Viral Diversity Threshold for Adaptive Immunity in Prokaryotes

Bacteria and archaea face continual onslaughts of rapidly diversifying viruses and plasmids. Many prokaryotes main- tain adaptive immune systems known as clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR- associated genes (Cas). CRISPR-Cas systems are genomic sensors that serially acquire viral and plasmid DNA fragments (spac- ers) that are utilized to target and cleave matching viral and plasmid DNA in subsequent genomic invasions, offering critical immunological memory. Only 50% of sequenced bacteria possess CRISPR-Cas immunity, in contrast to over 90% of sequenced archaea. To probe why half of bacteria lack CRISPR-Cas immunity, we combined comparative genomics and mathematical mod- eling. Analysis of hundreds of diverse prokaryotic genomes shows that CRISPR-Cas systems are substantially more prevalent in thermophiles than in mesophiles. With sequenced bacteria disproportionately mesophilic and sequenced archaea mostly ther- mophilic, the presence of CRISPR-Cas appears to depend more on environmental temperature than on bacterial-archaeal taxon- omy. Mutation rates are typically severalfold higher in mesophilic prokaryotes than in thermophilic prokaryotes. To quantita- tively test whether accelerated viral mutation leads microbes to lose CRISPR-Cas systems, we developed a stochastic model of virus-CRISPR coevolution. The model competes CRISPR-Cas-positive (CRISPR-Cas) prokaryotes against CRISPR-Cas- negative (CRISPR-Cas) prokaryotes, continually weighing the antiviral benefits conferred by CRISPR-Cas immunity against itsfitness costs. Tracking this cost-benefit analysis across parameter space reveals viral mutation rate thresholds beyond which CRISPR-Cas cannot provide sufficient immunity and is purged from host populations. These results offer a simple, testable viral diversity hypothesis to explain why mesophilic bacteria disproportionately lack CRISPR-Cas immunity. More generally, funda- mental limits on the adaptability of biological sensors (Lamarckian evolution) are predicted. IMPORTANCE A remarkable recent discovery in microbiology is that bacteria and archaea possess systems conferring immunolog- ical memory and adaptive immunity. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR- associated genes (CRISPR-Cas) are genomic sensors that allow prokaryotes to acquire DNA fragments from invading viruses and plasmids. Providing immunological memory, these stored fragments destroy matching DNA in future viral and plasmid inva- sions. CRISPR-Cas systems also provide adaptive immunity, keeping up with mutating viruses and plasmids by continually ac- quiring new DNA fragments. Surprisingly, less than 50% of mesophilic bacteria, in contrast to almost 90% of thermophilic bac- teria andArchaea, maintain CRISPR-Cas immunity. Using mathematical modeling, we probe this dichotomy, showing how increased viral mutation rates can explain the reduced prevalence of CRISPR-Cas systems in mesophiles. Rapidly mutating vi- ruses outrun CRISPR-Cas immune systems, likely decreasing their prevalence in bacterial populations. Thus, viral adaptability may select against, rather than for, immune adaptability in prokaryotes.