Twenty-four Burkholderia arboris -like isolates obtained from samples of persons with cystic fibrosis and environmental sources were analysed using genomic approaches to clarify their taxonomic positions. Phylogenomic and overall genome relatedness index analyses revealed three distinct clusters. One cluster comprised the B. arboris type strain and thus corresponded to B. arboris , while the other two represented novel species within the Burkholderia cepacia complex, for which the names Burkholderia pulmonis sp. nov. (with LMG 33096ᵀ=CCUG 77266ᵀ as type strain) and Burkholderia torrens sp. nov. (with LMG 34232 T =TSD-620 T as type strain) are proposed. Closed genomes were obtained for all 24 isolates through hybrid assembly of Illumina data and Oxford Nanopore Technologies long-read sequencing data. The genome sizes ranged from 7.05 to 8.64 Mbp and exhibited the characteristic multi-replicon structure of Burkholderia , comprising two major replicons and a third, smaller, replicon (~0.96–1.27 Mbp) called pC3, except in B. pulmonis strains R-18413 and R-72673 and B. arboris strains R-132 and R-16920, which lost the third replicon. One or two small plasmids (24–355 kbp) were detected in several B. pulmonis and B. arboris strains. Several pairs or clusters of clonally related isolates were detected and included isolates with and without pC3.
Two novel yeast strains, designated NYNU 211158 and NYNU 211179, were recovered from decaying wood samples collected in the Baotianman Nature Reserve, Henan Province, central China. Molecular phylogenetic analyses based on the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) regions indicated that the closest known relative of these strains is the described species Effuseotrichosporon vanderwaltii . Sequence comparisons revealed that the novel strains differ from the type strain of E. vanderwaltii by 15 nucleotide substitutions (2.2%) in the D1/D2 domain and five nucleotide substitutions (1.0%) in the ITS region. Physiologically, the novel strains can be distinguished from E. vanderwaltii by their capacity to assimilate lactose, raffinose, inulin, N -acetyl- d -glucosamine, glycerol, erythritol, ethanol, methanol, citrate, 2-keto- d -gluconate, 5-keto- d -gluconate and ethylamine. On the basis of these molecular and phenotypic divergences, the strains are proposed to represent a novel species, Effuseotrichosporon baotianmanense sp. nov., with the holotype designated as CICC 33543 T (MycoBank MB 864553).
Two novel strains MAHUQ-55 T and MAHUQ-62 T were isolated from the rhizosphere soils of rice and pumpkin, respectively. Both strains were Gram-negative, catalase- and oxidase-positive, motile and rod-shaped. Strains MAHUQ-55 T and MAHUQ-62 T grew at 10–45 °C and 10–40 °C and pH 5.5–10.0 and 5.0–10.0 and tolerated 0–3.0% and 0–4.0% (wt/v) NaCl, respectively. Both strains hydrolysed l -tyrosine, Tween 20 and Tween 80. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MAHUQ-55 T and MAHUQ-62 T belong to the genus Metapseudomonas , showing the highest sequence similarities to Metapseudomonas furukawaii KF707 T (98.9%) and Metapseudomonas lalkuanensis PE08 T (99.4%), respectively. The genome sizes of strains MAHUQ-55 T and MAHUQ-62 T were 6,415,999 and 6,038,011 bp, respectively, with DNA G+C contents of 65.1 and 63.0 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains and their closest relatives were below the species delineation thresholds (ANI: 95–96%; dDDH: 70%). Both strains exhibited ubiquinone 9 as the predominant respiratory quinone and C 12 : 0 , C 16 : 0 , summed feature 3 (C 16 : 1 ω 7c and/or C 16 : 1 ω 6c) and summed feature 8 (C 18 : 1 ω7c and/or C 18 : 1 ω 6c) as major fatty acids. Based on dDDH, ANI value, genotypic analysis and chemotaxonomic and physiological data, strains MAHUQ-55 T and MAHUQ-62 T represent two novel species within the genus Metapseudomonas . Therefore, the names Metapseudomonas agri sp. nov. (type strain MAHUQ-55 T =KACC 22002 T =CGMCC 1.18516 T ) and Metapseudomonas agrisoli sp. nov. (type strain MAHUQ-62 T =KACC 22243 T =CGMCC 1.18999 T ) are proposed.
Three bacterial strains, designated RWH2-10P3 T , RWH1-P55 and W4-P8 T , were isolated from water samples collected from Xizang Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all three strains belong to the genus Mesocryomonas , with the highest sequence similarities to Mesocryomonas glaciei B5-2 T (98.1–98.4%), according to the EzBioCloud database. The draft genomes of the three strains were fully assembled, with genome sizes of 5.16–5.30 Mb and DNA G+C contents of 66.0–66.3%. Phylogenomic analysis based on single-copy genes confirmed that strains RWH2-10P3 T and RWH1-P55 would form a distinct clade, and strain W4-P8 T clustered together as a separate clade within the genus Mesocryomonas . Genome-scale comparative taxonomic analyses, including the digital DNA–DNA hybridization values, average nucleotide identity values and average amino acid identity, showed that the corresponding values between the novel strains and the closest relative species M. glaciei B5-2 T were below 23.2, 80.1 and 76.6%, respectively, which were well below the species delineation thresholds. Chemotaxonomic analysis showed that the major fatty acids of novel strains were summed feature 8 (C 18 : 1 ω7 c and/or C 18 : 1 ω6 c). The predominant isoprenoid quinone was Q-10, and the major polar lipids included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sulfoquinovosyldiacylglycerol and several unidentified lipids. Phenotypically, the novel strains exhibited distinct characteristics in growth conditions, carbon source utilization and enzyme activities compared to closely related species. Based on the polyphasic taxonomic data, strains RWH2-10P3 T and RWH1-P55 represent one novel species, named Mesocryomonas lacus sp. nov., with the type strain RWH2-10P3 T (=CGMCC 1.66487 T =KCTC 18568 T ) and the strain RWH1-P55 (=CGMCC 1.66488=KCTC 18566). Strain W4-P8 T represents another novel species, for which the name Mesocryomonas fontinalis sp. nov. is proposed, with the type strain W4-P8 T (=CGMCC 1.66489 T =KCTC 18567 T ).
The genus Arthrobacter Conn and Dimmick 1947 (Approved Lists 1980) encompasses a large and taxonomically complex assemblage of species within the family Micrococcaceae , many of which were described before whole-genome sequencing became a routine practice of prokaryotic taxonomy. During a comparison of genome sequences of Arthrobacter type strains, the type strain of Arthrobacter vasquezii Valenzuela-Ibaceta et al. 2023 (EH-1B-1 T ), isolated from Antarctic soil, was found to be genomically indistinguishable from the type strain of Arthrobacter parietis Heyrman et al. 2005 (LMG 22281 T ), isolated from a deteriorated mural painting. Pairwise comparison of the two type-strain genome sequences yielded a digital DNA–DNA hybridization (dDDH) value of 90.1% (95% CI 87.8–92.0%), an average nucleotide identity (ANI) of 98.96% and an average amino acid identity (AAI) of 99.15%, all well above the accepted thresholds for species delineation (dDDH ≥70%; ANI/AAI ≥95–96%). This congruence is further supported by all 16S rRNA gene sequence-based tree topologies and core genome phylogenomics and is consistent with comparative carbohydrate-active enzyme profiling and phenotypic analyses. As A. parietis Heyrman et al. 2005 has nomenclatural priority, we propose that A. vasquezii Valenzuela-Ibaceta et al. 2023 be reclassified as its later heterotypic synonym.
