Experimental evolution of root-associated microbial communities
Microbial communities associated with plants are dynamic ecosystems whose structure and functions influence host health and fitness. While the ecological roles of these communities are increasingly well understood, the evolutionary dynamics that shape them over time remain unclear. Experimental evolution constitutes a powerful tool to study microbial adaptation, but so far, its application has been mostly limited to single-species populations. Here, we use a long-term evolution experiment to test whether synthetic bacterial communities can adapt to novel plant hosts. We show that replicate microbial communities undergo rapid and parallel genomic evolution, with measurable gains in colonization fitness. Adaptation involves mutations in regulatory processes, motility, and core metabolism, leading to significant fitness gains. Our findings demonstrate that the plant host can drive microbiome evolution without disrupting community stability.