Viral diversity and host-virus interactions in the model crenarchaeon Sulfolobus islandicus

Viruses are pervasive evolutionary forces and key players shaping natural populations. Our understanding of viral impact on host physiology however, is based on a few model systems that represent a small fraction of the life-history strategies employed by hosts or viruses across the three domains of life. The factors that define these host-virus coevolutionary dynamics are not easily approached in complex natural systems. Microbes and the viruses that infect them provide a framework to study these coevolutionary interactions because evolution can be observed in real time in systems that are experimentally tractable. Acidic hot springs serve as a model system to study these interactions in natural populations because they provide low-complexity and geographically isolated environments with a limited number of microbial hosts where viruses are the only known predator. Within these springs we find the hyperthermophilic crenarchaeon Sulfolobus islandicus which represents one of the few genetically tractable systems within the TACK (Thaumarchaeota, 'Aigarchaeota', Crenarchaeota and Korarchaeota) archaea. In this dissertation I focus on broadening our understanding of host-virus interactions in this system. In Chapter 2 we investigate the impact of SSV9 (Sulfolobus spindle - shaped virus 9) challenge on CRISPR immune and CRISPR deficient S. islandicus hosts and demonstrate that CRISPR-Cas immunity is active in S. islandicus against a naturally occurring virus. Surprisingly, we uncovered that SSV9 induces a population-wide dormancy response at a low multiplicity of infection (MOI) from which only cultures with CRISPR immunity were able to recover. Dormancy was independent of productive infection since challenge with UV inactivated SSV9 particles caused cultures to go dormant. Further, continuous exposure to inactivated particles, mimicking the continuous production of SSV9 particles in CRISPR deficient cultures, resulted in cell death. In Chapter 3 we investigate the cost of CRISPR-Cas immunity and dormancy as compared to other virus resistance mechanisms by performing direct competitions in co-cultures of CRISPR immune and immune deficient resistant cells with and without SSV9 challenge. We established that under laboratory conditions, a non-immune resistant mutant had a competitive advantage over CRISPR immune strains only when challenged with virus. In Chapters 4 and 5 we explore the diversity and distribution of viruses from two geographically isolated geothermal regions: Yellowstone National Park (USA) and Kamchatka (Russia) to understand whether differences between these two viral populations are important drivers of the evolutionary trajectories of local S. islandicus populations. We isolated, purified, sequenced and established in culture eight new SIRVs (Sulfolobus islandicus rod-shaped viruses) and two SSVs from Yellowstone National Park and eight new SSVs from Kamchatka, thus augmenting the number of crenarchaeal viruses in culture by 40%. In Chapter 4 we examine the diversity and biogeographic distribution of Sulfolobus spindle-shaped viruses and in Chapter 5 we perform, for the first time, comparative genomic analyses of SIRVs from Yellowstone National Park. Our findings highlight the importance of looking beyond the established model systems and examine natural variation in order to understand how viruses are driving host-virus coevolutionary dynamics in natural populations