International journal of systematic and evolutionary microbiology最新文献

A hydrogenotrophic methanoarchaeon, designated strain FWC-SCC4^T, was isolated from cold seep sediment of Four-Way Closure Ridge, offshore southwestern Taiwan. Strain FWC-SCC4^Tutilizes H₂/CO₂ or formate, but not acetate, secondary alcohols, methylamines, methanol or ethanol for growth and methane production. Yeast extract is required for growth. The cell morphology is coccoid, with a diameter of 0.8-1.2 µm, and the cell envelope is composed of S-layer protein with M_r about 137.00 kDa. Cells possess multiple flagella and usually occur singly. Strain FWC-SCC4^T grows at a temperature range of 20-40 °C (optimum 37 °C) and a pH range of 5.4-7.2 (optimum 7.0). The NaCl range for growth is 0-0.86 M (optimum 0.09 M). The result of phylogenetic analysis of 16S rRNA gene sequences indicates that the most closely related species are Methanoplanus limicola M3^T and Methanoplanus endosymbiosus MC1^T, with similarities of 95.95 and 95.63%, respectively. The G+C content of the genomic DNA is 40.3 mol%. The overall genome-relatedness indexes (OGRIs) and concatenated ribosomal protein (RBP) phylogenic analysis indicate that strain FWC-SCC4^T is a novel lineage of Methanomicrobiaceae. In addition to strain FWC-SCC4^T, the differences between Methanomicrobium antiquum MobH^T and Methanomicrobium mobile BP^T demonstrated by comparative analysis of genomic G+C content and phylogenetic analysis with non-type strain genomes are enough to support the establishment of a novel genus. In conclusion, strain FWC-SCC4^T (BCRC AR10058^T= NBRC 114595^T) is proposed as the type strain of Methanochimaera problematica gen. nov., sp. nov., and Methanoeremita antiquus gen. nov., comb. nov. is proposed as the new name for Methanomicrobium antiquum MobH^T (=DSM 21220^T= NBRC 104160^T).

Three Gram-stain-positive aerobic bacteria, characterized by branched mycelia with putative sporangia, were isolated from forest soil inside a decayed bamboo stem from a geothermal area in West Java, Indonesia. The strain S3.2.2.5^T grew at 15-37 °C (optimum 30 °C), at pH 5.0-7.0 (optimum 7.0) and in the presence of 0-1% NaCl (optimum 0%). Strain S3.2.2.5^T was able to hydrolyse cellulose, xylan, starch and skim milk. The cell-wall sugars were composed of xylose and mannose, and the peptidoglycan hydrolysates contained d-glutamic acid, glycine, d-alanine, l-alanine, β-alanine and l-ornithine. The major fatty acids (>10%) were anteiso-C_17:0, iso-C_17:0, C_16:1 2-OH and iso-C_16:1. The major polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, unidentified glycolipids and unidentified phospholipids. The major menaquinone was MK-9 (H₂). The results of the analysis of the phylogenetic tree based on the 16S rRNA gene indicated that these three isolates belong to the genus Dictyobacter and they were most closely related to the type strain of species Dictyobacter aurantiacus S-27^T (97.41-98.00%). The strain S3.2.2.5^T exhibited a genome size of 9.41 Mbp, which was significantly larger than the known Dictyobacter species. The G+C content was 54.3 mol%. The average nucleotide identity (90.77%) and the digital DNA-DNA hybridization values (42.6%) between strain S3.2.2.5^T and D. aurantiacus S-27^T were below the threshold value for species delineation. Based on the phenotypic, chemotaxonomic and molecular characteristics of strain S3.2.2.5^T, a novel species of the genus Dictyobacter, for which the name Dictyobacter halimunensis sp. nov., is proposed. The type strain is S3.2.2.5^T (= UICC B-128^T = CGMCC 1.61913^T = KCTC 43728^T).

A novel Gram-stain-positive, black-pigmented bacterium, designated as WL48A ^T, was isolated from the surface of badland sedimentary rock in the Red Desert of Wyoming and characterized using a polyphasic taxonomic approach. Good growth occurred at 28-32 °C, pH 7-9, and NaCl less than 1% (w/v). Colonies, growing well on International Streptomyces Project media (ISP) 3 and ISP 7, were black and adhering to the agar. Phylogenetic analyses based on 16S rRNA gene and draft genome sequences showed that strain WL48A^T belongs to the family Geodermatophilaceae, forming a distinct sub-branch with Geodermatophilus bullaregiensis DSM 46841^T. The organism showed 16S rRNA gene sequence similarity of 98.8% with G. bullaregiensis DSM 46841^T. Digital DNA-DNA hybridization value between the genome sequences of strain WL48A ^T and G. bullaregiensis DSM 46841^T was 51.8%, below the threshold of 70% for prokaryotic species delineation. The chemotaxonomic investigation revealed the presence of galactose, glucose, mannose, xylose and ribose as well as meso-DAP in the peptidoglycan layer. The polar lipid profiles contained phosphatidylcholine (PC), phosphatidylinositol (PI), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) phosphoglycolipid, phospholipids and an unidentified lipid. The menaquinone profile consisted of MK-9(H₄) (98.2%) and MK-9(H₂) (10.8%). The major fatty acid profile (>15%) comprised iso-C_15 : 0 and iso-C_16 : 0. Based on phenotypic, genetic and genomic data, strain WL48A^T (=DSM 116197^T = NCIMB 15483^T=NCCB 100957^T =ATCC TSD-376^T) merits to be considered as a novel species for which the name Geodermatophilus maliterrae sp. nov. is proposed.

