Leveraging alfalfa variety trials to measure seasonal and host-specific selection on nitrogen-fixing rhizobial bacteria
J. SUTHERLAND, G. BLEDSOE, E. BINGMAN, P. SYDOW, E. PAILLAN, J. HARRIS, L. BURGHARDT
Department of Plant Science, Penn State University, 103 Tyson Bldg., University Park, PA 16801, USA

The rhizobia-legume interaction could be a sustainable alternative to synthetic nitrogen fertilizers, particularly in perennial systems. Yet, we have a limited understanding of the drivers of rhizobial evolutionary ecology in agroecosystems. Here, we track selection on the rhizobial species Sinorhiozbium meliloti, associating with alfalfa (Medicago sativa), an important perennial legume forage crop. We sampled ~300 pools of ~75 nodules sampled seasonally across three years for five varieties in repeated, randomized, replicated alfalfa field trials. We used whole-genome shotgun sequencing and read mapping to call SNPs. Then, we identified the relative contributions of our predictors (i.e., season and host-plant variety) on the genome-wide shifts in allele frequencies. We compared the efficacy of several computational approaches, including a redundancy analysis and two machine-learning methods. Identifying 26 potential loci under seasonal selection, we provide the first insight into drivers of rhizobial symbiont evolution in a critical perennial agroecosystem, which could enable innovative, sustainable solutions to address global synthetic nitrogen use challenges.