International journal of systematic and evolutionary microbiology最新文献

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.

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 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.

Two Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacteria, designated as strains S88^T and W115^T, exhibiting catalase- and oxidase-positive reactions, were isolated from marine red algae in South Korea. Strain S88^T exhibited growth at 20-30 °C, pH 6.0-9.0 and 2.0-5.0% (w/v) NaCl, while strain W115^T grew at 20-30 °C, pH 7.0-9.0 and 2.0-5.0% (w/v) NaCl. Strain S88^T contained summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_16 : 0 and C_16 : 0 2-OH as major fatty acids (>5%), with major polar lipids being phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. Strain W115^T contained summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and C_16 : 0 as major fatty acids (>5%), with major polar lipids including phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and unidentified lipids. Ubiquinone-10 was the sole respiratory quinone in both strains, and the genomic DNA G+C contents were 57.0% for strain S88^T and 56.5% for strain W115^T. Despite 99.86% 16S rRNA gene sequence similarity, strains S88^T and W115^T shared 88.8% average nucleotide identity (ANI) and 36.8% digital DNA-DNA hybridization (dDDH) value, indicating different species. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences, respectively, revealed that strains S88^T and W115^T formed a phylogenetic lineage within the genus Roseovarius. ANI and dDDH values of both strains with other type strains were less than 73.7 and 20.3%, respectively, confirming that they represent novel species. Based on phenotypic, chemotaxonomic and molecular characteristics, strains S88^T and W115^T represent two novel species of the genus Roseovarius, for which the names Roseovarius phycicola sp. nov. (S88^T =KACC 23423^T =JCM 36647^T) and Roseovarius rhodophyticola sp. nov. (W115^T =KACC 23690^T =JCM 36651^T) are proposed, respectively.

Six urease-negative Campylobacter strains were isolated from cattle faeces over a 19-month period from 2009 to 2010. These strains were initially identified as Campylobacter sputorum by 16S rRNA gene and atpA typing. Initial studies characterizing these strains by multilocus sequence typing and genome sequencing further supported their classification as C. sputorum but indicated that these strains form a divergent clade within the species. A polyphasic study was undertaken here to clarify their taxonomic position. Phylogenetic analyses were performed based on 16S rRNA gene sequences and the concatenated sequences of 330 core genes, with the latter analysis also placing the six strains into a clade distinct from the three C. sputorum biovars. Pairwise digital DNA-DNA hybridization values identified these strains as C. sputorum, and the pairwise average nucleotide identity values were consistent with those observed between current Campylobacter subspecies pairs. Standard phenotypic testing was also performed. All strains are microaerobic, anaerobic, motile, Gram-negative and oxidase- and catalase-positive; cells are curved rods or spirals. Strains can be distinguished from the C. sputorum biovars by the presence of alkaline phosphatase activity and triphenyltetrazolium chloride reduction and absence of nitrate reduction. The data presented here show that these strains represent a novel subspecies within C. sputorum, for which the name C. sputorum subsp. bovis subsp. nov. (type strain RM8705^T=LMG 32300^T=CCUG 75470^T) is proposed.

Two Gram-stain-negative bacterial strains, BSw22131^T and DMSP-1^T, were isolated from seawater of Arctic Kongsfjorden in the Ny-Ålesund area, Svalbard. Strains BSw22131^T and DMSP-1^T were within the genus Pseudomonas and presented 98.1 and 99.8% 16S rRNA gene sequence similarity to Pseudomonas piscicola P50^T and Pseudomonas paracarnis V5/DAB/2/5^T, respectively. However, the results of multilocus sequence analysis (concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences) and whole-genome sequence analysis indicated that BSw22131^T and DMSP-1^T were most closely related to Pseudomonas petrae P2653^T and Pseudomonas lactis DSM 29167^T, respectively. The genome G+C contents of strains BSw22131^T and DMSP-1^T were 58.2 and 60.0%, respectively. The two isolates presented digital DNA-DNA hybridization and average nucleotide identity values of less than 70 and 96%, respectively, with type strain genomes of their close relatives. BSw22131^T contained summed feature 3 (C_16 : 1  ω6c/C1_6 : 1  ω7c), C_16 : 0 and summed feature 8 (C_18 : 1  ω6c/C1_8 : 1  ω7c) as the major cellular fatty acids, whereas DMSP-1^T contained an additional C_17 : 0-cyclo as the major fatty acid. The major quinones of both strains were Q-9 (57.5-77.2%) and Q-8 (22.8-37.2%), and their major cellular polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. BSw22131^T could be differentiated from its related species by positive ornithine decarboxylase, esterase (C8) and l-rhamnose and d-fructose-6-PO₄ utilization, whereas DMSP-1^T could be differentiated by positive acid phosphatase but negative p-hydroxyphenylacetic acid utilization. The two strains were negative for the reduction of nitrates but contained genes related to dimethylsulfoniopropionate catabolism. The results of the polyphasic taxonomy analysis revealed that strains BSw22131^T and DMSP-1^T represent two novel species of the genus Pseudomonas, for which the names Pseudomonas huanghezhanensis sp. nov. (type strain BSw22131^T = CCTCC AB 2019135^T = JCM 36635^T = DSM 117336^T) and Pseudomonas fjordensis sp. nov. (type strain DMSP-1^T = CCTCC AB 2019124^T = JCM 36636^T = DSM 117337^T) are proposed.

