Assistant Professor Pennsylvania State University State collage, Pennsylvania
The nitrogen-fixing symbiosis between legumes and rhizobia represents fertile ground to infer principles underlying the functional genomics of beneficial plant-microbe interactions. Here we use a twist on an ‘evolve and resequence’ methodology to measure the relative success of scores of co-existing rhizobia isolates when associating with plant hosts. We measured relative Sinorhizobium meliloti fitness in the nodules of legume host (Medicago) at three scales of genetic variation— 30 individual mutations in M. truncatula symbiosis genes, 202 accessions of M. truncatula, and 15 Medicago species. We found that variation in isolate fitness increased as levels of host genetic differentiation increased. Examining rhizobial fitness correlations across scales, we found positive fitness correlations when individual host genes were perturbed and among host accessions. Negative fitness correlations indicative of evolutionary constraint only occur between host species. To examine the genetic basis of these phenotypic patterns, we used genome-wide association analysis to identify putative rhizobial genes underlying adaptation and ask if overlapping candidate gene regions determine rhizobial fitness across scales. Our results support the hypothesis that co-occurring species maintain rhizobial genetic diversity in soils and suggest the possibility of leveraging host genetic variation at the species level to manipulate rhizobial communities in natural and agricultural contexts.