International journal of systematic and evolutionary microbiology最新文献

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.

The high carbon to nitrogen ratio in oil-contaminated environments limits the efficiency of bioremediation. Therefore, isolating nitrogen-fixing bacteria from oil-contaminated environments will provide functional strain resources for improving bioremediation efficiency. A novel Gram-stain-negative, spiral-shaped and nitrogen-fixing bacterium, designated strain DQ9^T, was isolated from the oil sludge of Daqing Oilfield, Daqing City, Heilongjiang Province, China. Cells grew at 18-45 °C (optimum of 40 °C), at pH of 6.5-9.0 (optimum of 7.0) and with 0-2.0% (w/v) NaCl (optimum of 0%). The respiratory quinone was ubiquinone 8 (Q-8). The major cellular fatty acids were summed feature 8 (C_18:1  ω7c and/or C_18:1  ω6c) (46.8%), summed feature 3 (C_16:1 ω7c and/or C_16:1  ω6c) (14.6%) and C_16:0 (17.4%). The polar lipids consisted of phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unidentified aminophospholipid (UAPL), an unidentified aminolipid (UAL) and two unidentified lipids (UL1-2). Strain DQ9^T exhibited the highest 16S rRNA gene sequence similarities with Novispirillum itersonii subsp. itersonii LMG 4337^T (94.10%), N. itersonii subsp. nipponicum LMG 7370^T (94.10%), Marispirillum indicum B142^T (94.04%) and Caenispirillum bisanense K92^T (93.44%). The genomic DNA G+C content was 69.8 mol%. Comparing strain DQ9^T with closely related type strains, the digital DNA-DNA hybridization values were 18.5-22.0%, the average nucleotide identity values based on blast+ were 67.88-73.76%, the average amino acid identity values were 58-62% and the percentage of conserved proteins values were 45.53-58.80%. In the phylogenetic trees based on 16S rRNA genes and whole-genome sequences, strain DQ9^T formed an independent branch within the family Rhodospirillaceae. Based on the results of phylogenetics, morphology, physiology and chemotaxonomy, strain DQ9^T represents a novel species of a novel genus in the family Rhodospirillaceae, for which the name Cauispirillum nitrogeniifigens gen. nov., sp. nov. is proposed. The type strain is DQ9^T (=KCTC 8951^T=CGMCC 1.65428^T).

A novel fructophilic lactic acid bacterium, designated strain 1H7-5^T, was isolated from fresh honey in Japan. The strain exhibited poor glucose assimilation under anaerobic conditions and required external electron acceptors for glucose metabolism, indicating a fructophilic lifestyle. Cells were non-motile, rod-shaped, catalase-negative and facultatively anaerobic. Strain 1H7-5^T grew at 20-37 °C and at pH 5.0-7.5. Comparative 16S rRNA gene sequence analysis and phylogeny based on core genome sequences revealed that strain 1H7-5^T is affiliated within the genus Apilactobacillus, showing the highest similarity to Apilactobacillus apinorum. Average nucleotide identity and digital DNA-DNA hybridization values between strain 1H7-5^T and type strains of Apilactobacillus species were below the thresholds for species demarcation. The major cellular fatty acids were C_16:0, C_18:1  ω9c and C_19:0 cyclo ω8c, and the genomic DNA G+C content was 34.5 mol%. Based on phenotypic, chemotaxonomic and genomic evidence, strain 1H7-5^T represents a novel species within the genus Apilactobacillus, for which the name Apilactobacillus pseudapinorum sp. nov. is proposed. The type strain is 1H7-5^T (=JCM 37175^T=DSM 118410^T).

