International journal of systematic and evolutionary microbiology最新文献

A polyphasic taxonomic study was carried out on strain T5W1^T, isolated from the roots of the aquatic plant Spirodela polyrhiza. This isolate is Gram-negative, rod-shaped, motile, aerobic and non-pigmented. Nearly complete 16S rRNA gene sequence homology related the strain to Pseudomonas, with 98.4% similarity to P. guineae, P. peli and P. leptonychotis. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbour of T5W1^T showed differences at the species level, further confirmed by differences in several physiological characteristics. The main fatty acids are summed feature 3 (C_{16 : 1   ω7c} and/or C_{16 : 1   ω6c}), C_{18 : 1   ω7c}, and C_16 : 0. The DNA G+C content is 59.3 mol%. Q-9 is the primary ubiquinone found, and phosphatidylethanolamine is the dominant polar lipid, with lesser amounts of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylserine. Based on the results obtained, this bacterium is assigned to the genus Pseudomonas as a new species with the name Pseudomonas spirodelae sp. nov., type strain T5W1^T (=NRRL B-65714^T =DSM 118085^T).

Four novel nontuberculous mycobacteria were discovered from a historical strain collection at the International Reference Laboratory of Mycobacteriology at Statens Serum Institut in Copenhagen, Denmark. Phylogenetic analysis combining the 16S rrs, internal transcribed spacer and 23S rrl elements, as well as a single-copy core-gene (hsp65, rpoB+C, secA and tuf) analysis of these freeze-dried mycobacteria, clinically isolated from gastric lavage samples between 1948 and 1955, showed to be associated with type strains grouping within the Terra and Fortuitum-Vaccae clade. Phenotypic characteristics, biochemical properties and fatty acid and mycolic acid profiles supported the classification as novel strains. A genomic comparison to the closest related type strain was done by calculating average nucleotide identity and in silico DNA:DNA hybridization values, which showed 87.9% and 33.0% for Mu0050, 85.2% and 27.4% for Mu0053, 85.3% and 27.6% for Mu0083 and 93.3% and 50.1% for Mu0102, respectively. The names proposed for the new species are Mycobacterium wendilense sp. nov. (Mu0050^T=ITM 501390^T=CCUG 77525^T), Mycobacterium burgundiense sp. nov. (Mu0053^T=ITM 501391^T=CCUG 77526^T), Mycobacterium kokjensenii sp. nov. (Mu0083^T=ITM 501392^T=CCUG 77527^T) and Mycobacterium holstebronense sp. nov. (Mu0102^T=ITM 501393^T=CCUG 77528^T).

Yeast strains representing a novel asexual ascomycetous species were isolated from seven Malva sylvestris flowers. Sequencing of the chromosomal regions coding for the D1/D2 domains of the large subunit ribosomal RNA, the ITS1-5.8S-ITS2 segments and parts of the gene coding for the small subunit ribosomal RNA showed that the isolates were conspecific. Comparative analysis of these sequences and the corresponding sequences of the type strains of ascomycetous yeasts revealed that the strains represent a hitherto undescribed species belonging to the sensu stricto subclade of the genus Starmerella. The new species is osmotolerant and can develop invasive pseudohyphae, but does not form spores. For the new species, the name Starmerella aleppica f.a. (forma asexualis) is proposed. The holotype, preserved in a metabolically inactive state, is CBS 12960^T (extype cultures: 2-1361 and CCY 90-2-1, NCAIM Y.02123). The GenBank accession numbers of barcode sequences are JX515983 (D1/D2 domain), JX515985 (ITS1-5.8S-ITS2 and partial 18S rRNA gene), PQ613837 (TEF1 partial sequence) and PQ613838 (RPB2 partial sequence). MycoBank: MB855459. The analysis of the D1/D2 and internal transcribed spacer (ITS) sequences of the type strains of species of the genus identified multiple multinucleotide indels that can be used as taxonomic markers (InDel markers). The indel patterns of the subclades are very different and homogeneous within the subclades. This result reinforces the idea raised, but also refuted, in previous studies that the Starmerella subclades may represent different genera.

