Bacterial biodiversity drives the evolution of CRISPR-based phage resistance in Pseudomonas aeruginosa

Approximately half of all bacterial species encode CRISPR-Cas adaptive immune systems 1 , which provide immunological memory by inserting short DNA sequences from phage and other parasitic DNA elements into CRISPR loci on the host genome 2 . Whereas CRISPR loci evolve rapidly in natural environments 3 , bacterial species typically evolve phage resistance by the mutation or loss of phage receptors under laboratory conditions 4,5 . Here, we report how this discrepancy may in part be explained by differences in the biotic complexity of in vitro and natural environments 6,7 . Specifically, using the opportunistic pathogen Pseudomonas aeruginosa and its phage DMS3 vir , we show that coexistence with other human pathogens amplifies the fitness trade-offs associated with phage receptor mutation, and therefore tips the balance in favour of CRISPR-based resistance evolution. We also demonstrate that this has important knock-on effects for P. aeruginosa virulence, which became attenuated only if the bacteria evolved surface-based resistance. Our data reveal that the biotic complexity of microbial communities in natural environments is an important driver of the evolution of CRISPR-Cas adaptive immunity, with key implications for bacterial fitness and virulence.