Theses and Dissertations at Montana State University (MSU)
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Item Soil legacy effects alter plant volatile emissions in response to diversified cropping systems(Montana State University - Bozeman, College of Agriculture, 2020) Malone, Shealyn Chelsea; Chairperson, Graduate Committee: David K. Weaver and Amy Trowbridge (co-chair); David K. Weaver, Fabian Menalled, Tim Seipel, Justin B. Runyon, Lila Hamburg, Megan L. Hofland and Amy M. Trowbridge were co-authors of the article, 'Cropping systems alter crop volatile cues important for insect pests through soil legacy effects' which is contained within this thesis.; David K. Weaver, Tim F. Seipel, Fabian D. Menalled, Megan L. Hofland, Justin B. Runyon and Amy M. Trowbridge were co-authors of the article, 'Soil microbes alter herbivore-induced volatile emissions in response to cereal cropping systems' submitted to the journal 'Plant and soil' which is contained within this thesis.Soil microbes can influence the emissions of plant volatile organic compounds (VOCs) that serve as host-location cues for insects and their natural enemies. The influence of the soil microbial community on the plasticity of plant VOC synthesis and emissions is particularly important in agricultural settings where crop rotations and management practices cause significant shifts in the soil microbiome. Studies have shown agricultural soils to influence plant-insect interactions through changes in foliar chemistry, but their potential to alter VOC emissions is unknown. To determine the effect of diversified agricultural practices on crop VOC emissions through microbe-mediated soil legacy effects, I measured VOCs from wheat (Triticum aestivum L.) in a series of field and greenhouse experiments. In Chapter II, I determined the effect of the soil microbiome on VOCs in the greenhouse by first measuring VOCs from wheat plants grown in sterilized soil or soil with added inoculum from an agricultural field. Next, to determine the effect of diversified agricultural practices on VOC phenotypes, I measured VOCs from wheat plants in the field in rotation with either fallow or a mixture of cover crops that was terminated by grazing cows. Finally, in Chapter III, I explored the interactive effect of herbivory and the soil microbiome on VOC emissions in a full factorial experiment in which wheat grown in soil inoculum from wheat-fallow or wheat-cover crop rotation that was subjected to larval feeding by the wheat stem sawfly (WSS; Cephus cinctus Norton), a major pest of wheat. Across all studies I found that soils associated with a higher microbial diversity--cover crop soils and inoculated soils--tended to emit more total VOCs and blends that would likely increase pest resistance to the WSS through 1) shifts in key bioactive compounds and 2) enhanced herbivore-induced VOC emissions. Results also suggest that soil microbes may be more likely to alter plant VOCs when plants experience abiotic or biotic stressors. Together, these results suggest that agricultural practices may indirectly influence plant resistance through microbe-altered VOCs, and these effects are more likely to occur when plants experience additional stressors, such as herbivory or drought.Item Impacts of crop rotations and nitrogen fertilizer on soil biological factors in semi-arid Montana(Montana State University - Bozeman, College of Agriculture, 2021) Fouts, Willa Constance; Chairperson, Graduate Committee: Catherine A. ZabinskiEvaluating the effects of cropping and fertilizing techniques is key to informing agricultural best practices. We must continue monitoring how we manipulate soils in order to preserve and cultivate high-quality soil ecosystems that can support us in the face of climate change and widespread soil loss and deterioration. We assessed the effects of common agricultural practices in Montana by measuring biological indicators of soil quality in the 18th year of a field plot experiment with 100% and 50% the recommended rate of synthetic nitrogen (N) fertilizer and crop rotations incorporating wheat, fallow, and legumes. The biological indicators measured were four soil extracellular enzymes, potentially mineralizable N (PMN), and microbial biomass. We sampled once in spring 2020 and subsampled in the fall. We also tested whether enzymes and PMN were correlated to aboveground plant residue, which was represented by the sum of the dried plant mass from past two years left on the plots after harvest. Plant residue was positively correlated with the C, N, and S-cycling enzymes and to PMN. The