Following a proposal to emend Recommendation 6(7), Rule 64 and Appendix 9, Section D of the International Code of Nomenclature of Prokaryotes to regulate the formation of prokaryote names from personal names, I hereby report the outcome of the ballot on this proposal by the members of the International Committee on Systematics of Prokaryotes.

A bacterial strain, designated as A6^T, was isolated from the rhizosphere soil of a healthy muskmelon in Wenchang, Hainan Province, China. The cells of strain A6^T were Gram-negative, aerobic, short rod and motile with a single polar flagellum. Strain A6^T could tolerate up to 55.0 mM Al³⁺ and inhibited the growth of Fusarium oxysporum f. sp. melonis, which is the pathogen of muskmelon Fusarium wilt. Growth occurred at 15-37 ℃ (optimum at 30 ℃), pH 4.5-8.0 (optimum pH 6.5) and with 0-3.0 % NaCl (w/v; optimum, 0.5%). Strain A6^T shared the highest 16S rRNA gene sequence similarities with Dyella lutea Sa^T (98.0%), followed by Dyella thiooxydans ATSB10^T (98.0%), Frateuria edaphi 5GH9-34^T (97.9%), Dyella nitratireducens DHG59^T (97.7%), Frateuria defendens DHo^T (97.7%) and Frateuria soli 5GH9-11^T (97.7%). Phylogenetic trees based on 16S rRNA gene and genomic sequences indicated that strain A6^T belonged to the genus Dyella and formed a subclade with Dyella lutea Sa^T and Dyella thiooxydans ATSB10^T. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between A6^T and its closely related type strains were 78.8-80.8 %, 70.0-71.7 % and 20.5-22.1 %, respectively. The sole respiratory quinone was ubiquinone-8 (Q-8). The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified aminophospholipids (APL1-2) and three unidentified phospholipids (PL1-3). The major cellular fatty acids (≥5 %) were iso-C_17 : 0, C_16 : 0, summed feature 9 (iso-C_17 : 1  ω9c and/or C_16 : 0 10-methyl), iso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The genome size of strain A6^T was 3.7 Mb with a DNA G+C content of 65.1%. Based on the phenotypic, phylogenetic, genotypic and chemotaxonomic features, strain A6^T represents a novel species in the genus Dyella, for which Dyella aluminiiresistens A6^T sp. nov. is proposed. The type strain is A6^T (= GDMCC 1.4640^T = KCTC 92542^T).

A Gram-stain-positive, facultatively anaerobic, rod-shaped strain, designated SPB1-3^T, was isolated from tree bark. This strain exhibited heterofermentative production of dl-lactic acid from glucose. Optimal growth was observed at 25-40 °C, pH 4.0-7.0, and in the presence of 3% (w/v) NaCl. The cell wall peptidoglycan contained lysine and aspartic acid. The predominant fatty acids identified were C_16:0 and the Summed feature 7 (C_19 :1  ω7c/C_19:1  ω6c and/or C_19:1  ω6c/ω7c/19cy). The polar lipid profile included phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol, along with two unidentified phospholipids, two unidentified amino lipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain SPB1-3^T within the genus Lentilactobacillus, showing a close relation to Lentilactobacillus kosonis NBRC 111893^T (99.86%) and Lentilactobacillus curieae CCTCC M 2011381^T (98.65%). The whole genome of strain SPB1-3^T comprised 1 932 998 base pairs with 1955 coding genes and a DNA G+C content of 37.8%. Digital DNA-DNA hybridization between strain SPB1-3^T and closely related type strains ranged from 19.50 to 27.20%. The average nucleotide identity ranged from 84.21 to 85.56%, and the average amino acid identity ranged from 57.25 to 85.99%, both falling below the established thresholds for species delineation. Strain SPB1-3^T was clearly distinguishable from related Lentilactobacillus species based on its phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence similarity and whole genome analysis. Additionally, the strain exhibited radical scavenging activity at 66.92% and demonstrated 82.32% inhibition in the tyrosinase inhibitory assay. These findings support the classification of strain SPB1-3^T as a novel species within the genus Lentilactobacillus, for which the name Lentilactobacillus terminaliae sp. nov. is proposed. The type strain is SPB1-3^T (=JCM 35081^T=TISTR 10005^T).

