The elite common bean Phaseolus vulgaris cultivar Pinto Saltillo hosts a rich and diverse array of plant-growth promoting bacteria in its rhizosphere.

Abstract

The rhizosphere of crop plants is a nutrient-rich niche that is inhabited by many microorganisms. Root-associated microorganisms play a crucial role in crop yields in agriculture. Given the ample diversity of varieties and cultivars of the common bean (Phaseolus vulgaris) used in agriculture, it is important to characterize their bacterial communities. In this study, we analyzed the bacterial rhizosphere components of the bean cultivar Pinto Saltillo, which is widely produced and consumed in Mexico. Bulk soil and rhizosphere samples from the P. vulgaris cultivar Pinto Saltillo were collected in situ from plots with and without cultivation history. Metagenomic analysis revealed that in both plots, the bacterial diversity in the bulk soil exceeded that in the rhizosphere. Moreover, diversity and taxonomic composition analysis confirmed the dominance of Proteobacteria in the rhizosphere. Comparisons with pairs of bulk soil-rhizosphere metagenomes of other cultivated plants (maize, wheat, tomato, cucumber, and the model plant Arabidopsis) indicated a pronounced rhizosphere effect of the cultivar Pinto Saltillo, particularly regarding the presence of bacterial genera already known as plant growth promoters, including Rhizobium. Metagenome-assembled genomes (MAGs) reconstructed from metagenomes confirmed a diverse set of species at the OTU level, closely related to this group of microorganisms. Our analysis underscores the association of R. sophoriradicis strains as the primary nodulating agent of common beans in the sampled agricultural fields. These findings imply that the success of common bean crops relies on microbial species that are still inadequately characterized beyond the established role of nitrogen-fixing bacteria. ImportanceSustainable agriculture is a long-term goal aimed at mitigating the impact of modern intensive and polluting agricultural technologies. Significant efforts are underway to understand the contributions of microorganisms to the health and productivity of crop plants. The common bean (Phaseolus vulgaris) is a domesticated leguminous plant native to Mesoamerica, that whose seeds provide sustenance for millions of people in America and Africa. Previous studies have illuminated the bacterial diversity of the rhizosphere microbiome in relation to plant resistance to pathogens and in the domestication process. These findings underscore the importance of investigating the bacterial rhizosphere communities in successful cultivars of the common bean. In this study, we demonstrate that the common bean cultivar Pinto Saltillo hosts a diverse array of plant-growth promoting bacteria in its rhizosphere. These findings suggest that the agricultural success of common bean cultivars could be attributed to the interplay between the plant and its rhizosphere bacterial community, rather than solely relying on nitrogen-fixing symbiosis.