Experimental evolution of root-associated microbial communities

Understanding how plant-associated microbial communities adapt to new environments and host species is critical for improving microbiome-based agricultural strategies. We investigated the evolutionary dynamics of synthetic root-associated communities (SynComs) derived from Arabidopsis thaliana and Lotus japonicus by experimentally evolving them on native and non-native hosts over 16 successive plant generations. Using a combination of community profiling, population genomics, and phenotypic assays, we found that repeated exposure to a novel host drove rapid, reproducible genomic changes in replicate bacterial populations, particularly in genes involved in orchestrating changes in transcriptional regulation and inter-microbial interactions. These adaptations led to significant increases in colonization fitness of roots of a new plant species, confirmed through competition experiments using whole genome-sequenced evolved isolates. Our results demonstrate that root-associated microbial communities can rapidly evolve host-specific adaptations, deepening our understanding of plant-microbiota associations and highlighting the potential of directed microbiome evolution for improving microbial inoculants for sustainable agriculture.