Deciphering Competitiveness of Root Colonizers with the Use of Synthetic Communities

Plant roots are home to a vast array of microorganisms, collectively known as microbiota. While many of these microbes have no discernible effect on the host, they play a crucial role in maintaining microbial homeostasis at the root-soil interface.

By studying the genomes of entire microbial communities, rather than just individual strains, we can gain access to microbial genetic elements that inform how microbe-microbe and host-microbe- interactions establish.

This approach allows us to identify genetic factors that contribute to niche supremacy, shedding light on the mechanisms by which symbionts and pathogens arise and how homeostasis can be maintained. To investigate, we introduced well-defined synthetic communities (SynCom) composed of 1000 soil-derived, fully sequenced bacteria into Arabidopsis, Lotus, and barley roots. Through metagenome sequencing, we pinpointed 40 isolates dominating specific niches.

Comparing the genomes and conducting Microbial Genome-Wide Association Studies (mGWAS) on these competitive colonizers unveiled molecular functions linked to colonization behavior. Notably, Lotus japonicus engages in root nodule symbiosis with Mesorhizobium loti. While previous studies focused on single inoculations to identify nitrogen-fixing symbiosis-related genes, our work examined symbiont and microbiome genes contributing to optimal symbiosis and host-soil microbe associations concurrently.

Our analysis highlighted genetic elements enriched in Lotus-compatible commensal bacteria and unique functions in symbiotic rhizobia compared to nonsymbiotic Mesorhizobium spp. Together, our studies unravelled novel functions enriched during root nodule symbiosis in a community setting, providing a solid fundament for genetic studies to underpin their role in root nodule symbiosis in the field conditions.