Transient CRISPR immunity leads to coexistence with phages

Phages play a major role in shaping the composition, evolution and function of bacterial communities. While bacteria and phages coexist in many natural environments, their coexistence is often short-lived in the lab due to the evolution of phage resistance. However, fitness costs associated with resistance and mutational loss of resistance alleles may limit the durability of acquired resistances, potentially allowing phages to re-invade the population. Here, we explore this idea in the context of bacteria that evolve CRISPR-based immunity against their phages. Consistent with previous studies, we found that the bacterium PA14 evolved high levels of CRISPR-based immunity and low levels of surface-based resistance following infection with phage DMS3vir, which led to rapid phage extinction. However, when these pre-immunized bacterial populations were subsequently challenged with the same phage, they failed to clear the infection and instead stably coexisted with the phage. Analysis of bacterial genotypes and phenotypes over time explained why CRISPR-Cas immunity provides only a transient advantage: in the absence of phage (i.e. following the initial phage extinction) formerly CRISPR-immune bacteria regain sensitivity due to evolutionary loss of spacers, whereas in the presence of phage (i.e. upon reinfection) selection favours surface-based resistance over CRISPR immunity. The latter results from an infection-induced fitness cost of CRISPR-immunity that is due to phage gene expression prior to target DNA cleavage by the immune system. Together, these results show that CRISPR-Cas immune systems provide only a transient benefit to bacteria upon phage infection and help to explain why bacteria and phages can coexist in natural environments even when bacteria carry CRISPR-Cas adaptive immune systems that allow for rapid acquisition of immunity against phages.