM 34539^T=FBCC-B5258^T).

Mangrove sediments are recognized as hotspots for methane emissions and harbour diverse methanogenic archaea. In this study, we describe two novel methanogens, strains T3^T and Mfa9^T, isolated from mangrove sediment samples in the Futian Mangrove Nature Reserve in Shenzhen, People's Republic of China. Cells of strains T3^T and Mfa9^T are irregularly coccoid in shape, with diameters of 0.7-1.4 µm and 0.6-1.7 µm, respectively. Both strains utilize methanol, methylamine, dimethylamine, trimethylamine, dimethyl sulphide and acetate as the sole carbon source for growth and methanogenesis, but not H₂/CO₂, formate, choline, betaine or pyruvate. Strain T3^T grew at 15-42 °C (optimum 37 °C), pH 6.0-8.0 (optimum 6.5) and 0-0.72 M NaCl (optimum 0.10 M NaCl). Strain Mfa9^T grew at 20-33 °C (optimum 25 °C), pH 5.5-7.5 (optimum 7.0) and 0-0.72 M NaCl (optimum 0.51 M NaCl). The genomic G+C contents of strains T3^T and Mfa9^T are 43.3 mol% and 46.2 mol%, respectively. Phylogenetic analyses revealed that both strains are classified within the genus Methanosarcina. Strain T3^T was mostly related to Methanosarcina siciliae T4/M^T, with 16S rRNA gene similarity of 99.7%, an average nucleotide identity of 88.8% and a digital DNA-DNA hybridization of 35.7%. By contrast, strain Mfa9^T shared 98.8% 16S rRNA gene similarity with Methanosarcina semesiae MD1^T. As M. semesiae MD1^T is unavailable and lacks genomic data, comparative analyses with its closer relative Methanosarcina sp. MTP4 (99.8% 16S rRNA gene identity), together with genomic and phenotypic differences from M. semesiae, support the designation of strain Mfa9^T as a novel species. In conclusion, two novel species of the genus Methanosarcina, Methanosarcina mangrovi sp. nov. and Methanosarcina sediminis sp. nov., are proposed. The type strain of M. mangrovi sp. nov. is T3^T (=CCAM 2189^T=JCM 39553^T), and the type strain of M. sediminis sp. nov. is Mfa9^T (=CCAM 2190^T=JCM 39554^T).