positive correlation between PMN and residue reflects that increased biomass inputs could increase easily mineralizable N. Soil with the high N-rate had a slightly higher geometric mean enzyme activity. This could be from the resulting increase in plant residue. The high N-rate treatment slightly decreased soil PMN but was not affected by crop rotation treatments. Fallow systems had lower enzyme function overall, indicating a lessened fertility and decomposition rate compared to continuously cropped treatments, which keep the soil covered with a crop for more months out of the year. The positive correlations of plant residue, along with the general lower performance of the fallow systems, especially the tilled fallow rotation, support that aboveground biomass inputs are a driver in soil ecosystem function. Continuous no-till crop rotations have increased aboveground plant organic matter, which could increase nutrient cycling and decomposition, and thereby soil biological quality and fertility.Item Microbial community composition and the transformation of dissolved organic matter in supraglacial environments(Montana State University - Bozeman, College of Agriculture, 2016) Smith, Heidi Jean; Chairperson, Graduate Committee: Christine Foreman; Markus Dieser and Christine Foreman were co-authors of the article, 'Organic matter shapes community compositon in glacial environments' submitted to the journal 'International Society for Microbial Ecology (ISME)' which is contained within this dissertation.; Rachel Foster, Diane McKnight, John Lisle, Daniela Tienken, Marcel Kuypers and Christine Foreman were co-authors of the article, 'Microbial formation of labile glacial organic carbon' submitted to the journal 'Nature geosciences' which is contained within this dissertation.; Michelle Tigges, Juliana D'Andrilli, Albert Parker, Brian Bothner and Christine Foreman were co-authors of the article, 'Supraglacial dissolved organic matter: a labile but unsustainable carbon source' submitted to the journal 'Limnology and oceanography' which is contained within this dissertation.; Amber Schmidt, Rachel Foster, Sten Littmann, Marcel Kuypers and Christine Foreman were co-authors of the article, 'Biofilms on glacial surfaces: hotspots for biological activity' submitted to the journal 'Nature biofilms and microbiomes' which is contained within this dissertation.Relating microbial community composition to ecosystem function is a fundamental goal in ecological analyses, with physico-chemical parameters largely controlling this relationship. This investigation aimed to elucidate the impact of physicochemical factors on biodiversity in glacial habitats, with an emphasis on dissolved organic matter (DOM). DOM is a complex mixture of organic compounds and the primary substrate for microbial activity. Considering the variety of DOM sources in aquatic systems, little is still known about the biological release and bio-transformation of microbially-derived, autochthonous DOM. Continental Antarctica, typically lacking terrestrial carbon inputs, is largely governed by autochthonous DOM, making it an ideal site to investigate microbial biodiversity and the microbial formation of DOM. Different glacial ecosystems were selected, with a strong focus on the supraglacial Cotton Glacier stream, to investigate: i) the microbial diversity and underlying environmental factors governing biogeographical trends, ii) the contribution of exuded carbon to the DOM pool and subsequent heterotrophic uptake/transformation, and iii) how biofilm influences nutrient cycling in supraglacial environments. Findings from this study highlight distinct microbial assemblages in meltwater streams/sediments, ice, snow, and cryoconite across local and regional geographic scales. Specifically, nutrient availability and DOM quality influenced trends in microbial diversity. In situ DOM exudation was sufficiently high to support bacterial carbon demands, while the spatial organization of microorganisms in biofilms was advantageous in transferring nutrients between community members. Furthermore, compared to other more recalcitrant and chemically heterogeneous DOM sources, the highly labile supraglacial DOM was unable to sustain the same magnitude of microbial metabolism. The present study revealed dynamic carbon cycling in supraglacial environments, mediated by the tight coupling between in situ carbon fixation, DOM exudation, and rapid consumption. Statistical analyses failed to show the impact of any physical parameters on community composition. However, data from the Greenland Ice Sheet imply that