Investigation of the Individual Soybean Root Nodule Microbiome

Soybean is a valuable crop that establishes a symbiotic association with nitrogen-fixing microorganisms. Previous research suggests members of the genus Bradyrhizobium are the major nitrogen-fixing inhabitants of soybean root nodules. However, results from recent studies identified the presence of other bacteria, so called non-rhizobial endophytes (NREs), inside root nodules. All previous research has pooled nodules of different plants for bacterial community analysis, but this study investigated the presence and relative abundance of rhizobia and NREs within multiple root nodules of a single plant. Three sites were selected on Kendrick Farm in Springfield, MO, where three plants and rhizosphere soil were collected at each (nine total plants). I have assessed the microbiomes of 193 individual soybean root nodules from nine different plants using Illumina MiSeq paired-end DNA sequencing. Bradyrhizobium japonicum strains were preferentially selected in high abundance within all root nodules despite the presence of other soybean nodulating rhizobia. Nitrobacter and Tardiphaga were the two nonrhizobial genera that were consistently detected in low abundance within almost all root nodules. DNA sequences related to other frequently reported soybean NREs were detected within a few nodules only. The overall, very low abundance and inconsistent presence of most commonly reported NREs within different root nodules of a single plant suggest that these NREs are not being preferentially selected as endophytes by host plants and most likely have a very limited role in plant growth as endophytes. However, these NREs may have a significant role in plant growth as free-living plant growth-promoting rhizobacteria, which was observed in several coinoculation-based studies