International journal of systematic and evolutionary microbiology最新文献

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.

Two novel bifidobacteria (designated F806-1^T and F814-1.1) isolated from the gut of honeybee (Apis mellifera) were characterized in the present study. 16S rRNA gene sequence analysis indicated that strains F806-1^T and F814-1.1 belonged to the Bifidobacterium asteroides group and were most closely related to Bifidobacterium apousia W8102^T and Bifidobacterium polysaccharolyticum W8117^T, having 98.9-99.4% 16S rRNA gene sequence similarities. Strains F806-1^T and F814-1.1 had the highest 16S rRNA gene sequence similarities (99.1 and 99.4 %) with B. polysaccharolyticum W8117^T. Strains F806-1^T and F814-1.1 had 73.2-90.5% average nucleotide identity, 21.5-40.8% digital DNA-DNA hybridization and 67.4-92.5% average amino acid identity values with type strains of all species in the B. asteroides group. Acid production from d-arabinose, l-arabinose, d-xylose, l-xylose, d-galactose, d-fructose, d-mannose and methyl-α-d-glucopyranoside; tolerance to 3% NaCl and activity of cystine arylamidase, N-acetyl-β-glucosaminidase, α-mannosidase and α-fucosidase could differentiate strains F806-1^T and F814-1.1 from the type strain of B. polysaccharolyticum. Based on the data obtained in the present study, a novel species, Bifidobacterium apicola sp. nov., is proposed, and the type strain is F806-1^T (=CCTCC AB 2024129^T=JCM 37002^T).

A bacterial strain was isolated from pathogenic lesions of Acer campestre tree leaves from the Teutoburg Forest in North Rhine-Westphalia, Germany, by culture on non-selective agar plates. 16S rRNA sequencing revealed 100% similarity to Sanguibacter keddieii and Sanguibacter inulinus, as well as 99% similarity to Sanguibacter gelidistatuariae and Sanguibacter antarcticus. Here, we used genome-based taxonomy with the Type (Strain) Genome Server (TYGS), which suggests the isolation of a novel prokaryotic strain. According to TYGS-analysis, using whole genome digital DNA-DNA hybridization, only 65.5% similarity to the closest relative S. inulinus was revealed, suggesting a novel species. Growth was observed at both aerobic and anaerobic conditions. Bacterial cells depicted coryneform motile rods, with a length of 1.1-3.3 µm and a constant diameter of 0.5 µm. Cells did not form spores under the tested conditions and stain Gram-positive. Growth occurred between 0.5 and 4% NaCl (optimal: 1%), at pH 5.5-9.5 (optimal: 8.0-9.0). The strain was mesophilic with an optimal growth at 25°C. Major cellular fatty acids of the novel strain were anteiso-C_15 : 0 and C_16 : 0.

Sphingobacterium, as the type genus of the family Sphingobacteriaceae, comprises a diverse array of species found in various environments. In this study, we aim to reassess and elucidate the taxonomic relationships of Sphingobacterium species. Based on 16S rRNA gene sequences, the phylogeny of 70 validly published Sphingobacterium species was reconstructed. Of which, 50 species with available genomes were further subjected to overall genome relatedness indices (OGRI) analysis, resulting in the identification of distinct pairs of closely related species. One such pair, consisting of the type strains of Sphingobacterium soli and Sphingobacterium cellulitidis, exhibited an average nucleotide identity (ANI) of 97.7%, a digital DNA-DNA hybridization (dDDH) of 80.1% and an average amino acid identity (AAI) of 98.3%, alongside a 16S rRNA gene sequence similarity of 99.8%. Based on the phylogenetic, OGRI and phenotypical evidence, we propose S. soli as a later heterotypic synonym of S. cellulitidis. Additionally, another pair of type strains, Sphingobacterium siyangense and Sphingobacterium cladoniae, possessed ANI, dDDH, AAI and 16S rRNA gene sequence similarity values of 96.3, 70.1, 96.0 and 99.0%, respectively. These values, together with differences in phenotypic traits, support the proposal of two subspecies within this taxonomic lineage. Thus, we propose the establishment of two new subspecies, S. siyangense subsp. siyangense subsp. nov. and S. siyangense subsp. cladoniae subsp. nov.

