Bradyrhizobium and the Soybean Rhizosphere: Species Level Bacterial Population Dynamics in Established Soybean Fields, Rhizosphere and Nodules — 106a — Sukhvir K. Sarao¹, Vincent Boothe¹, Bikram K. Das^2,3, Jose L. Gonzalez Hernandez², and Volker S. Brözel^1,4

Departments of Biology and Microbiology¹, Agronomy, Horticulture and Plant Science² and Chemistry, Biochemistry and Physics³, South Dakota State University, Brookings, SD 57006, and Department of Biochemistry, Genetics and Microbiology; Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa⁴

Bradyrhizobium, is an agriculturally important soil bacterium that fixes nitrogen for soybeans within nodules. Although a lot is known about the behavior of Bradyrhizobium in nodules, little is known about their ecophysiology in bulk soil. Previous studies identified Bradyrhizobium only to the genus level due to partial 16S rRNA gene sequences from culture-independent methods. Our goal was to achieve species-level identification of Bradyrhizobium in soybean environments and trace its population dynamics from bulk soil to the rhizosphere and ultimately to nodules. Samples were collected from established soybean fields in South Dakota. We utilized Oxford Nanopore Technology’s MinION for full 16S rRNA gene sequencing, providing higher fidelity and specificity. Using EPI2ME software, we categorized sequences to the species level. Our findings unveiled diverse Bradyrhizobium species and their community dynamics in both bulk soil and the rhizosphere across three sites, with a total of 10,855 bacterial species identified, including 74 Bradyrhizobium species. Associative nitrogen-fixing Bradyrhizobium species were notably enriched in the rhizosphere. B. liaoningense, B. americanum, and B. diversitatus were prevalent in bulk soil and the rhizosphere but absent from nodules. In contrast, nodule isolates primarily comprised B. japonicum, B. elkanii, and B. diazoefficiens, which were present in lower proportions in bulk soil and the rhizosphere. Interestingly, several Bradyrhizobium species persisted in soybean field soil independent of potential nodulating partners over extended periods, suggesting a non-nodulating lifestyle. This study enhances our understanding of Bradyrhizobium population dynamics at the species level in soybean fields, providing valuable insights for optimizing microbial inoculant use by soybean farmers and paving the way for further research on interactions between nodulating and non-nodulating species.

South Dakota State University
Dr. Volker Brozel