interactions between community composition and meltwater dynamics are susceptible to environmental changes, shifting ecosystem function and microbial communities, with unforeseen consequences to downstream environments. A multi-scale approach contributed to a better understanding of microbial biogeography, carbon cycling, and cellular spatial organization in glacial surface environments.Item Microbially mediated biogeochemical cycles in polar ice covered lakes(Montana State University - Bozeman, College of Agriculture, 2016) Michaud, Alexander Bryce Olson; Chairperson, Graduate Committee: John C. Priscu; Trista J. Vick-Majors, Mark L. Skidmore and John C. Priscu were co-authors of the article, 'Field testing of a clean, hot water drill used for access to subglacial aquatic environments' submitted to the journal 'Antarctic science' which is contained within this dissertation.; Mark L. Skidmore, Andrew C. Mitchell, Trista J. Vick-Majors, John C. Priscu, Carlo Barbante, Clara Turetta and Will vanGelder were co-authors of the article, 'Solute sources and geochemical processes in subglacial Lake Whillans, west Antarctica' in the journal 'Geology' which is contained within this dissertation.; John E. Dore, Trista J. Vick-Majors, Mark L. Skidmore and John C. Priscu were co-authors of the article, 'Microbial methane transformations beneath the west Antarctic ice sheet' submitted to the journal 'Science' which is contained within this dissertation.; This dissertation contains one article of which Alexander Bryce Olson Michaud is not the main author.Lakes are important sites for globally-relevant biogeochemical cycles mediated by microorganisms. In the Arctic, seasonally ice covered thermokarst lakes are a large component in Earth's carbon cycle due to their methane emissions from organic carbon degradation. In the Antarctic, over 400 unexplored lakes exist beneath the Antarctic ice sheet with unknown biogeochemical contributions to the Earth system. This dissertation seeks to investigate the biogeochemical role of microorganisms in the lake habitat and how they interact with the seasonal and permanent ice covers of lakes in polar environments. Microbiologically clean hot water drilling was used to access a subglacial lake beneath Antarctica's ice to collect, for the first time, intact sediment and water samples. Laboratory experiments on Arctic and Antarctic, seasonally and perennially, respectively, ice covered lakes were used to investigate the impact of lake ice freezing regimes on microorganisms. My results show that subglacial lake sediments beneath the West Antarctic Ice Sheet contain solute ratios that suggest relict marine sediments were deposited during previous interglacial periods. Microbial activity overprints the marine geochemical signature to produce fluxes of ions into the Subglacial Lake Whillans water column, which ultimately drains to the Southern Ocean. Microbial activity in Subglacial Lake Whillans is partially fueled by biologically-formed methane diffusing from below our deepest collected (~38 cm) subglacial sediment samples. The ice above Subglacial Lake Whillans appears to be an important source of molecular oxygen for microorganisms to drive oxidative physiologies. My experimental evidence shows microorganisms incorporate into lake ice cover to, potentially, avoid increasing stressors from progressive lake ice freezing. Taken together, the results from this dissertation reinforce the hypothesis that subglacial environments beneath the Antarctic ice sheet are habitats for life. Further, the microorganisms in subglacial lakes participate in globally-relevant biogeochemical cycles. Here, I extend the extent of the biosphere and show sediments at the base of ice sheets are an active component of the Earth system.Item Biogeochemical processes in Antarctic aquatic environments: linkages and limitations(Montana State University - Bozeman, College of Agriculture, 2016) Vick-Majors, Trista Juliana; Chairperson, Graduate Committee: John C. Priscu; John C. Priscu and Linda Amaral-Zettler were co-authors of the article, 'Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered antarctic lakes' in the journal 'The ISME journal ' which is contained within this dissertation.; John C. Priscu was a co-author of the article, 'Partitioning of inorganic carbon-fixation in permanently ice-covered Antarctic lakes' submitted to the journal 'Microbial ecology' which is contained within this dissertation.; Amanda Achberger, Pamela Santibanez, John E. Dore, Timothy Hodson, Alexander B. Michaud, Brent C. Christner, Jill Mikucki, Mark