A novel Stenotrophomonas species was isolated as a contaminant in viral transport media at the District of Columbia Department of Forensic Sciences Public Health Laboratory. Phylogenomic and biochemical analyses of the isolate determined that it represented a novel species within Stenotrophomonas. Related strains in public genome databases suggested that this novel species is associated with clinically acquired infections, similar to closely related Stenotrophomonas maltophilia. The name Stenotrophomonas forensis sp. nov. is proposed. Comparative genomic and phylogenetic analyses of the S. maltophilia complex reveal that Stenotrophomonas africana is an independent species and is not a later heterotypic synonym of S. maltophilia. We also propose the transfer of two misclassified Pseudomonas species into Stenotrophomonas as Stenotrophomonas beteli comb. nov. and Stenotrophomonas hibiscicola comb. nov. The type strain for S. forensis sp. nov. is DFS-20110405^T (=ATCC TSD-272^T=NCTC 14893^T).

A new species of bacterial predator (PP10^T) was isolated from a biocrust sample taken from near Potter Cove, King George Island, Antarctica (62°14'15.62″S 58°43'15.65″W). The Bdellovibrio and like organism was vibrio-shaped and employed a single polar flagellum for motility. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that this isolate clustered within the genus Bacteriovorax in the family Bacteriovoracaceae. The 16S rRNA gene sequence similarities between isolate PP10^T and the type strain (Bacteriovorax stolpii DSM 12778^T) were only 97.14%. The draft genome of PP10^T has a size of 4.243 Mbps, with 4148 genes and a G+C content of 38.49%. While the optimal temperature for its growth was 25 °C, PP10^T was active at 4 °C, classifying it as psychrotolerant. The results of genetic and physiological tests indicated phenotypic differentiation of strain PP10^T from the type strain Bx. stolpii DSM 12778^T. Based on physiological and phylogenetic analyses, as well as the prey spectrum, isolate PP10 represents a novel species within the genus Bacteriovorax, for which the name Bacteriovorax antarcticus sp. nov. is proposed. The type strain is PP10^T (= KCTC 8097^T = DSM 116241^T).

Two yeast strains, NYNU 224191 and NYNU 22411, were isolated from plant leaves of Cyclobalanopsis jenseniana and Schisandra sp. harvested from Qingyuan Mountain, Quanzhou City, Fujian Province, southeast China. Molecular phylogenetic analyses demonstrated that these two strains represent a novel species in the genus Meira. They are more closely related to M. marina, M. nashicola, M. plantarum and M. pileae than other Meira species based on phylogenetic analysis of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit (LSU) rRNA gene. The novel species differed from its closest relatives, M. marina, M. nashicola, M. plantarum and M. pileae, by 1.8-2% sequence divergence (11-12 substitutions and 1-2 gaps) in the D1/D2 domain and over 6.7% sequence divergence (40-60 substitutions and 53-77 gaps) in the ITS region, respectively. We propose the name Meira qingyuanensis sp. nov. (Holotype CICC 33567; Mycobank MB 855328) for the new species, which differs phenotypically from M. marina, M. plantarum and M. pileae in its ability to assimilate methyl-α-d-glucoside and the inability to assimilate salicin, and from M. nashicola in its ability to assimilate nitrate and nitrite and grow at 30 °C.