A bacterial strain, designated as P4^T, was isolated from an oil-contaminated soil sample. The cells were Gram-stain-positive, short rod-shaped and motile with a single lateral flagellum. Growth of the strain was observed at 20-40 °C (optimum at 30 °C), at pH 6.0-11.0 (optimum at pH 7.0) and with 0-5.0 % (w/v) NaCl (optimum at 1.0%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain P4^T was closely related to the members of genus Cellulomonas, with the highest sequence similarity to Cellulomonas hominis DSM 9581^T (99.5%), followed by Cellulomonas endometrii Marseille-Q7820^T (99.1%), Cellulomonas pakistanensis NBRC 110800^T (99.0%) and Cellulomonas denverensis NBRC 110783^T (98.1%). The draft genome sequence of strain P4^T was 3.98 Mb in length, with a DNA G+C content of 75.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain P4^T and the closely related type strains were in the range of 78.6-84.4 % and 21.9-28.2 %, respectively. The predominant cellular fatty acids of strain P4^T included anteiso-C_15 :0, C_16:0, C_14:0, iso-C_15:0 and anteiso-C_17:0. The main polar lipid was composed of diphosphatidylglycerol, glycophospholipid, glycolipid and three phosphatidylinositol mannosides and the major menaquinone was MK-9(H4). Based on the polyphasic characterization, strain P4^T (=KCTC 49393^T=CCTCC AB 2019402^T) represents a novel species of the genus Cellulomonas, for which the name Cellulomonas olei sp. nov. is proposed.

Fifteen Gram-stain-negative, rod-shaped bacterial strains, motile by means of a monopolar flagellum, were isolated from glaciers located on the Tibetan Plateau, P.R. China. These strains, designated MDT1-19^T, MDB2-8^T, HLS12-2^T, HLX7-2^T, LB2P49^T, LB2P70^T, LB3P112^T, LB3P118^T, LB2P10^T, RB2R34^T, ZB1P44^T, RB2P8^T, GB1R12^T, GB4P2^T and RT4P48^T, belong to the genus Janthinobacterium based on 16S rRNA gene sequences analysis. The average nucleotide identity and digital DNA-DNA hybridization values between these strains and species with validly published names were below 96% and 70%, respectively. Based on the phylogenetic, genotypic and phenotypic evidence, these 15 strains are proposed to represent fifteen novel species within the genus Janthinobacterium, with the following proposed names: Janthinobacterium algoris sp. nov. (MDT1-19^T=CGMCC 1.9797=NBRC 116353^T), Janthinobacterium breve sp. nov. (MDB2-8^T=CGMCC 1.9853^T=NBRC 116354^T), Janthinobacterium darwini sp. nov. (HLS12-2^T=CGMCC 1.9980^T=NBRC 116355^T), Janthinobacterium woesei sp. nov. (HLX7-2^T=CGMCC 1.9990^T=NBRC 116356^T), Janthinobacterium salmonicoloratum sp. nov. (LB2P49^T=CGMCC 1.11246^T=NBRC 116357^T), Janthinobacterium violaceum sp. nov. (LB2P70^T=CGMCC 1.11252^T=NBRC 116358^T), Janthinobacterium leeuwenhoeki sp. nov. (LB3P112^T=CGMCC 1.11294^T=NBRC 116359^T), Janthinobacterium pasteuri sp. nov. (LB3P118^T=CGMCC 1.11299^T=NBRC 116360^T), Janthinobacterium paucivorans sp. nov. (LB2P10^T=CGMCC 1.11332^T=NBRC 116361^T), Janthinobacterium longum sp. nov. (RB2R34^T=CGMCC 1.11894^T=NBRC 116362^T), Janthinobacterium glycogeni sp. nov. (ZB1P44^T=CGMCC 1.23234^T=NBRC 116363^T), Janthinobacterium kochi sp. nov. (RB2P8^T=CGMCC 1.23776^T=NBRC 116364^T), Janthinobacterium goodfellowi sp. nov. (GB1R12^T=CGMCC 1.24272^T=NBRC 116365^T), Janthinobacterium lyxosi sp. nov. (GB4P2^T=CGMCC 1.24307^T=NBRC 116366^T) and Janthinobacterium amylolyticum sp. nov. (RT4P48^T=CGMCC 1.24355^T=NBRC 116367^T).

