Divergent molecular strategies drive convergent evolutionary adaptation to kin competition in biofilms

Abstract

Biofilms are a hotspot of bacterial social interactions that are characterized by cooperation and competition. Even a mono-species biofilm would evolve and diversify into polymorphic subpopulations so that bacterial kins of different genotypes would compete for limited nutrient and space. However, the specific biological functions underlying biofilm diversification and competition adaptation are poorly demonstrated. Here, we launched and monitored the experimental evolution of Pseudomonas aeruginosa biofilms, finding that two competition-adaptive derivatives rapidly emerged with variable capacities in forming biofilm. Further investigations identified that two novel divergent molecular trajectories were adopted for convergent adaptation to kin competition: one involved hijacking bacteriophage superinfection to aggressively inhibit kin competitors, while the other induced a subtle change in c-di-GMP signaling to gain a positional advantage via enhanced early biofilm adhesion. Bioinformatics analyses implicated that similar evolutionary strategies were prevalent among clinical P. aeruginosa strains, indicative of parallelism between natural and experimental evolution. Divergence in the molecular bases illustrated the adaptive values of genomic plasticity for gaining competitive fitness in the biofilm. Finally, we demonstrated that these competition-adaptive mutations reduced bacterial virulence. Our findings showed how kin competition shaped the P. aeruginosa biofilm evolution. More importantly, it revealed new insights into molecular targets for the treatment of recalcitrant biofilm infections formed by this clinically relevant pathogen.