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.

Based on phylogenetic analysis of whole-genome sequencing of Yersinia pestis 2.MED1 strains of the medieval biovar, combined with epizootic, epidemiological, and climatic data over a 100-year period, we have reconstructed the most probable directions of distribution of plague in Eastern Europe and Central Asia (EECA) in the 20th and 21st centuries. The data suggest the important role of three great lakes—the Caspian, Aral, and Balkhash—in the circulation and preservation of Y. pestis 2.MED1 in EECA. Three main directions of Y. pestis 2.MED1 expansion have been identified: Caspian (Caspian Sea region foci, 1912–1945; Caucasus, 1953–1986), North Aral (Northern Aral Sea region foci, 1945–1959; Caspian Sea region foci, 1945–2015; Pre-Caucasus, 1999–2003; Karakum, 1949–1965) and Central Asian (Kyzylkum, 1924, 1983–2020; Balkhash foci, 1939–2020; Northern Aral Sea region foci, 1967–2020; Eastern Caspian Sea region foci, 1968–1985). Favorable climatic conditions in the Caspian Sea region, the Northern Aral Sea region, and the Balkhash region in the 20th and 21st centuries contributed to the rapid formation of stable natural plague foci and the long-term persistence of Y. pestis 2.MED1 strains of the medieval biovar, with their further introduction into other foci of EECA. Periodic introductions of the pathogen are one of the reasons for the plague re-emergence and activation of plague foci in the EECA region.

Based on phylogenetic analysis of whole-genome sequencing of Yersinia pestis 2.MED1 strains of the medieval biovar, combined with epizootic, epidemiological, and climatic data over a 100-year period, we have reconstructed the spread of plague in Eastern Europe and Central Asia (EECA) in the 20th and 21st centuries. The data suggest the important role of three great lakes—the Caspian, Aral, and Balkhash—in the spread and preservation of Y. pestis 2.MED1 in EECA. Three waves of Y. pestis 2.MED1 spread have been identified: Caspian (Caspian Sea region foci, 1912-1945; Caucasus, 1953-1986), North Aral (Northern Aral Sea region foci, 1945-1959; Caspian Sea region foci, 1945-2015; Pre-Caucasus, 1999-2003; Karakum, 1949-1965) and Central Asian (Kyzylkum, 1924, 1983-2020; Balkhash foci, 1939-2020; Northern Aral Sea region foci, 1967-2020; Eastern Caspian Sea region foci, 1968-1985). Favorable climatic conditions in the Caspian Sea region, the Northern Aral Sea region, and the Balkhash region in the 20th and 21st centuries contributed to the rapid formation of stable natural plague foci and the long-term persistence of Y. pestis 2.MED1 strains of the medieval biovar, with their sporadic spread into other foci of EECA. Periodic introductions of the pathogen are one of the reasons for the plague re-emergence and activation of plague foci in the EECA region.