Cross-continental biogeography of the common bean rhizosphere microbiome reveals a persistent core membership

Plants recruit soil microbes that provide nutrients, promote growth and protect against pathogens. However, the full potential of microbial communities for supporting plant health and agriculture is unrealized, in part because rhizosphere members key for plant health are difficult to prioritize. Microbes that ubiquitously associate with a plant species across large spatial scales and varied soil conditions provide a practical starting point for discovering beneficial members. Here, we quantified the structures of bacterial/archaeal and fungal communities in the common bean rhizosphere (Phaseolus vulgaris), and assessed its core membership across two evolutionarily-distinct genotypes. Beans were grown in field conditions across five major growing regions in the United States. We discovered a conserved core microbiome of 271 bacterial, archaeal and fungal taxa that were consistently associated with the common bean, despite different soil types, management, climates and genotypes. Neutral models of abundance-occupancy relationships and co-occurrence networks suggest that these core taxa are in intimate relationships with the plant, rather than important members of the local soil microbiome. We expanded our study to leverage rhizosphere samples inclusive of eight additional common bean genotypes that were grown in Colombian soils. Surprisingly, there were 48 persistent bacterial taxa that were detected in all samples, inclusive of U.S. and Colombian-grown beans. Many of the core taxa were yet-uncultured and affiliated with Proteobacteria; these taxa are prime targets for functional investigation in support of sustainable common bean agriculture. More generally, our approach provides insights into microbial taxa that can be prioritized towards translational studies of plant-microbiome. management.