A novel bacterium, designated 19SA41, was isolated from the air of the Icelandic volcanic island Surtsey. Cells of strain 19SA41 are Gram-stain-negative, strictly aerobic, non-motile rods and form pale yellow-pigmented colonies. The strain grows at 4-30 °C (optimum, 22 °C), at pH 6-10 (optimum, pH 7.5) and with 0-4% NaCl (optimum, 0.5%). Phylogenetic analyses based on 16S rRNA gene sequences showed that 19SA41 belonged to the genus Flavobacterium and is most similar to Flavobacterium xinjiangense DSM 19743^T, with a sequence similarity of 96.52%. The new strain contained iso-C_15 : 0 (22%) and summed feature 3 (C_16∶1ω6c/C_16∶1ω7c) (20%) as the predominant fatty acids. The major respiratory quinone was menaquinone-6 (100%). The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized amino lipids, glycolipids and lipids. The genome of the new strain was 4.01 Mbp, and its G+C content was 33.2 mol%. Based on characterization and comparative results, using a polyphasic taxonomic approach, we propose that the new isolate represents a novel species of the genus Flavobacterium with the name Flavobacterium aerium sp. nov. The type strain is ISCaR-07695^T (=DSM 116640^T =UBOOC-M-3567^T).

A novel Pseudonocardia strain DW16-2^T, isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8^T (98.8%), followed by Pseudonocardia tropica YIM 61452^T (98.7%), Pseudonocardia antarctica DVS 5a1^T (98.7%) and Pseudonocardia alni DSM 44104^T (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2^T and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2^T were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2^T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H₄). The cellular fatty acids (>5 %) were iso-C_16 : 0, iso-C_16 : 1 H, summed feature 3: C_16 : 1 ω7c/C_16 : 1 ω6c; C_16 : 1 ω6c/C_16 : 1 ω7c, C_17 : 1 ω8c and anteiso-C_17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2^T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2^T = TBRC 16418^T = NBRC 115857^T) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.

A hybrid in-person and online open plenary meeting of the International Committee on Systematics of Prokaryotes (ICSP) was held on 22 October 2024 at the Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Florence, Italy, and via Teams just prior to the IUMS 2024 Congress. To comply with Articles 4(d) and 5(d) (1) of the statutes of the ICSP, the minutes of this meeting are published here.

An obligately anaerobic, spore-forming sulphate-reducing bacterium, strain SB140^T, was isolated from a long-term continuous enrichment culture that was inoculated with peat soil from an acidic fen. Cells were immotile, slightly curved rods that stained Gram-negative. The optimum temperature for growth was 28 °C. Strain SB140^T grew at pH 4.0-7.5 with an optimum pH of 6.0-7.0 using various electron donors and electron acceptors. Yeast extract, sugars, alcohols and organic acids were used as electron donors for sulphate reduction. SB140^T additionally used elemental sulphur and nitrate as electron acceptors but not sulphite, thiosulphate or iron(III) provided as ferrihydrite and fumarate. The 16S rRNA gene sequence placed strain SB140^T in the genus Desulfosporosinus of the phylum Bacillota. The predominant cellular fatty acids were iso-C_15 : 0 (52.6%) and 5,7 C_15 : 2 (19.9%). The draft genome of SB140^T (5.42 Mbp in size) shared 77.4% average nucleotide identity with the closest cultured relatives Desulfosporosinus acididurans M1^T and Desulfosporosinus acidiphilus SJ4^T. On the basis of phenotypic, phylogenetic and genomic characteristics, SB140^T was identified as a novel species within the genus Desulfosporosinus, for which we propose the name Desulfosporosinus paludis sp. nov. The type strain is SB140^T (=DSM 117342^T=JCM 39521^T).