evolution of virulence; biodiversity 19 20 21Approximately half of all bacterial species encode CRISPR-Cas adaptive immune 22 systems 1 , which provide immunological memory by inserting short DNA sequences 23 from phage and other parasitic DNA elements into CRISPR loci on the host genome 2 . 24Whereas CRISPR loci evolve rapidly in natural environments 3 , bacterial species 25 typically evolve phage resistance by the mutation or loss of phage receptors under 26 laboratory conditions 4,5 . Here, we report how this discrepancy may in part be explained 27 by differences in the biotic complexity of in vitro and natural environments 6,7 . 28
Specifically, using the opportunistic pathogen Pseudomonas aeruginosa and its phage 29DMS3vir, we show that coexistence with other human pathogens amplifies the fitness 30 trade-offs associated with phage receptor mutation, and therefore tips the balance in 31 favour of CRISPR-based resistance evolution. We also demonstrate that this has 32 important knock-on effects for P. aeruginosa virulence, which became attenuated only if 33 the bacteria evolved surface-based resistance. Our data reveal that the biotic complexity 34 of microbial communities in natural environments is an important driver of the 35 evolution of CRISPR-Cas adaptive immunity, with key implications for bacterial fitness 36 and virulence. 37
38Pseudomonas aeruginosa is a widespread opportunistic human pathogen that thrives in a 39 range of different environments, including hospitals, where it is a common source of 40 nosocomial infections. In particular, it frequently colonises the lungs of cystic fibrosis 41 patients, in whom it is the leading cause of morbidity and mortality 8 . In part fuelled by a 42 renewed interest in the therapeutic use of bacteriophages as antimicrobials (phage 43 therapy) 9,10 , many studies have examined if and how P. aeruginosa evolves resistance to 44 phage (reviewed in ref. 11). The clinical isolate P. aeruginosa strain PA14 has been reported 45 to predominantly evolve resistance against its phage DMS3vir by the modification or 46 complete loss of the phage surface receptor 12 when grown in nutrient-rich medium 4 despite 47