Prolonged inoculation of soya bean (Glycine max L.) farms with exotic strains of Bradyrhizobium species starting in the 1960s resulted in the establishment of populations of Bradyrhizobium strains in the soils of several soya bean farms in South Africa. With the increasing number of new soya bean genotypes in the country, it is challenging to determine which genotypes are highly compatible with a given rhizobium strain. In this study, we investigated the symbiotic compatibility of native rhizobial isolates and the strains from the South African Rhizobium Culture Collection (SARCC) on ten selected locally available soya bean genotypes. A glasshouse soil trap experiment using soil samples collected from Lothair, Bothaville, and Standerton was performed on five cultivars. The trapped rhizobial strains were further screened in the glasshouse to authenticate their nodulation compatibility with the different soya bean cultivars. The rhizobial strains showed significant nodulation compatibility with the selected cultivars. These strains were also tested for beneficial traits in vitro and characterized using DNA sequencing methods to elucidate their taxonomic identity. Some of the most nodulation-compatible strains characterized as Bradyrhizobium and Sinorhizobium species exhibited significant symbiotic performance in terms of plant biomass, nodule number, and nodule dry weight. The study generated valuable data that provide information on the extent of symbiotic compatibility of some of the existing cultivars used in South Africa with native rhizobia and whether inoculation of soya bean with commercial products is vital on some soya bean farms.

Prior to the introduction of the exotic inoculant strain of Bradyrhizobium , South African soils lacked the rhizobia that nodulate soybean. Five decades of soybean inoculation practice resulted in the establishment of the Bradyrhizobium population in many soybean growing fields. However, there is no record of the magnitude of this establishment and its impact on the taxonomic and functional abundance of other microbes. Here we use a shotgun metagenomics approach to elucidate the taxonomic and functional profiles of the soil microbes from selected commercial soybean farms in South Africa. Metagenomics of the total sequences revealed that Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria and Bacteroitedes are the prevalent phyla which differed in their relative abundance. Bradyrhizobium was the predominant genus at all three locations. Predicted functions detected genes essential for nitrogen metabolism, including nitrogen fixation, which have been unveiled in this study at a higher rate in all locations investigated. This study uncovers the microbial communities associated with soybean soils in South Africa. The study also generated vital information on the establishment of Bradyrhizobium spp. in the soils of soybean farms, providing a clue on whether inoculation of soya beans is always necessary. The findings, however, warrant further field investigations before any recommendations are rendered.