Two Gram-stain-negative, aerobic, rod-shaped, non-endospore-forming bacteria, designated as strain MH1^T and MH2^T, were isolated from branches of wilted pepper plants (Capsicum annuum) collected from a farmland in Machong town, Guangdong, China, and investigated using a polyphasic approach. MH1^T grew at temperatures of 4-42 °C (optimum 28 °C), with 0-6.0 % (w/v) NaCl and at pH 4.0-10.0 (optimum pH 4.0). MH2^T grew at temperatures of 4-42 °C (optimum 28 °C), with 0-6.0% (w/v) NaCl and at pH 4.0-10.0 (optimum pH 5.0). Analysis of the 16S rRNA gene sequence indicated that MH1^T belongs to Stenotrophomonas and MH2^T belongs to Pseudomonas. Genome-based phylogenetic analysis further established that MH1^T shares the closest evolutionary relationships with Stenotrophomonas humi DSM 18929 and Stenotrophomonas terrae DSM 18941, and MH2^T is sister to Pseudomonas wayambapalatensis RW3S1. Whole-genome comparisons between MH1^T and known Stenotrophomonas species revealed average nucleotide identity (ANI) values up to 84.5%, as well as digital DNA-DNA hybridization (dDDH) values up to 28.3%, both substantially lower than the accepted thresholds for species delineation (ANI: 95%; dDDH: 70%). The ANI and dDDH values between MH2^T and known Pseudomonas species were at most 94.6 and 59.2 %, respectively. Additional biochemical and physiological analyses further support that MH1^T and MH2^T represent a novel species in Stenotrophomonas and Pseudomonas, respectively. Notably, the differences in carbon source utilization could differentiate MH1^T and its close relatives in Stenotrophomonas. The major fatty acids were iso-C_15 : 0, iso-C_16 : 0 and iso-C_14 : 0 for MH1^T and were C_16 : 0, C_18 : 1 ω7c/C_18 : 1 ω6c (summed feature 8), C_16 : 1 ω7c/C_16 : 1 ω6c (summed feature 3) and C_17 : 0 cyclo for MH2^T. Therefore, we propose a new species Stenotrophomonas capsici sp. nov., with MH1^T (=GDMCC 1.3749^T=JCM 36317^T) as the type strain, and a new species Pseudomonas machongensis sp. nov., with MH2^T (=GDMCC 1.3750^T=JCM 36318^T) as the type strain. The MH1^T genome has a size of 4.18 Mb and a GC-content of 67.19 mol%, while the MH2^T genome has a size of 5.71 Mb and a GC-content of 63.12 mol%.

In the survey of yeast diversity in high-temperature Daqu, which is a fermentation starter for Chinese sauce-flavoured Baijiu, six yeast strains representing one novel species of the genus Starmerella were isolated from samples of Daqu and surrounding environments collected in Zunyi city, Guizhou Province, China. Phylogenetic analyses of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene indicate that these six strains are conspecific with three other strains isolated from flowers and duckweed collected in Samoa, India and Thailand. The representative strain QFC-8 of the new species differs from the closet species Starmerella caucasica resolved by the D1/D2 sequence analysis by 13 (3.1 %, 12 substitutions and 1 gap) and 40 (10.3 %, 9 substitutions and 31 gaps) mismatches in the D1/D2 domain and ITS region, respectively. The results suggest that the novel group represents an undescribed species in the genus Starmerella, for which the name Starmerella fangiana sp. nov. is proposed. The holotype strain is CGMCC 2.7773.

The present study was carried out to clarify the taxonomic assignment of two closely related Spiroplasma species. Genomic information for 26 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Spiroplasma atrichopogonis (Koerber et al. 2005) and Spiroplasma mirum (Tully et al. 1982), are conspecific. The 16S rRNA gene sequences of the two species possess 99.78% sequence similarity. Furthermore, whole-genome sequence comparisons showed that S. atrichopogonis GNAT3597^T (CP011855.1) GCA 001029245.1 and S. mirum ATCC 29335^T (CP002082.1) GCA 000517365.1 shared 99.99% average nucleotide identity, 99.99% average amino acid identity and 100% digital DNA-DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Furthermore, the phylogenomic analysis based on the core proteome of the strains under study confirmed that S. atrichopogonis GNAT3597^T (CP011855.1) GCA 001029245.1 and S. mirum ATCC 29335^T (CP002082.1) GCA 000517365.1 formed a monophyletic clade. Based on this evidence, we propose the reclassification of S. atrichopogonis Koerber et al. 2005 as a later heterotypic synonym of S. mirum Tully et al. 1982.

