Alfalfa varieties can weakly choose beneficial nitrogen-fixing bacteria from a population isolated from a single field

Legumes recruit rhizobial bacteria from the soil to fix nitrogen in root nodules. The legume-rhizobia symbiosis is an early example of humans using microbes to improve crop yields. Rhizobia/microbe-based bioinoculant products often perform inconsistently in the field, across locations, and years. Rather than engineering a one-size-fits-all inoculant, identifying crop varieties that select for and reward beneficial bacteria within each field's diverse microbial community could eliminate the need for repeated inoculant applications as beneficial microbial populations increase over time. Although legume crops have not been explicitly bred to recruit and enrich beneficial rhizobia, the model legume Medicago truncatula can selectively enrich beneficial strains. Here, we investigated whether its perennial relative, Medicago sativa (alfalfa), a globally important forage crop, also has this ability. To test this, we first isolated and sequenced a collection of 117 Sinorhizobium meliloti strains from nodules of three alfalfa varieties in a field trial. Despite being isolated from nodules less than three meters apart, we found high intraspecific genetic diversity in both single-nucleotide polymorphisms and gene presence-absence, with little phylogenetic clustering by source variety. Single-strain inoculations in a nitrogen-free greenhouse experiment revealed substantial variation in nitrogen-fixation ability across strains, with the best-performing strains differing by alfalfa variety. When varieties were inoculated with a mix of all strains, no variety accumulated as much biomass as with the best single strain for that variety, indicating a lack of ability to select only the best strain when given a choice. To confirm, we evaluated relative strain fitness in nodules and found that two of the three varieties weakly enriched for beneficial strains. Our results suggest that alfalfa varieties ability to enrich beneficial rhizobial populations is a variable, breedable trait, opening the door to developing varieties optimized to enrich these populations. Ultimately, breeding hosts to enhance mutualism could improve the reliability and sustainability of field nitrogen fixation.