Phage-mediated resolution of genetic conflict alters the evolutionary trajectory of Pseudomonas aeruginosa lysogens

The opportunistic human pathogen Pseudomonas aeruginosa is naturally infected by a large class of temperate, transposable, Mu-like phages. We examined the genotypic and phenotypic diversity of P. aeruginosa PA14 populations as they resolve CRISPR autoimmunity, mediated by an imperfect CRISPR match to the Mu-like DMS3 prophage, and show that lysogen evolution is profoundly impacted by CRISPR autoimmunity and phage transposition around the chromosome. After 12 days of evolution, we measured a decrease in spontaneous induction in both exponential and stationary phase growth. Co-existing variation in spontaneous induction rates in exponential phase corresponded to a difference in the type of CRISPR self-targeting resolution, mediated either by host mutation or phage transposition. Multiple mutational modes to resolve genetic conflict between host and phage resulted in coexistence in evolved populations of single lysogens that maintained CRISPR immunity to other phages and polylysogens that have lost immunity completely. This work highlights a new dimension of the role of lysogenic phages in the evolution of their hosts. Importance The chronic opportunistic multi-drug resistant pathogen Pseudomonas aeruginosa is persistently infected by temperate phages. We assess the contribution of temperate phage infection to the evolution of the clinically relevant strain UCBPP-PA14. We found that a low level of CRISPR-mediated self-targeting resulted in polylysogeny evolution and large genome rearrangements in lysogens; we also found extensive diversification in CRISPR spacers and cas genes. These genomic modifications resulted in decreased spontaneous induction in both exponential and stationary phase growth, increasing lysogen fitness. This work shows the importance of considering latent phage infection in characterizing the evolution of bacterial populations. ### Competing Interest Statement The authors have declared no competing interest.