Theses and Dissertations at Montana State University (MSU)
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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 Geomicrobiology of hydrogen in Yellowstone Hot Springs(Montana State University - Bozeman, College of Letters & Science, 2019) Lindsay, Melody Rose; Chairperson, Graduate Committee: Eric Boyd; Daniel R. Colman, Maximiliano J. Amenabar, Kirsten E. Fristad, Kristopher M. Fecteau, Randall V. Debes, John R. Spear, Everett L. Shock, Tori M. Hoehler and Eric S. Boyd were co-authors of the article, 'Geological source and biological fate of hydrogen in Yellowstone hot springs' which is contained within this dissertation.; Maximiliano J. Amenabar, Kristopher M. Fecteau, R. Vincent Debes II, Maria Clara Fernandes, Kirsten E. Fristad, Huifang Xu, Tori M. Hoehler, Everett L. Shock and Eric S. Boyd were co-authors of the article, 'Subsurface processes influence oxidant availability and chemoautotrophic hydrogen metabolism in Yellowstone hot springs' in the journal 'Geobiology' which is contained within this dissertation.Hydrogen (H 2) connects the geosphere and biosphere in rock-hosted ecosystems and has likely done so since early in Earth's history. High temperature hydrothermal environments, such as hot springs, can be enriched in H 2 and were likely widespread on early Earth. As such, linking the geological processes that supply H 2 to contemporary hot springs and the distribution of extant thermophilic organisms that can utilize H 2 as a component of their energy metabolism can provide insights into the environment types that supported early H 2 dependent life. Using a series of geochemical proxies, I developed a model to describe variable H 2 concentrations in Yellowstone National Park (YNP) hot springs. The model invokes interaction between water and crustal minerals that generates H 2 that can partition into the vapor phase during decompressional boiling of ascending hydrothermal waters. Fractures and faults in bedrock, combined with topographic features such as high elevation, allow for vapor to migrate and concentrate in certain areas of YNP leading to elevated concentrations of H 2. Metagenomes from chemosynthetic communities in YNP springs sourced with vapor-phase gas are enriched in genes coding for enzymes predicted to be involved in H 2-oxidation. A spring in an area of YNP (Smokejumper, SJ3) sourced with vapor-phase gas, that has the highest concentration of H 2 measured in YNP, and that is enriched in hydrogenase encoding genes was chosen to further examine the biological fate of H 2. SJ3 harbors a hyperdiverse community that is supported by mixing of oxidized meteoric fluids and volcanic gases. Transcripts coding for genes involved in H 2 uptake and CO 2 fixation were detected. The processes that control the availability of oxidants and their effect on the activity and abundance of H 2 dependent organisms was also investigated in two paired hot springs. H 2-oxidizing chemoautotrophs utilized different oxidants in the two springs and this underpinned differences in H2 oxidation activity and their identity. Together, these observations indicate that the subsurface geological processes of decompressional boiling and phase separation influence the distribution, identity, and activity of hydrogenotrophs through their combined effects on the availability of H 2 and oxidants.Item Biogeography of thermophilic cyanobacteria and the importance of isolation to the evolution of microorganisms(Montana State University - Bozeman, College of Agriculture, 2002) Papke, Robertson ThaneItem A study of cultivation methods of sulphur bacteria found in thermal waters of Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 1948) Kathrein, Henry R.