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Item Virus host interactions at the single cell level in hot springs of Yellowstone National Park(Montana State University - Bozeman, College of Letters & Science, 2019) Munson-McGee, Jacob Hampton; Chairperson, Graduate Committee: Mark J. Young; Jamie C. Snyder and Mark J. Young were co-authors of the article, 'Introduction to archaeal viruses' in the journal 'Genes' which is contained within this dissertation.; Ross Hartman was an author and Mark J. Young were co-authors of the article, 'vFish for the quantification of viral infection in natural environments' submitted to the journal 'Environmental microbiology' which is contained within this dissertation.; Erin K. Field, Mary Bateson, Colleen Rooney, Ramunas Stepanauskas and Mark J. Young were co-authors of the article, 'The identification and characterization of a nanoarchaeota, its cellular host and a nanoarchaeal virus across Yellowstone National Park hot springs' which is contained within this dissertation.; Colleen Rooney and Mark J. Young were co-authors of the article, 'An uncultivated virus infecting a nanoarchaeal parasite in the hot springs of Yellowstone National Park' submitted to the journal 'Virology' which is contained within this dissertation.; Shengyun Peng, Samantha Dewerff, Ramunas Stepanauskas, Rachel J. Whitaker, Joshua Weitz and Mark J. Young were co-authors of the article, 'A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments' in the journal 'The ISME journal' which is contained within this dissertation.Viruses are the most abundant biological entities on the planet and virus-host interactions are some of the most important factors in shaping microbial community structure and function and global chemical cycling. The high temperature low pH hot spring of Yellowstone National Park contain simplified microbial communities of 8-10 Archaeal species, and comparatively simple viral communities. These idealized communities that contain only viruses and their Archaeal hosts represent a model natural environment for the study of viruses and their hosts. This work presented here builds on previous population level studies of the viral and microbial communities to examine virus-host interactions at the single cell level. The identification of viral infection has long been a scourge of environmental virologist. In order to identify viral infection in natural environments we have adapted Fluorescent in situ hybridization (FISH) techniques to directly identify viral sequences. We further advance this technique to be compatible with flow cytometry analysis for the rapid quantification of viral infection of uncharacterized viruses in natural environments. This technique is used to quantify viral infection of two different viruses, previously only characterized by metagenomic sequencing analysis, in four geographically separate low pH high temperature hot springs of Yellowstone National Park. Finally, we combine viral and cellular metagenomics with cellular transcriptomics and single cell genomics to identify virus host interactions at the single cell level and identify viruses that are replicating in the hot springs. This work suggests that a majority of cells in the hot springs are interacting with viruses and that a majority of the cells are interacting with multiple viruses at any given time. We also identify RNA sequences from a majority of the viral types present in the hot springs suggesting that viral replication is occurring and is an important force in determining the structure and function of the microbial communities in these hot springs. Together these works represent a significant advancement of our understanding of virus host interactions in natural environments as well as new techniques to be used in future studies.Item Biological and structural properties of wild-type and mutant mengoviruses(Montana State University - Bozeman, College of Agriculture, 1984) Anderson, KevinItem Archaeal host virus interactions(Montana State University - Bozeman, College of Letters & Science, 2011) Wirth, Jennifer Fulton; Chairperson, Graduate Committee: Mark J. YoungViruses are the most abundant biological entity on earth, and virus-host interactions are one of the most important factors shaping microbial populations (Suttle, 2007b). The study of both the cellular and viral members of the domain Archaea is a relatively new field. Thus, the viruses (and their cellular hosts) of Archaea are poorly understood as compared to viruses of Bacteria and Eukarya. This work has sought to expand our understanding of archaeal viruses by two general approaches. The first is by developing and implementing the use of a genetic system for a crenarchaeal virus, Sulfolobus turreted icosahedral virus (STIV), isolated from a hot (82°C) acidic (pH 2.2) pool in Yellowstone National Park, USA. The second approach has been to look at viral communities and their interactions with their cellular hosts in natural environments. We have developed a genetic tool, an infectious clone for STIV, which has allowed for genetic analysis of this virus. A number of viral genes have been knocked out, and their functions investigated using this tool. We have determined that at least three viral genes, A197, B345 and C381, are required for viral replication, while one gene, B116, is not essential. Work continues investigating function for other STIV genes as well as specific interactions with its host, Sulfolobus solfataricus. We have performed total community sequencing (metagenomics) for both the cellular and viral populations of several hot springs in Yellowstone National Park. We have been able to assemble a near full-length putative novel viral genome from one of these sites. We have also performed an in depth analysis of the function of a newly described bacterial and archaeal adaptive immune system (CRISPR/Cas) in a natural environment. This study has provided insights into the function of this immune system in a complex nutrient limited environment, which would not have been observed by studying cultured isolates in a laboratory.