Interbacterial competition triggers stress-induced CRISPR immunity against bacteriophages

Summary Bacteria–phage interactions are often studied in relatively simple experimental systems involving a single bacterial strain infected by a single phage1. In natural environments, however, bacteria typically inhabit complex multispecies communities where species compete for limited resources and ecological niches2-4. Recent studies show that the microbial community context can have profound effects on the evolution of phage resistance5. For example, Pseudomonas aeruginosa evolves phage resistance primarily through receptor loss when grown in isolation, but switches to CRISPR-based immunity in the presence of bacterial competitors6,7. Previous work showed that interspecies competition can favour CRISPR-immune bacteria over surface mutants after phage resistance has evolved6. However, it remains unknown whether competition also alters the initial generation of CRISPR immunity by changing CRISPR-Cas expression and spacer acquisition before selection among resistance phenotypes occurs. Here, we show that interbacterial competition can trigger CRISPR-Cas activation and adaptation in P. aeruginosa. When co-cultured with Acinetobacter baumannii, P. aeruginosa exhibited markedly increased expression of CRISPR-Cas genes and a higher frequency of new spacer acquisition, whereas no such induction occurred in monoculture or mixed communities lacking A. baumannii. This upregulation was associated with markers of DNA damage and stress signalling, indicating that competition-induced stress primes the bacterial adaptive immune response. These findings identify interbacterial antagonism as an ecological and physiological trigger for CRISPR activation, linking competitive interactions to enhanced antiphage defence. More broadly, our results suggest that bacteria sense and respond to competitive stress in complex microbial communities by increasing the generation of more adapted genotypes.