L. Skidmore, Ross Powell, W. Peyton Adkins, Carlo Barbante, Andrew Mitchell, Reed Scherer and John C. Priscu were co-authors of the article, 'Biogeochemistry and microbial diversity in the marine cavity beneath the McMurdo Ice Shelf, Antarctica' submitted to the journal 'Limnology and oceanography' which is contained within this dissertation.; Alexander B. Michaud and John C. Priscu were co-authors of the article, 'Subglacial carbon and nutrient fluxes fertilize the Southern Ocean under the Ross Ice Shelf' submitted to the journal 'Nature' which is contained within this dissertation.; This dissertation contains two articles of which Trista Juliana Vick-Majors is not the main author.The research presented in this dissertation focused on microbially-mediated biogeochemical processes and microbial ecology in Antarctic lakes and seawater. The major objective of my research was to examine the impact of environmentally imposed energetic constraints on nutrient cycling in mirobially-dominated systems. I used three ice-covered aquatic environments as natural laboratories for my investigations. The permanently ice-covered lakes of the McMurdo Dry Valleys (MCM) are located in Victoria Land, East Antarctica. The MCM have been studied intensively as part of the McMurdo Long Term Ecological Research Project since 1993. My work built on the extensive MCM dataset via high-throughput DNA sequencing to examine microbial communities from all three domains of life during the transition to winter, and by quantifying rates of dark inorganic carbon-fixation. This worked showed the importance of flexible metabolisms in the microbial ecosystems of the MCM lakes. The ocean beneath the McMurdo Ice Shelf (MIS) is the gateway between the Ross Sea and the dark ocean of the Ross Ice Shelf cavity. The area supports a biological carbon pump that is important in ocean biogeochemistry. Ice shelves around Antarctica are under threat of collapse, but little is known about the ecosystems beneath them. My work used a combination of biogeochemical measurements and assessment of microbial community structure to characterize the ecosystem beneath the MIS and its connections to the open ocean. The data showed the importance of nutrients advected from open water to the MIS cavity and projected an organic carbon deficit farther from the ice shelf edge. Subglacial Lake Whillans lies 800 m beneath the surface of the West Antarctic Ice Sheet near the end of a hydrological continuum that terminates in the ocean beneath the Ross Ice Shelf. Primarily through the use of biogeochemical rate measurements and determinations of organic matter quantity and quality, this work established the presence of an active microbial ecosystem in the subglacial lake, and estimated the annual subglacial flux of carbon and nutrients to the ocean under the ice shelf. Together, these projects show the importance of microbial activity in regional biogeochemical processes and of metabolic flexibility under energy-limited conditions.Item Factors influecing the abundance of microorganisms in icy environments(Montana State University - Bozeman, College of Agriculture, 2016) Santibanez-Avila, Pamela Alejandra; Chairperson, Graduate Committee: John C. Priscu; Joseph R. McConnell and John C. Priscu were co-authors of the article, 'A flow cytometric method to measure prokaryotic records in ice cores: an example from the Wais Divide drilling site' submitted to the journal 'Journal of glaciology: instruments and methods' which is contained within this dissertation.; Mark Greenwood, Joseph R. McConnell and John C. Priscu were co-authors of the article, 'Prokaryotic concentration changes between the last glacial maximum and the early Holocene from the Wais Divide ice core' submitted to the journal 'Quaternary science reviews' which is contained within this dissertation.; Alexander B. Michaud, Trista J. Vick-Majors, Juliana D'Andrilli, Amy Chiuchiolo and John Priscu were co-authors of the article, 'Bacterial response to progressive freezing in perennially and seasonally ice-covered lakes' submitted to the journal 'Journal of geophysical research (JGR) biogeosciences' which is contained within this dissertation.Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides' (Falkowski et al., 2008). Despite of the key role of microbes on Earth, microbial community characteristics are not explicitly part of climate models because our understanding of their responses to long-term environmental and climatic processes is limited. In this study, I developed a Flow Cytometric protocol to access a long-term record of non-photosynthetic prokaryotic cell concentration archived in the West Antarctic Ice-Sheet (WAIS; chapter 2). The WD ice core was retrieved between 2009 and 2011 to a depth of 3,405 m, extending back to 68,000 before 1950. Once a 17,400 year-record of prokaryotic cell concentration was acquired, I investigated its temporal variability and patterns, determined the potential sources of prokaryotic cells between the Last Glacial Maximum and the early Holocene, and assessed the environmental factors that might have the largest influence on the prokaryotic response (chapter 3). The observed patterns in the prokaryotic record are linked to large-scale controls of the Southern Ocean and West Antarctica Ice-Sheet. The main research findings presented here about the first prokaryotic record are: (i) airborne prokaryotic cell concentration does respond to long-term climatic and environmental processes, (ii) the processes of deglaciation, sea level rise and sea-ice fluctuation were key; the abundance of prokaryotic cells covariate with ssNa and black carbon, and (iii) the prokaryotic cell record variate on millennial time scale with cycles of 1,490-years. In addition, I studied 'congelation ice' (i.e., ice forms as liquid water freezes) from ice-covered lakes to understand prokaryotic cell segregation between liquid and solid phases during the physical freezing process. Five mesocosm experiments were designed to understand prokaryotic responses to the progressive freezing in concert with field observations from ice-covered lakes from Barrow, Alaska. As a result of this last study (chapter 4), I concluded that prokaryotic cells are preferentially incorporated in the ice with segregation coefficients (K eff) between 0.8 - 4.4, which are higher than for major ions. Prokaryotic cells avoid rejection more effectively from the ice matrix.Item Ecosystem dynamics and temporal variations in a microbially dominated, coastal antarctic lake(Montana State University - Bozeman, College of Agriculture, 2009) Dieser, Markus; Chairperson, Graduate Committee: John C. Priscu; Christine Foreman (co-chair)This study investigated the microbial ecology of Pony Lake, Antarctica. The main objectives of this research were to 1) characterize physicochemical parameters in Pony Lake during the transition from ice covered to ice free, 2) highlight seasonal and inter-seasonal alterations in lake parameters, 3) relate the physicochemical conditions in the ice and water column to microbial processes and community structure, 4) characterize the effects of phototransformation of dissolved organic matter (DOM) on its bioavailability to bacteria, and 5) demonstrate the role of carotenoid pigments in protecting cells against environmental stresses. Also included are results from three McMurdo Dry Valley lakes on the survivability of microbes encapsulated within the lake ice covers. The results of this study highlight the sensitivity of Antarctic environments and the close coupling of environmental conditions and biological processes. Inter-seasonal differences in weather conditions and snow accumulation strongly affected the physicochemistry of this lacustrine system. Biological processes were closely tied to the physicochemical lake conditions. As a consequence planktonic abundances, production rates, and community structure evolved distinctly in each year. Bacterial production was regulated by the quality of DOM. Whereas nutrient availability appeared to play a minor role in eutrophic Pony Lake water, it became more critical for microbial communities found within the ice column of Antarctic lakes. Especially in the ice cover of the McMurdo Dry Valley lakes, enhanced microbial diversity and survivability was associated with particles (nutrient enriched micro-zones) within an otherwise ultra-oligotrophic habitat. In Pony Lake ice, microbial activity and community structure differed with respect to different strata within the ice column, induced by freeze-concentration of solutes, bioavailability of DOM, and oxygen gradients. A comparison of carotenoid pigmented and non-pigmented heterotrophic bacteria indicated that pigmentation provides enhanced resistance to environmental stresses such as freeze-thaw cycles or solar radiation. Collectively, the Pony Lake data demonstrated that microorganisms that persist throughout the year were able to survive much more severe conditions while entrapped within the ice compared to those observed in the lake water during summer months. Further, this study contributes to a better understanding of the biogeochemical carbon cycle in a microbially dominated system.