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.
Highlights
The discovery of diverse and novel viruses that infect bacteria [1,2,3] and archaea [4,5,6] has revived interest in the viruses of microbes
September and 20 samples fromofsix springs in the National Park collected between June and September 2010 and 20 samples from six springs in the Mutnovsky Volcano in Kamchatka, Russia, were screened on a panel of diverse S. islandicus hosts
To further test SIRV biogeographic patterns, we looked at the signatures of host-virus interactions interactions recorded in the CRISPR-Cas adaptive immune system, which is present in all Sulfolobus recorded in the CRISPR-Cas adaptive immune system, which is present in all Sulfolobus islandicus islandicus strains sequenced to date and has been demonstrated to confer immunity against natural strains sequenced to date and has been demonstrated to confer immunity against natural viral infection viral infection in this species [31]
Summary
The discovery of diverse and novel viruses that infect bacteria [1,2,3] and archaea [4,5,6] has revived interest in the viruses of microbes. Like bacteria and archaea, different viruses are represented by one or two variants isolated on a single host. This poses a bottleneck in studying and understanding the vast and uncharacterized “viral dark matter” uncovered by metagenomics [12,13] or predicting their impact on the environment. In the past few decades, a great effort has been made to study and characterize the viruses that infect the crenarchaeal species that inhabit these types
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