Bacterial Strains from Soybean Nodules in the Lower Volga Region Belong to a New Subspecies Bradyrhizobium japonicum subsp. saratovii subsp. nov.

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 <i>Bradyrhizobium japonicum</i> USDA 6^T and 96.3% with <i>Bradyrhizobium barranii</i> 144S4^T, forming a distinct cluster in phylogenetic trees. No significant differences were detected between <i>B. japonicum</i> and <i>B. barranii</i> that would explain the species boundary. Therefore, it is proposed to unite all novel strains into the subspecies <i>Bradyrhizobium japonicum</i> subsp. <i>saratovii</i> subsp. nov., and all other strains of <i>B. japonicum</i> and <i>B. barranii</i> we suggest dividing into four subspecies: <i>Bradyrhizobium japonicum</i> subsp. <i>japonicum</i> subsp. nov., <i>Bradyrhizobium japonicum</i> subsp. <i>barranii</i> comb. nov., <i>Bradyrhizobium japonicum</i> subsp. <i>apii</i> comb. nov., and <i>Bradyrhizobium japonicum</i> subsp. <i>saratovii</i> 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 <i>Bradyrhizobium</i> spp. in previously unexplored regions.