Dissecting plant-associated bacterial genetic architecture on host performance reveals discrepancies among contrasted environments

Elucidating the mechanisms through which microbes confer benefits to their hosts provides valuable opportunities for designing sustainable and environmentally friendly approaches to improve host health and performance. However, the exploration of the genetic diversity within bacterial species has been overlooked in the search for novel microbial mechanisms that confer beneficial effects to the host. In this study, we characterized the genetic architecture of the effect of the plant-associated bacterium Pseudomonas siliginis on the vegetative growth of its native host, Arabidopsis thaliana . Using a bacterial genome-wide association (BGWA) mapping approach based on multiple long-read-based reference genomes, we uncovered a highly polygenic architecture that drastically differs across nine A. thaliana genotypes and between in vitro and field conditions. Altogether, our findings revealed an extensive genetic diversity within P. siliginis and highlight the remarkable flexibility of its genetic architecture, depending on host genotype and environmental conditions. These factors might help drive innovations in the design of synthetic communities for precision agriculture.