Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia

Abstract

Strains of the genus Bradyrhizobium associated with agronomically important crops such as soybean ( Glycine max ) are increasingly studied; however, information about symbionts of wild Glycine species is scarce. Australia is a genetic centre of wild Glycine species and we performed a polyphasic analysis of three Bradyrhizobium strains—CNPSo 4010 T , CNPSo 4016 T , and CNPSo 4019 T —trapped from Western Australian soils with Glycine clandestina , Glycine tabacina and Glycine max , respectively. The phylogenetic tree of the 16S rRNA gene clustered all strains into the Bradyrhizobium japonicum superclade; strains CNPSo 4010 T and CNPSo 4016 T had Bradyrhizobium yuanmingense CCBAU 10071 T as the closest species, whereas strain CNPSo 4019 T was closer to Bradyrhizobium liaoningense LMG 18230 T . The multilocus sequence analysis (MLSA) with five housekeeping genes— dnaK , glnII , gyrB , recA and rpoB —confirmed the same clusters as the 16S rRNA phylogeny, but indicated low similarity to described species, with nucleotide identities ranging from 93.6 to 97.6% of similarity. Considering the genomes of the three strains, the average nucleotide identity and digital DNA–DNA hybridization values were lower than 94.97 and 59.80 %, respectively, with the closest species. In the nodC phylogeny, strains CNPSo 4010 T and CNPSo 4019 T grouped with Bradyrhizobium zhanjiangense and Bradyrhizobium ganzhouense , respectively, while strain CNPSo 4016 T was positioned separately from the all symbiotic Bradyrhizobium species. Other genomic (BOX-PCR), phenotypic and symbiotic properties were evaluated and corroborated with the description of three new lineages of Bradyrhizobium . We propose the names of Bradyrhizobium agreste sp. nov. for CNPSo 4010 T (=WSM 4802 T =LMG 31645 T ) isolated from Glycine clandestina , Bradyrhizobium glycinis sp. nov. for CNPSo 4016 T (=WSM 4801 T =LMG 31649 T ) isolated from Glycine tabacina and Bradyrhizobium diversitatis sp. nov. for CNPSo 4019 T (=WSM 4799 T =LMG 31650 T ) isolated from G. max .