Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism

Abstract

Theory, simulation, and experimental evolution demonstrate that diversified CRISPR-Cas immunity to lytic viruses can lead to stochastic virus extinction due to a limited number of susceptible hosts available to each potential new protospacer escape mutation. Under such conditions, theory predicts that to evade extinction, viruses evolve toward decreased virulence and promote vertical transmission and persistence in infected hosts. To better understand the evolution of host-virus interactions in microbial populations with active CRISPR-Cas immunity, we studied the interaction between CRISPR-immune Sulfolobus islandicus cells and immune-deficient strains that are infected by the chronic virus SSV9. We demonstrate that Sulfolobus islandicus cells infected with SSV9, and with other related SSVs, kill uninfected, immune strains through an antagonistic mechanism that is a protein and is independent of infectious virus. Cells that are infected with SSV9 are protected from killing and persist in the population. We hypothesize that this infection acts as a form of mutualism between the host and the virus by removing competitors in the population and ensuring continued vertical transmission of the virus within populations with diversified CRISPR-Cas immunity. IMPORTANCE Multiple studies, especially those focusing on the role of lytic viruses in key model systems, have shown the importance of viruses in shaping microbial populations. However, it has become increasingly clear that viruses with a long host-virus interaction, such as those with a chronic lifestyle, can be important drivers of evolution and have large impacts on host ecology. In this work, we describe one such interaction with the acidic crenarchaeon Sulfolobus islandicus and its chronic virus Sulfolobus spindle-shaped virus 9. Our work expands the view in which this symbiosis between host and virus evolved, describing a killing phenotype which we hypothesize has evolved in part due to the high prevalence and diversity of CRISPR-Cas immunity seen in natural populations. We explore the implications of this phenotype in population dynamics and host ecology, as well as the implications of mutualism between this virus-host pair.

Intraspecific antagonism through viral toxin encoded by chronicSulfolobusspindle-shaped virus

“…As shown in figure 4, supernatant from RJW004/pOE-SSV11p29 and RJW004/pOE-SSV11p29&p30 produced zones of inhibition, but supernatant of strains with vectors encoding the SSV13 genes had no discernible effect. This is inconsistent with the data suggesting that SSV13 confers a competitive phenotype [17].…”

“…In previous work, we demonstrated the competitive advantage of chronically SSV-infected strains over other host types, such as CRISPR-Cas immune strains. We previously hypothesized that this phenotype evolved in Kamchatka under conditions of high distributed CRISPR-Cas immunity where susceptible hosts are rare as a strategy to promote viral fitness through vertical transmission [17,[35][36][37][38][39]. Given the metapopulation structure seen in hot spring locations, the killing phenotype would theoretically benefit the host not only in invasion of a new hot spring environment but also in helping it to maintain dominance in an already established population [17,34,40].…”

“…We previously hypothesized that this phenotype evolved in Kamchatka under conditions of high distributed CRISPR-Cas immunity where susceptible hosts are rare as a strategy to promote viral fitness through vertical transmission [17,[35][36][37][38][39]. Given the metapopulation structure seen in hot spring locations, the killing phenotype would theoretically benefit the host not only in invasion of a new hot spring environment but also in helping it to maintain dominance in an already established population [17,34,40]. However, the present work highlights the potential for competitive dynamics between host strains chronically infected with different viruses.…”

Introduction: the secret lives of microbial mobile genetic elements

“…Chronic infection imposes only a small fitness cost, because SSV9 reproduces by budding from host cells, without lysis. In fact, in communities, SSV9 provides a competitive advantage over uninfected strains [50]. DeWerff et al [51] demonstrate that this advantage is due to a virusencoded specific toxin protein that kills competitors.…”

Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales

“…The Sulfolobales viruses that have been described so far belong to six different archaeal virus families and are characterized by an impressive diversity regarding their morphologies, as well as genome structures and life cycles [203,254]. While viruses of bacteria are mostly lytic, the majority of archaeal viruses rather seem to persist in their host cells in a stable carrier state [255], which sometimes is beneficial for the host [256]. Similar to prophage lambda, some temperate archaeal viruses can be activated by various stimuli, such as the well described Fuselloviridae infecting Sulfolobales, however they do not always cause cell lysis after induction of virion production.…”