Cover crop microbiomes affect legume cash crop growth but not consistently through enriching nitrogen-fixing rhizobia

Harnessing plant-microbe interactions offers a promising path toward reducing chemical inputs and enhancing crop resilience in agricultural systems. However, microbial inoculants often fail to persist or function consistently across soils, which limits their broad utility. Here, we explore whether legume cover crops can be used to manipulate and enrich for rhizobial bacteria that improve nodulation and nitrogen fixation in downstream legume cash crops. In a greenhouse experiment, we inoculated cash crops with rhizosphere and nodule microbiomes derived from different legume cover crops. We found that bacterial communities were markedly different between the rhizosphere and nodules of cover crops, indicating strong habitat differentiation. Interestingly, the cover crop inoculum did not substantially alter the taxonomic composition of cash crop nodule communities, suggesting strong partner selectivity by the cash crop host. However, cover crop identity strongly affected nodule formation and, to a lesser extent, total biomass of cash crops. For alfalfa and soybean, a higher abundance of their respective rhizobial partners in cover crop nodule inocula increased total biomass and nodule number for these cash crop species, respectively. These findings emphasize the importance of selecting cover crops that foster the availability of effective microbial partners to support more sustainable legume cropping systems.