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Item Analysis of archaeal viruses and characterization of their communities in Yellowstone National Park(Montana State University - Bozeman, College of Letters & Science, 2014) Bolduc, Benjamin Ian; Chairperson, Graduate Committee: Mark J. Young; Daniel P. Shaughnessy, Yuri I. Wolf, Eugene Koonin, Francisco F. Roberto, and Mark J. Young were co-authors of the article, 'Identification of novel positive-strand RNA viruses by metagenome analysis of archaea-dominated Yellowstone hot springs' in the journal 'Journal of virology' which is contained within this thesis.; Jennifer Wirth, Aurélien Mazurie, and Mark J. Young were co-authors of the article, 'Viral community composition in Yellowstone acidic hot springs assessed by network analysis' submitted to the journal 'ISME Journal' which is contained within this thesis.; Mark J. Young was a co-author of the article, 'Characterization of viral communities in Yellowstone hot springs by deep-sequencing' which is contained within this thesis.Viruses infecting the Archaea - the third domain of life - are the least understood of all viruses. Despite only 100 archaeal viruses being described, work on these viruses revealed a remarkable level of morphological and genetic diversity unmatched by their bacterial and eukaryotic counterparts, whose numbers range over 6000. Study of these archaeal viruses could gain insight into fundamental aspects of biology and reveal underlying evolutionary connections spanning the three domains of life, including the origin of life. In addition, we understand very little about their community structures in natural environments. To address these daunting tasks, a viral metagenomics approach was undertaken using next generation sequencing technologies. Despite this, only a fragmented view of the viral communities is possible in natural ecosystems. Therefore, this dissertation sought to apply a network-based approach in combination with viral metagenomics to not only describe natural viral communities, but to find and characterize the first RNA viruses out of acidic, high-temperature hot springs in Yellowstone National Park, USA. These hot springs harbor low complexity cellular communities dominated by several species of hyperthermophilic Archaea. The results of this dissertation show that this approach can identify distinct viral populations and provide insights into the viral community. Furthermore, the viral communities of these hot springs are relatively stable over the course of the sampling time period. In addition, a number of viral clusters - each representing a viral family at the taxonomic level - are likely previously uncharacterized DNA viruses infecting archaeal hosts. This approach demonstrates the utility of combining viral community sequencing with a network analysis to understand viral community structures in natural ecosystems. Additional analysis of these viral metagenomes led to the identification of novel RNA viral genome segments. Since no RNA virus infecting Archaea is known to exist, this dissertation also sought to more fully characterize these sequences. Genes for RNA-dependent RNA polymerases, a hallmark of positive-strand RNA viruses were identified, suggesting the existence of novel positive-strand RNA viruses likely replicating in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses infecting eukaryotes and are even more distant from known bacterial RNA viruses.