Bacillus adaptation to Pseudomonas secondary metabolites enhances its root competitiveness

Abstract Bacillus velezensis is a widely used plant growth-promoting rhizobacterium whose effectiveness under natural conditions is strongly influenced by interactions with surrounding microorganisms. While bacterial secondary metabolites are known to shape these interactions, little is known about their long-term evolutionary consequences. Here, we show that repeated exposure of B. velezensis GA1 to secondary metabolites produced by the competing rhizobacterium Pseudomonas sessilinigenes CMR12a drives the emergence of an adapted subpopulation with enhanced ecological fitness. Multi-omics analyses revealed extensive metabolomic and transcriptional changes associated with altered growth dynamics, sporulation, motility, and biofilm formation. Importantly, the evolved variant exhibited improved tomato root colonization and reduced the abundance of the competing Pseudomonas strain in planta . Together, our results demonstrate that prolonged exposure to diffusible bacterial metabolites can drive rapid adaptive diversification in rhizosphere-associated bacteria and highlight the importance of long-term interbacterial interactions in shaping the outcome of plant microbiome assembly and biocontrol performance.