Abstract
The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multiscale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of existent strains, such that populations have very low similarity compared over the long term. However, in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains (as single strains and coalitions) and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active.
Highlights
The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune system which defends against foreign genetic material, for
VIRAL AND HOST DIVERSIFICATION IN A MULTIPLE SPACER, MULTIPLE PROTOSPACER MODEL Here, we examine the dynamics of a host–virus community in which each host possesses multiple spacers and each virus possesses multiple protospacers
We find that hosts rapidly acquire CRISPR immunity through directed incorporation of spacers
Summary
Growth rate (1/h) Carrying capacity (1/mL) Burst size Adsorption rate (mL/h) Viral decay rate (1/h) Mutation rate Density cutoff (1/mL). ECOLOGICAL COMPONENT We consider a community comprised of hosts (either bacteria or archaea), viruses, and implicitly modeled resources. We focus on a rather simplified ecological context, where resources are considered implicitly and host populations would increase to their carrying capacity in the absence of viruses. Each host strain has a unique genomic state which we denote by Si , corresponding to the set of spacers it contains that confer it with CRISPR-derived immunity. Each viral strain has a unique genomic state which we denote by G j , corresponding to the set of protospacers it contains for which hosts may or may not be immune. Viruses decay at a density-independent rate of m Together these rules lead to the following dynamical equations: Host division and mortality dNi = dt
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