Two novel strains were isolated from the mudflat of Suaeda japonica colonies in Incheon, Republic of Korea. Designated as DGU5^T and DGU6^T, these strains were Gram-stain-negative, facultatively anaerobic and rod-shaped and had yellowish colonies. Both strains were determined to belong to the genus Aurantiacibacter through phylogenetic analysis of their 16S rRNA sequences and draft genomes. The cells of strain DGU5^T were non-motile and grew at temperatures ranging between 7-45°C (optimum, 25-30°C), pH 6.0-10.0 (optimum, 7.0-8.0) and in the presence of 0-11.0% NaCl (optimum, 2.0%). The cells of strain DGU6T were non-motile and grew in temperatures ranging from 10-45 °C (optimum, 30-35°C), pH 3.0-10.0 (optimum, 7.0-8.0) and in the presence of 0-11.0% NaCl (optimum, 2.0%). Overall genome relatedness index calculations revealed average nucleotide identity values (72.3-88.6%) and digital DNA-DNA hybridization values (18.8-35.9%) aligning with those of the genus Aurantiacibacter. The major fatty acids in both strains were C_17:1 ω6c and summed feature 8 (C_18:1 ω6c/C_18:1 ω7c), while the predominant polar lipids were sphingoglycolipid, phosphatidylglycerol, and diphosphatidylglycerol. Phylogenetic, average nucleotide identity, digital DNA-DNA hybridization, physiological, and biochemical data collectively demonstrated the distinctiveness of the novel strains from other members within the family Erythrobacteraceae. We propose the names A. flavus sp. nov. (type strain DGU5^T = KACC 23720^T = TBRC 19015^T) and A. gilvus sp. nov. (type strain DGU6^T = KACC 23721^T = TBRC 19016^T) for the two strains.

A novel actinomycete, designated strain ZYX-F-249^T, was isolated from the gill of a leopard coral grouper in Yongxing Island, Hainan Province, China. Based on 16S rRNA gene sequence analysis, strain ZYX-F-249^T belonged to the genus Microbispora, with high similarities to Microbispora rosea ATCC 12950^T (98.7 %), Microbispora hainanensis 211020^T (98.5 %), Microbispora clausenae CLES2^T (98.4 %), Microbispora bryophytorum NEAU-TX2-2^T (98.1 %) and Microbispora oryzaeRL4-1S^T (98.0 %). Phylogenetic analysis of the 16S rRNA gene sequence of strain ZYX-F-249^T showed that the strain formed a stable subclade with Microbispora rosea ATCC 12950^T in the genus Microbispora. The cell wall of the novel isolate contained meso-diaminopimelic acid, while whole-cell sugars were madurose, glucose and ribose. The predominant menaquinones were MK-9(H₆), MK-9(H₄), MK-9(H₂) and MK-9(H₀). The characteristic phospholipids (PLs) were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol mannoside, glycophospholipids and an unknown PL. The major cellular fatty acids (>10%) were iso-C_16 : 0 and iso-C_18 : 0. Genome sequencing showed a DNA G+C content of 71.6%. The low average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values demonstrated that strain ZYX-F-249^T could be readily distinguished from closely related species. Based on data from these phylogenetic, chemotaxonomic and physiological characteristics, strain ZYX-F-249^T represents a novel species of the genus Microbispora, for which the name Microbispora maris sp. nov. is proposed. The type strain is ZYX-F-249^T (=CCTCC AA 2023030^T =JCM 36778^T).

The order Caryophanales, belonging to class Bacilli, is globally distributed in various ecosystems. Currently, this order comprised 12 families that show vast phenotypic, ecological and genotypic variation. The classification of Caryophanales at the family level is currently mainly based on 16S rRNA gene sequencing analysis and the presence of shared phenotypic characteristics, resulting in noticeable anomalies. Our present study revises the taxonomy of Caryophanales based on 1080 available high-quality genome sequences of type strains. The evaluated parameters included the core-genome phylogeny, pairwise average aa identity, lineage-specific core genes, physiological criteria and ecological parameters. Based on the results of this polyphasic approach, we propose that the order Caryophanales be reclassified into 41 families, which include the existing 12 families, 17 families in a recent Validation List in the IJSEM (Validation List no. 215) and 12 novel families for which we propose the names Aureibacillaceae, Cytobacillaceae, Domibacillaceae, Falsibacillaceae, Heyndrickxiaceae, Lottiidibacillaceae, Oxalophagaceae, Pradoshiaceae, Rossellomoreaceae, Schinkiaceae, Sulfoacidibacillaceae and Sutcliffiellaceae. This work represents a genomic sequence-based and systematic framework for classifying the order Caryophanales at the family level, providing new insights into its evolution.

The photosynthetic microorganisms within the coral holobiont produce energy and organic compounds through photosynthesis, which are vital for the biocalcification and heat tolerance of coral hosts. However, aerobic anoxygenic phototrophic bacteria (AAPB), which are one of the most important photosynthetic microorganisms, have not been thoroughly investigated in this environment. In this study, a novel AAPB, SCSIO 66989^T, was isolated from the reef-building coral Favia sp. and considered a beneficial microorganism for corals (BMC). The polyphasic taxonomic analysis showed that it had the highest similarities with Parasphingorhabdus litoris DSM 22379^T (95.9%) and Altererythrobacter ishigakiensis ATCC BAA-2084^T (95.7%). Phylogenetic analysis showed that it formed an independent clade, distinguishing it from other genera within the family Sphingomonadaceae. The predominant fatty acids were C_18 : 1  ω7c and/or C_18 : 1  ω6c and C_16 : 0. The major respiratory quinone was ubiquinone-10 (Q-10). Sphingolipid, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the diagnostic polar lipids. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between SCSIO 66989^T and the type strains of P. litoris DSM 22379^T and A. ishigakiensis ATCC BAA-2084^T were 69.2-70.0%, 58.6-61.2% and 19.2-19.7%, respectively. These results indicate that strain SCSIO 66989^T represents a new species of a novel genus in the family Sphingomonadaceae, for which the name Alterisphingorhabdus coralli gen. nov. sp. nov. is proposed.