The isolation of locally adapted rhizobial strains with high symbiotic activity represents an effective strategy for increasing soybean yield under extreme environmental conditions. In this study, seven novel strains were isolated from nodules of soybeans grown in a greenhouse using field soil from the Lower Volga region. Five genomes were assembled into complete circular chromosomes, whereas two strains yielded near-complete chromosomes containing single repeat-mediated junctions. All strains had putative plasmids that were independently validated as circular by long-read mapping and confirmed by the presence of characteristic replication and conjugation-associated genes. Genome sequences of strains were about 11 Mb, and GC contents were 63.1–63.3%. Comparative genome analyses demonstrated that all strains had average nucleotide identity values of 95.4% with Bradyrhizobium japonicum USDA 6^T and 96.3% with Bradyrhizobium barranii 144S4^T, forming a distinct cluster in phylogenetic trees. No significant differences were detected between B. japonicum and B. barranii that would explain the species boundary. Therefore, it is proposed to unite all novel strains into the subspecies Bradyrhizobium japonicum subsp. saratovii subsp. nov., and all other strains of B. japonicum and B. barranii we suggest dividing into four subspecies: Bradyrhizobium japonicum subsp. japonicum subsp. nov., Bradyrhizobium japonicum subsp. barranii comb. nov., Bradyrhizobium japonicum subsp. apii comb. nov., and Bradyrhizobium japonicum subsp. saratovii subsp. nov. The proposed taxonomic framework expands current knowledge of the biodiversity of soybean symbiotic bacteria and contributes to a better understanding of the distribution and the evolution of bacteria Bradyrhizobium spp. in previously unexplored regions.

The Aksai high-mountain focus is part of the Tien Shan focus, which has recently shown constant epizootic activity. In 2024, Yersinia pestis cultures were isolated from the Aksai focus for the first time in the 21st century. The aim of the study was molecular identification of Y. pestis strains collected in the Aksai focus in 2024, their phylogenetic analysis to establish their origin and obtain whole-genome sequences that are reference ones for this focus in the mo dern period. Materials and methods. The genomes of Y. pestis strains were sequenced on a MinIon genetic analyzer (Oxford Nanopore Technologies, UK). Sequencing libraries were prepared using the Native Barcoding Kit 24 v14 (SQKNBD114.24) and sequenced on an R10.4.1 flow cell. Core SNPs were identified applying pair wise alignment of the obtained whole-genome sequences to the genome of Y. pestis CO92 strain using Snippy v4.6.0 software. The Maximum Likelihood dendrogram was constructed using PhyML 3.1. Results and discussion. According to the phylogenetic analysis of whole-genome sequences, it has been established that the Y. pestis strains isolated in the Aksai focus in 2024 belong to the phylogenetic branch 0.ANT3 of antique biovar. The Y. pestis strains of 2024 fall under the 0.ANT3 polytomy, which also includes all 0.ANT3 strains of the 20th century from the Aksai, Upper Naryn and Alai high-mountain foci and strains from the Xinjiang province in China. The genetic differences between the 0.ANT3 strains of the current and last centuries are small, which proves the continuity of the preservation of this population in the 20th–21st centuries and the local origin of the 2024-strains. Strains 0.ANT3 were previously isolated across large areas of the Upper Naryn, Aksai, Alai plague foci and on the adjacent territories of China, which indicates the existence of a mega-focus of 0.ANT3 Y. pestis there. Strains 0.ANT3 are highly virulent and epidemically significant. The activation of the Aksai natural plague focus requires increased epidemiological surveillance of this autonomous plague focus in the Tien Shan.

The aim of the study is to obtain a comprehensive characterization of Yersinia pseudotuberculosis strains from the Aksai high-mountain and Balkhash desert foci of plague in Central Asia. Materials and methods. Investigation of the cultural, morphological and biochemical properties of the examined strains was carried out using conventional methods of laboratory diagnostics. Ion S5 XL System (Thermo Fischer Scientific) was used for whole-genome sequencing. Data processing and sequence assembly of raw reads de novo were performed using Ion Torrent Suite software package 5.12 and Newbler gsAssembler 2.6 (454 Life Sciences). To search for marker SNPs, the Wombac 2.0 program based on the BioLinux 8.0 operating system was applied. When constructing the dendrogram, the Maximum Likelihood method, the PhyML 3.1 program and the HKY85 model were used. Results and discussion. The studied strains from the Aksai high-mountain and Balkhash desert foci have properties characteristic of the Y. pseudotuberculosis species, are prototrophs and do not contain the pYV plasmid. According to phylogenetic analysis based on identified 109,641 core SNPs, they are closely related to strains of the pseudotuberculosis microbe from the Sarydzhaz high-mountain focus in the Kyrgyz Republic and the Republic of Kazakhstan, as well as to the O:3 serovar strain from Turkmenistan. The cluster of these Central Asian strains on the phylogenetic tree of Y. pseudotuberculosis is localized next to strains of the pseudotuberculosis microbe of O:3 serovar from various regions of the world. The results obtained testify to the circulation of a separate phylogeographic population of Y. pseudotuberculosis in the territory of natural plague foci in Central Asia. The characterized Y. pseudotuberculosis strains and their whole genome sequences can be used as reference ones for the Aksai and Balkhash natural plague foci of Central Asia.

Multilocus variable number tandem repeat analysis (MLVA) is one of the highest-resolution methods for subtyping genetically monomorphic pathogens of especi

Seven indigenous strains of Bradyrhizobium japonicum subsp. saratovii isolated from soybean nodules (Glycine max (L.) Merr.) grown in the arid Lower Volga region of Russia were investigated. A complete set of the major symbiotic genes was detected in all strains. Single synonymous nucleotide substitutions were identified in nifH and nifD, whereas a missense mutation, Ser149Phe, was found in the nifK gene of strain II-2. Homology modelling showed that this substitution did not cause any noticeable rearrangement of the overall structure of the nitrogenase β-subunit, although it was located near the conserved Cys152 residue. The nodB and nodC genes were completely conserved; the nodC sequence corresponded to symbiovar glycinearum. Structural disruptions in the nap operon were detected in strains II-2 and III-2, which was consistent with the absence of nitrate-reducing activity. Comparison of the genomic data with the inoculation results showed that the most effective strain, II-2, combined strong growth-promoting and yield-enhancing effects with the presence of a complete set of symbiotic genes and disruption of napA. These findings indicate that the integration of genomic analysis with phenotypic assessment improves the accuracy of selecting promising indigenous Bradyrhizobium strains for soybean inoculation.