A bacterial strain designated HT6-4^T was isolated from soil samples collected from the Flaming Mountain, Xinjiang, PR China. The purpose of this study was to describe a novel species and its characteristics, through genome sequencing and analysis of the relationship between the members of the genus Blastococcus, and explore the antiradiation, antioxidation and antibacterial capabilities of strain HT6-4^T. The polyphasic study confirmed the affiliation of strain HT6-4^T with the genus Blastococcus. Strain HT6-4^T was aerobic, Gram-stain-positive, non-budding, non-motile, catalase-positive and oxidase-negative. It grew at 10-37 °C, pH 5.0-8.0 and 0-4% (w/v) NaCl. Colonies were circular, smooth and bright orange in colour. In addition, strain HT6-4^T was drought tolerant. The predominant menaquinone was MK-9, with MK-8 as the minor component. The polar lipids of strain HT6-4^T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phospholipids, an unidentified aminolipid and two unidentified phospholipids. Whole-cell hydrolysates contain meso-diaminopimelic acid as the diagnostic diamino acid and ribose and galactose as diagnostic sugars. Its major fatty acids were iso-C_{16 :  0}, C_{17 :  1} ω8c and C_{18 :  1} ω9c. The genome of strain HT6-4^T was 4.30 Mb in the whole-genome shotgun project. The G+C content was 73.9 mol%. The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain HT6-4^T was closely related to Blastococcus jejuensis KST3-10^T(97.9%), Blastococcus capsensis BMG 804^T(97.8%), Blastococcus aggregatus DSM 4725^T(97.5%), Blastococcus saxobsidens BC 444^T(97.5%), Blastococcus xanthinilyticus BMG 862^T(97.5%) and Blastococcus litoris GP-S2-8^T(97.5%). The average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values among strain HT6-4^T and B. jejuensis KST3-10^T, B. capsensis BMG 804^T, B. aggregatus DSM 4725^T, B. saxobsidens BC 444^T, B. xanthinilyticus BMG 862^T and B. litoris GP-S2-8^T were below the species delimitation thresholds. The genome of strain HT6-4^T contained antiradiation genes, antioxidant genes and antibacterial genes. Based on its morphological, physiological and chemical taxonomic characteristics, strain HT6-4^T (=KCTC 59234^T =GDMCC 1.4386^T) should be classified as a novel species of the genus Blastococcus with the proposed name Blastococcus montanus sp. nov.

Three Gram-stain-negative, aerobic, short rod-shaped and motile strains (FXH3W^T, SHGZ20W and SMYT11W^T) were isolated from freshwater environments in China. Comparisons based on the 16S rRNA gene sequences indicated that strains FXH3W^T and SHGZ20W showed the highest 16S rRNA gene sequence similarity of about 99.6% to 'Luteimonas cellulosilyticus' MIC 1.5, and strain SMYT11W^T showed the highest 16S rRNA gene sequence similarity of 99.8% to Luteimonas fraxinea D4P002^T, respectively. Observing the phylogenetic trees reconstructed based on the 16S rRNA gene sequences, the species of genera Luteimonas and Lysobacter were not monophyletic and often mixed together. The further reconstructed phylogenomic tree and Genome Taxonomy Database also showed that the species of both genera were polyphyletic, implying that the current taxonomic status of the species of both genera was questionable. The calculated OrthoANIu, digital DNA-DNA hybridization and average amino acid sequence identity (AAI) values supported that strains FXH3W^T and SHGZ20W should belong to the same novel species and strain SMYT11W^T should also represent an independent novel species. Combining the AAI values and phylogenomic analyses, the species of genera Luteimonas and Lysobacter should be reassigned to 12 genera (Luteimonas, Lysobacter, Cognatiluteimonas, Noviluteimonas, Pseudoluteimonas, Solilutibacter, Agrilutibacter, Cognatilysobacter, Marilutibacter, Novilysobacter, Montanilutibacter and Aerolutibacter). The AAI values 69.5-76.0% were also proposed as the Lysobacteraceae-specific thresholds for genus delineation. Strain SMYT11W^T should represent a novel species of the genus Luteimonas, for which the name Luteimonas flava sp. nov. (type strains SMYT11W^T=GDMCC 1.4275^T=KCTC 8304^T) is proposed. Strains FXH3W^T and SHGZ20W should represent a novel species of a new genus Aquilutibacter rugosus gen. nov., sp. nov. The type strain of the type species is FXH3W^T (=GDMCC 1.4096^T=KCTC 8154^T).

A Gram-stain-negative, facultatively aerobic, rod-shaped and motile bacterium, designated as CCTCC AB 2023082^T, was isolated from leaves of Calanthe triplicata in China. Optimal growth occurred at 4-45 ℃ and pH 4.0-10.0 and in the presence of 0-7% (w/v) NaCl. The major fatty acids of the strain CCTCC AB 2023082^T were C16 : 0, sum of C16 : 1 ω7c/C16 : 1 ω6c, C17 : 0 cyclo and C18 : 1 ω7c. The polar lipids included unidentified lipids, phospholipids, phosphatidylethanolamine, phosphatidylglycerol and amino phospholipid. The DNA G+C content of strain CCTCC AB 2023082^T was 54.2 mol%. 16S rRNA gene sequence analysis indicated that strain CCTCC AB 2023082^T formed a distinct lineage within the genus Kosakonia and exhibited the highest similarity to Kosakonia quasisacchari, with a 97.9% 16S rRNA gene sequence similarity. Moreover, the preliminary analysis of the organism's genome suggested its potential as a biostimulant for augmenting plant growth. According to its genotypic, phenotypic, phylogenetic and chemotaxonomic characteristics, strain CCTCC AB 2023082^T should be categorized as a novel species in the genus Kosakonia. The novel species was named Kosakonia calanthes sp. nov., and its type strain is CCTCC AB 2023082^T (=JCM 36393^T).