Three Gram-negative, aerobic and non-motile bacterial strains, BT552^T, BT553^T and KR1UV-12^T, were isolated from soil samples in Gwangju-si and Gangneung-si, the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequence showed that strains BT552^T, BT553^T and KR1UV-12^T clustered to a distinct clade within the family Sphingomonadaceae (order Sphingomonadales, class Alphaproteobacteria). The strains exhibited the highest genetic similarity with representatives of the genus Sphingomonas; moreover, strains BT552^T and BT553^T tightly clustered with Sphingomonas melonis DAPP-PG 224^T (98.2 and 98.1 %) and Sphingomonas aquatilis JSS-7^T (98.1 and 98.0 %), while strain KR1UV-12^T clustered with S. melonis DAPP-PG 224^T (97.9%) and Sphingomonas rubra BH3^T (97.8%), respectively. The major cellular fatty acids of all three strains were summed feature 8 (C_18:1 ω7c/C_18:1 ω6c), comprising 44.7, 46.4 and 48.5%. Additionally, their respiratory quinone is Q-10, and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids, sphingolipid and phosphatidylcholine. They all grow well at an optimum temperature of 25 °C, at pH 7. The draft genomes of strains BT552^T, BT553^T and KR1UV-12^T measures 4 035 561 bp, 3 941 714 bp and 3 418 792 bp, respectively, comprising 3 804 3648 and 3236 coding sequences and 50, 48 and 45 RNA genes. The average nucleotide identity analysis and digital DNA-DNA hybridization values between BT552^T, BT553^T and KR1UV-12^T and closely related Sphingomonas species range from 72.7 to 80.2% and 19.4 to 24.3%, respectively. Based on phenotypic, genotypic and chemotaxonomic data, these three strains BT552^T, BT553^T and KR1UV-12^T represent three novel bacterial species within the genus Sphingomonas for which the names Sphingomonas longa sp. nov. (type strain BT552^T= KCTC 82094^T =NBRC 114993^T), Sphingomonas mollis sp. nov. (type strain BT553^T =KCTC 82095^T =NBRC 114994^T) and Sphingomonas aurea sp. nov. (type strain KR1UV-12^T = KCTC 92959^T = TBRC 18506^T) are proposed.

A Gram-stain-negative, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP47G, was isolated from the hindgut of a silver drummer (Kyphosus sydneyanus) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on the 16S rRNA gene sequence of the isolate indicated that it belonged to the family Oscillospiraceae in the phylum Bacillota. The gene sequence of BP47G was most similar to Oscillibacter valericigenes with 95.23% sequence identity. Isolate BP47G grew on agar medium containing mannitol and fish gut fluid as the sole carbon sources. Clear colonies of ~1 mm diameter grew within a week at 20-28 °C (optimum 28 °C) and pH 7.1-8.5 (optimum 8.5). BP47G tolerated the addition to the medium of up to 1% NaCl. Formate and butyrate were the major fermentation products. The major cellular fatty acids were C_12:0, C_13:0, iso-C_14:0, C_16:0 and C_16:1 cis 7. Genomic analyses comparing BP47G with its closest relatives indicated low genomic relatedness based on the average nucleotide identity, average amino acid identity, percentage of conserved protein and in silico DNA-DNA hybridization. Supported by the phenotypic and taxonomic characteristics observed in this study, a novel genus and species Bengtsoniella intestinalis gen. nov., sp. nov. is proposed for isolate BP47G (=ICMP 24688=JCM 35770).

Six Pseudomonas strains isolated from muskmelon and watermelon seedlings affected by stem rot and wilting in Serbia were reported as P. cichorii based on pathogenicity, LOPAT and cell wall fatty acid analyses. Recent bacterial isolates from cucurbit crops displaying P. cichorii-like symptoms in Alabama, USA, were identified as P. capsici, prompting polyphasic re-evaluation of the Serbian strains. All six strains were found to cause severe disease in watermelon and squash seedlings under greenhouse conditions. Strains KFB 138 and KFB 140 underwent whole-genome sequencing and were found to have the highest level of 16S rRNA similarity to P. lijiangensis LJ2^T (both 99.87%). Phylogenies based on housekeeping genes and core-genome analysis placed both strains into phylogroup 11 of the Pseudomonas syringae species complex, with KFB 138 forming a lineage basal to all other phylogroup 11 members. In core-genome phylogeny, KFB 140 was placed into a clade alongside P. lijiangensis LJ2^T. Average nucleotide identity based on blast (ANIb) identified KFB 140 as a member of P. lijiangensis (95.85%), though KFB 138 did not produce an ANIb value over 95% to any Pseudomonas type strain to which it was compared. Values for in silico DNA-DNA hybridization for both strains were below 70% to all reference strains tested, though KFB 140 was found to be most similar to P. lijiangensis (68.2%). KFB 138 and KFB 140 were further characterized using the online Type Genome Server, biochemical profiling with the Biolog Gen III MicroPlate system, matrix-assisted laser desorption/ionization time of flight mass spectrometry and imaged with transmission electron microscopy. From the results of the above analyses, we conclude that KFB 140 is a member of the species P. lijiangensis and that KFB 138 represents a novel Pseudomonas species, for which we propose the name Pseudomonas serbiensis (KFB 138^T, NCPPB 4762=LMG 33366), named for its location of isolation.