Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations

Abstract

In the past decade, molecular surveys of viral diversity have revealed that viruses are the most diverse and abundant biological entities on Earth. In culture, however, most viral isolates that infect microbes are represented by a few variants isolated on type strains, limiting our ability to study how natural variation affects virus-host interactions in the laboratory. We screened a set of 137 hot spring samples for viruses that infect a geographically diverse panel of the hyperthemophilic crenarchaeon Sulfolobus islandicus. We isolated and characterized eight SIRVs (Sulfolobus islandicus rod-shaped viruses) from two different regions within Yellowstone National Park (USA). Comparative genomics revealed that all SIRV sequenced isolates share 30 core genes that represent 50–60% of the genome. The core genome phylogeny, as well as the distribution of variable genes (shared by some but not all SIRVs) and the signatures of host-virus interactions recorded on the CRISPR (clustered regularly interspaced short palindromic repeats) repeat-spacer arrays of S. islandicus hosts, identify different SIRV lineages, each associated with a different geographic location. Moreover, our studies reveal that SIRV core genes do not appear to be under diversifying selection and thus we predict that the abundant and diverse variable genes govern the coevolutionary arms race between SIRVs and their hosts.

Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1

“…Here we studied two different viruses. The rudivirus SIRV3 contains characteristic linear dsDNA genome with inverted terminal repeats and covalently linked ends [13,29] and the virions exhibit a major coat protein gp19/ORF134 [13] and three minor components (Table 1); some differences were observed in the minor protein components from those described earlier for SIRV2 [20]. SMV1 carries a circular dsDNA genome [15] and 16 virion proteins (Table 1) and is related to the bicaudavirus ATV [21].…”

Surface resistance to SSVs and SIRVs in pilin deletions of Sulfolobus islandicus

“…(Figure ). In addition, a panel of unrelated SIRV viruses isolated from Yellowstone National Park, USA, (Bautista et al, ) was not able to infect ΔA1Δ6068 (Figure ). Susceptibility to all SIRVs and SSVs was restored by either pilA1 or pilA2 .…”

“…To test if pili provide a mechanism of attachment to the cellular envelope, we conducted adsorption assays with SSV9 (Bautista, Black, Youngblut, & Whitaker, ). Figure shows that SSV9 adsorbs to ΔA1Δ6068, Δ pibD::argD in addition to RJW002 that contains pilA1 and pilA2 , or the pilA1 and pilA2 complemented strains (data not shown).…”

The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification

“…Russia This dataset consists of a set of S. islandicus strains isolated from Kamchatka, Russia (in 2000) and sympatric chronic viruses (Sulfulobus spindle-shaped viruses: SSVs) [68].…”

“…These three springs have shown to share a single well-mixed population of S. islandicus hosts [67]. Viruses were collected from contemporary populations and CRISPR spacers and virus isolates suggest that these are dominated by the lytic virus SIRV [68]. The second data set is from S. islandicus strains isolated from several springs in the Mutnovsky Volcano in Kamchatka Russia that also were shown to share populations of hosts.…”