Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns

Africa is known for its rich legume diversity with a significant number of endemic species originating in South Africa. Many of these legumes associate with rhizobial symbionts of the genus Bradyrhizobium, of which most represent new species. Yet, none of the Bradyrhizobium species from South Africa have been described. In this study, phylogenetic analysis of 16S rRNA gene sequences of fourteen strains isolated in southern Africa from root nodules of diverse legumes (i.e., from the tribes Crotalarieae, Acacieae, Genisteae, Phaseoleae and Cassieae) revealed that they belong to the Bradyrhizobium elkanii supergroup. The taxonomic position and possible novelty of these strains were further interrogated using genealogical concordance of five housekeeping genes (atpD, dnaK, glnII, gyrB and rpoB). These phylogenies consistently recovered four monophyletic groups and one singleton within Bradyrhizobium. Of these groups, two were conspecific with Bradyrhizobium brasilense UFLA 03321(T) and Bradyrhizobium ivorense CI-1B(T), while the remaining three represented novel taxa. Their existence was further supported with genome data, as well as metabolic and physiological traits. Analysis of nodA gene sequences further showed that the evolution of these bacteria likely involved adapting to local legume hosts and environmental conditions through the acquisition, via horizontal gene transfer, of optimal symbiotic loci. We accordingly propose the following names Bradyrhizobium acaciae sp. nov. 10BB(T) (SARCC 730(T) = LMG 31409(T)), Bradyrhizobium oropedii sp. nov. Pear76(T) (SARCC 731(T) = LMG 31408(T)), and Bradyrhizobium altum sp. nov. Pear77(T) (SARCC 754(T) = LMG 31407(T)) to accommodate three novel species, all of which are symbionts of legumes in South Africa.

Automated summary

This study isolated fourteen strains of Bradyrhizobium bacteria from root nodules of legumes in South Africa and determined their taxonomic position and possible novelty through gene sequence analysis. The existence of these novel species was supported by genome data and metabolic characteristics.