The diversity of Bradyrhizobium strains associated with indigenous South African Genisteae
South Africa is the centre of origin for the legume tribe Genisteae and the centre of diversity for many of its genera. In other parts of the world the Genisteae are predominantly nodulated by Bradyrhizobium species, however not much is known about the diversity of rhizobia that associate with members indigenous to South Africa. The aim of this study was therefore to investigate this rhizobial diversity across the native range of nine indigenous Genisteae species. A set of 77 rhizobial isolates were obtained from root nodules of these species and were identified to genus level based on 16S rRNA sequence analyses. Sequence comparisons showed that most strains belong to Mesorhizobium (i.e., 40 strains), while 18 of the remaining strains represent Bradyrhizobium isolated from nodules of A. rupestre, A. sericeum, A. harveyanum and A. robustum, while a strain of Rhizobium was obtained from a Melolobium sp. The final sixteen strains which associate with Argyrolobium spp. (A. robustum, A. tomentosum, A. rupestre, and A. sericeum) and Melolobium spp. formed part of genera not considered to contain rhizobia. To identify the Bradyrhizobium strains to species level, we followed a genealogical concordance approach based upon five core genes (glnII, recA, dnaK, rpoB and gyrB). The resulting phylogenies revealed the consistent grouping of several strains into two putative novel Bradyrhizobium lineages while the remaining three groups were conspecific to B. arachidis, “B. brasilense”, and B. ivorense, respectively. Six representative strains were characterized by establishing their temperature, pH, and salt tolerance, as well as their ability to assimilate different carbon and nitrogen sources. Values of the calculated Average Nucleotide Identity comparisons were below the species circumscription threshold at 93.35% with B. japonicum USDA 6T and 78.78% with B. paxllaeri LMTR 21T for Arg816 and Arg237L, respectively. These were the two proposed type strains for the two putative lineages. Only Arg816 and representative strains were able to nodulate both cowpea and siratro, while Arg237L, 31Arga, and 31Argb strains failed to nodulate both hosts. The strains 31Arga and 31Argb, 62Arga19 and 68Arga19 formed part of the South African Clade XV, while the remainder of the strains belong to the cosmopolitan Clade III based on the nodA gene. Taken together, our findings thus show that Genisteae indigenous to South Africa are more likely to be nodulated by Mesorhizobium than Bradyrhizobium, although it would appear that there are novel lineages of Bradyrhizobium capable of interacting with these legumes.