Bradyrhizobium population dynamics in soybean fields

In the competitive environment of the rhizosphere, nodule forming Bradyrhizobium must compete with numerous other bacteria seeded from bulk soil. We asked which Bradyrhizobium species occur in soybean field bulk soil, which of these occur in the soybean rhizosphere, and which of these end up in nodules. We hypothesized that the nodulating species B. japonicum, B. diazoefficiens and B. elkanii would predominate in soils under long term soybean cultivation. To characterize microbial communities to species level we obtained full 16SrRNA gene sequences using Oxford Nanopore technologies. The results did not support our hypothesis. Surprisingly, we found a diversity of Bradyrhizobium species, as well as many members of other associative nitrogen fixing genera in the bulk soil to be enriched in the rhizosphere of soybeans grown in different soil types. As expected, nodules formed in this diverse diazotroph environment contain only B. japonicum, B. diazoefficiens or B. elkanii.