Bradyrhizobium and the soybean rhizosphere: Species level bacterial population dynamics in established soybean fields, rhizosphere and nodules

Bradyrhizobium fixes nitrogen symbiotically with soybean and is an agriculturally significant bacterium. Much is known about the Bradyrhizobium species that nodulate soybeans. Conversely, prevalence of Bradyrhizobium in soil and the rhizosphere is known only to the genus level as culture independent approaches have provided only partial 16S rRNA gene sequences, so that nodulating and non-nodulating species could not be distinguished.

To track which species in bulk soil proliferate in the rhizosphere, and then nodulate, we sought to study population dynamics of Bradyrhizobium in soybean fields and rhizosphere at the species level. Recent advances in Oxford Nanopore Technologies provided us with higher fidelity and increased number of reads which enabled us to track Bradyrhizobium populations at the species level.

We found evidence for 74 species of Bradyrhizobium within a community of 10,855 bacterial species in bulk soil and rhizosphere from three different soybean fields in South Dakota. The most predominant species in bulk soil and rhizosphere included B. liaoningense, B. americanum, and B. diversitatus, however none of these were isolated from nodules. Isolates from nodules included B. japonicum, B. elkanii and B. diazoefficiens. These nodulators also maintained populations in bulk soil and rhizosphere, although they were not the most prevalent Bradyrhizobium.

Our findings reveal the rich diversity and community dynamics of Bradyrhizobium species in soybean field soil as well as in the rhizosphere. Our results showed that many species of the genus maintain populations in soybean field soil, even in the long-term absence of potential nodulating partners.