In vivo plant-bacteria interaction rather than root exudates exploitation determines the evolution of bacterial rhizosphere adaptation

Plants dominates niche and functional differentiation between rhizosphere and bulk soil microorganisms, however, the dominant driving force directing evolution from uncompetitive root colonizers (bulk soil habitants) to competitive ones (rhizosphere habitants), are still being questioned. In the present evolutionary experiment, transferred growth of Bacillus amyloliquefaciens DSM7 ^T (a weak root colonizer) in root exudates in vitro improved metabolism competitiveness but failed to enhance its root colonization capacity. Conversely, in vivo evolution in plant rhizosphere significantly promoted bacterial root association, which is attributed to the evolved biofilm formation and indole-3-acetic acid production. Genome sequencing also identified hotspot mutations relevant to rhizosphere adaptation.