A peach-pigmented strain FW153^T and a yellow-pigmented FW199^T were isolated from marsh water located at Fort Whyte, Manitoba, Canada. Both produce an anoxygenic photosynthetic apparatus, with a reaction centre encircled by a light-harvesting I complex containing bacteriochlorophyll a. They do not produce RuBisCo and do not grow anaerobically or autotrophically, supporting the classification of both as aerobic anoxygenic phototrophs. Sequencing of the 16S rRNA gene showed similarity to Rhizorhabdus phycosphaerae (99.93%), Rhizorhabdus wittichii (98.73%) and Rhizorhabdus histidinilytica (98.52%) for FW153^T, while for FW199^T, it was Sphingomonas molluscorum (97.47%), Sphingomonas dokdonensis (97.44%) and Sphingomonas kyeonggiensis (97.08%). Polyphasic analysis identified differences in physiology and cellular fatty acid composition, as well as within the genome, with average nucleotide identity (<95%) and digital DNA-DNA hybridization values (<70%) between each strain and their closest relatives supporting species designation. Therefore, we propose that FW153^T (=NCIMB 15610^T=DSM 120042^T) and FW199^T (=NCIMB 15611^T=DSM 120043^T) be classified as the type strains of new species with the names Rhizorhabdus antheiae sp. nov. and Sphingomonas eleionomae sp. nov., respectively.

A novel Agromyces strain, designated as M3QZ16-3^T, was isolated from the rhizosphere soil of Excoecaria agallocha, collected from the Maowei Sea Mangrove Nature Reserve in the Guangxi Zhuang Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M3QZ16-3^T was closely related to species of the genus Agromyces and shared the highest similarity of 99.26% with Agromyces kandeliae Q22^T. The average nucleotide identity and digital DNA-DNA hybridization values between strain M3QZ16-3^T and the type strain of A. kandeliae Q22^T were 88.2% and 34.4%, respectively. The polar lipids of strain M3QZ16-3^T comprised diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified polar lipid and two unidentified lipids. The major cellular fatty acids were anteiso-C_15:0, anteiso-C_17:0, iso-C_15:0 and iso-C_16:0, and the predominant menaquinones (MK; vitamin K₂) were MK-12 (78.3%) and MK-11 (14.3%). Cell-wall amino acids were 2,4-diaminobutyric acid, glutamic acid, glycine and alanine. The genome size of strain M3QZ16-3^T was 3.8 Mb, with a DNA G+C content value of 71.7 mol%. Based on the above descriptions, we propose strain M3QZ16-3^T to represent a novel species of the genus Agromyces, for which the name Agromyces excoecariae sp. nov. is proposed. The type strain is M3QZ16-3^T (=MCCC 1K07179^T=JCM 34940^T).

The obligately anaerobic, Gram-stain-positive coccobacilli strains OB7620^T and OB7656^T were isolated from faecal samples of healthy Japanese volunteers. Strain OB7620^T showed the highest 16S rRNA gene sequence similarity to Coprococcus comes ATCC 27758^T (98.4%) and Clostridium nexile DSM 1787^T (96.3%). Strain OB7656^T showed the highest 16S rRNA gene sequence similarity to 'Gluceribacter canis' NATH-2371^T (97.7%), C. nexile DSM 1787^T (94.8%) and Faecalimonas umbilicata EGH7^T (94.8%). These findings indicate that the two strains represent novel species. Genomic analysis clarified the phylogenetic relationship of C. comes with the species cluster designated as Coprococcus sensu stricto, which includes the type species, C. eutactus. As C. comes is distinct from the species of Coprococcus sensu stricto, C. comes is reclassified into a novel genus, Allocoprococcus, as Allocoprococcus comes gen. nov., comb. nov. Although strain OB7620^T is closely related to C. comes, it is a distinct species. Therefore, we propose the name Allocoprococcus similis gen. nov., sp. nov. The type strain is OB7620^T (=DSM 118890^T=JCM 37173^T). Because Coprococcus catus differs from Coprococcus sensu stricto, it has been placed in a novel genus, Pseudocoprococcus, as Pseudocoprococcus catus gen. nov., comb. nov. We also concluded that Coprococcus immobilis and Coprococcus intestinihominis are the same species and belong to the new genus Pseudocoprococcus. As C. immobilis has priority, we propose the name Pseudocoprococcus immobilis gen. nov., comb. nov. We also concluded that C. nexile and Clostridium phoceensis are the same species in the genus Faecalimonas. As C. nexile has priority, we propose the name Faecalimonas nexilis comb. nov. Coprococcus mobilis and 'G. canis' should also be reclassified within the genus Faecalimonas. Therefore, we propose the name Faecalimonas mobilis comb. nov. and Faecalimonas canis sp. nov. As strain OB7656^T is related to 'G. canis' but is a different species, we propose the name Faecalimonas hominis sp. nov. The type strain is OB7656^T (=DSM 118889^T=JCM 37172^T).