Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics

ABSTRACT Prokaryotes can acquire antivirus immunity via two fundamentally distinct types of processes: direct interaction with the virus, as in clustered regularly interspaced short palindromic repeats (CRISPR)-Cas adaptive immunity systems, and horizontal gene transfer (HGT), which is the main route of transmission of innate immunity systems. These routes of defense evolution are not mutually exclusive and can operate concomitantly, but observations suggest that at least in some bacterial and archaeal species, one or the other route dominates the defense landscape. We hypothesized that the observed dichotomy stems from different life-history trade-offs characteristic of these organisms. To test this hypothesis, we analyzed a mathematical model of a well-mixed prokaryote population under a stochastically changing viral prevalence. Optimization of the long-term population growth rate reveals two contrasting modes of defense evolution. In stable, predictable environments, direct interaction with the virus is the optimal route of immunity acquisition. In fluctuating, unpredictable environments with a moderate viral prevalence, horizontal transfer of defense genes is preferred. In the HGT-dominant mode, we observed a universal distribution of the fraction of microbes with different immune repertoires. Under very low virus prevalence, the cost of immunity exceeds the benefits such that the optimal state of a prokaryote is complete absence of defense systems. By contrast, under very high virus prevalence, horizontal spread of defense systems dominates regardless of the stability of the virome. These findings might explain consistent but enigmatic patterns in the spread of antivirus defense systems among prokaryotes, such as the ubiquity of adaptive immunity in hyperthermophiles contrasting their patchy distribution among mesophiles. IMPORTANCE The virus-host arms race is a major component of the evolutionary process in all organisms that drove the evolution of a broad variety of immune mechanisms. In the last few years, over 200 distinct antivirus defense systems have been discovered in prokaryotes. There are two major modes of immunity acquisition: innate immune systems spread through microbial populations via HGT, whereas adaptive-type immune systems acquire immunity via direct interaction with the virus. We developed a mathematical model to explore the short-term evolution of prokaryotic immunity and showed that in stable environments with predictable viral repertoires, adaptive-type immunity is the optimal defense strategy, whereas in fluctuating environments with unpredictable virus composition, HGT dominates the immune landscape.