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Item Daily signals in nitrate processing provide a holistic perspective on stream corridor hydrologic and biogeochemical function(Montana State University - Bozeman, College of Agriculture, 2023) Foster, Madison Jo; Chairperson, Graduate Committee: Robert A. Payn; This is a manuscript style paper that includes co-authored chapters.Understanding interactive pathways of biogeochemical reaction and water movement in stream corridors is critical given the role stream corridors play in mitigating nitrate loading from agricultural watersheds. However, few studies consider the interactive effects of nitrate loading, riparian processing, and stream ecosystem processing, which may limit abilities to predict downstream nitrate delivery. Riparian groundwater inputs and stream ecosystem processing may vary due to daily cycles in evapotranspiration or stream ecosystem primary production. Recent advances in high-frequency monitoring of stream chemistry throughout the day exhibit potential to explore both hydrologic and biogeochemical influences on nitrate attenuation. In this thesis, I explore how diel variations in stream reach nitrate processing can provide holistic perspectives on the attenuation of nitrate along stream corridors within a watershed that is heavily influenced by agricultural land use. Nitrate processing is defined as the evident changes in nitrate concentration in parcels of water as they travel along a given reach of a stream, as measured from nitrate sensors located at the head and base of ca. 0.5 km reaches. To understand controls on diel variation in nitrate processing, we measured diel processing signals in agricultural headwater reaches in Central Montana, USA spanning variable atmospheric and flow conditions from March through August in 2020-2022. Across 168 days with valid data, most signals exhibited little diel variation (n = 106) and this lack of variation occurred most frequently during cooler and shorter days. In contrast, signals with greater variation were common during longer days, warmer temperatures, and lower flows (n = 62). This seasonal shift in patterns suggests that solar radiation and stream flow are primary controls on diel nitrate processing signals in these low-order reaches. In addition to diel variation, less overall nitrate attenuation in the study reach with direct inputs of high-nitrate upland waters suggest that the degree of hydrologic connection to upland aquifers influences apparent reach nitrate processing. This work highlights how understanding the drivers of diel processing signals may lead to a more holistic understanding of how multiple interacting processes in stream corridors influence nitrate delivery to downstream ecosystems.Item The application of mass spectrometry in environmental chemistry: investigating biological cycling of arsenic, mercury and glycine betaine in aquatic ecosystems(Montana State University - Bozeman, College of Letters & Science, 2019) Alowaifeer, Abdullah Mohammed; Chairperson, Graduate Committee: Timothy R. McDermott; Brian Bothner (co-chair); Masafumi Yoshinaga, Patricia E. Bigelow, Brian Bothner and Timothy R. McDermott were co-authors of the article, 'Biological cycling of arsenic and mercury in Yellowstone Lake' which is contained within this thesis.; Qian Wang, Brian Bothner and Timothy R. McDermott were co-authors of the article, 'Examining the role of photoautotrophs contributing to glycine betaine, methylated amines and methane in oxic waters' which is contained within this thesis.Elemental cycling is a complex process that occurs abiotically and biotically. While abiotic cycling is well defined, biological cycling is more complex as it involves different microbes, animals and enzymes that govern its form and fate. In my project, I investigated the biological cycling of two of the most toxic elements known, arsenic and mercury. I examine their bioavailability, bioaccumulation and biomagnification in freshwater aquatic systems using Yellowstone Lake as a study model. In addtion, the sources and sinks of glycine betaine, an important aquatic metabolite that contributes to the carbon and nitrogen cycle, is investigated in Yellowstone Lake and three rivers located around the state of Montana. This research presented in this dissertation offers new insight on how arsenic and mercury cycle in aquatic systems and introduces a new hypothesis of the possible source of glycine betaine in freshwater ecosystem. Additionally, this project highlights a new and promising methodology to detect and quatify methylated amines in water samples.Item Scaling nitrogen retention from trees to forests through succession(Montana State University - Bozeman, College of Agriculture, 2016) Scott-Klingborg, Aaron James; Chairperson, Graduate Committee: Jack Brookshire; Jack Brookshire was an author of the article, 'Large trees dominate nitrogen retention across forest succession' submitted to the journal 'Ecology letters' which is contained within this thesis.; Jack Brookshire was an author of the article, 'Expression of sink-driven and transactional nitrogen limitation following stand-replacing disturbance in an inland pacific northwest coniferous forest' submitted to the journal 'Ecosystems' which is contained within this thesis.We seek to understand how the ability of trees to acquire and retain nitrogen (N) changes throughout their lifetimes. This capacity enables trees to act as carbon (C) sinks individually and collectively in forest ecosystems over successional time scales. We evaluate how properties that govern nutrient retention change with tree size and forest age, and how allometric relationships scale up to influence ecosystem-level patterns of N cycling and retention. Most generally, we hypothesized that changes in N uptake and recycling efficiency with increasing tree size would vary with forest age and N availability. Additionally, we evaluated changes in ecosystem-level C and N accumulation throughout secondary forest succession following clear-cut logging disturbances in an effort to understand how N limitation may become expressed over time and interact with forest successional dynamics. Our findings highlight the importance of large trees in ecosystem N cycling and growth. We find that increasing mass growth rates are matched by an increasing capacity to acquire and retain N without necessitating increases in growth efficiency. Research findings indicate that mortality of single trees may hold profound consequences for stand-level N retention in addition to C storage. At the ecosystem scale, we find N accumulation and limitation are dynamic processes that fluctuate in strength and source over forest succession, and that ecosystem accumulation of N was driven predominately by increasing N in plant biomass rather than in soil pools.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 A generalized optimization model of microbially driven aquatic biogeochemistry based on thermodynamic, kinetic, and stoichiometric ecological theory(2014-12) Payn, Robert A.; Helton, A. M.; Poole, Geoffrey C.; Izurieta, Clemente Ignacio; Burgin, A. J.; Bernhardt, E. S.We have developed a mechanistic model of aquatic microbial metabolism and growth, where we apply fundamental ecological theory to simulate the simultaneous influence of multiple potential metabolic reactions on system biogeochemistry. Software design was based on an anticipated cycle of adaptive hypothesis testing, requiring that the model implementation be highly modular, quickly extensible, and easily coupled with hydrologic models in a shared state space. Model testing scenarios were designed to assess the potential for competition over dissolved organic carbon, oxygen, and inorganic nitrogen in simulated batch reactors. Test results demonstrated that the model appropriately weights metabolic processes according to the amount of chemical energy available in the associated biochemical reactions, and results also demonstrated how simulated carbon, nitrogen, and sulfur dynamics were influenced by simultaneous microbial competition for multiple resources. This effort contributes an approach to generalized modeling of microbial metabolism that will be useful for a theoretically and mechanistically principled approach to biogeochemical analysis.Item Linkages between soils and lake ice sediments biogeochemistry : Taylor Valley, southern Victoria Land Antarctica(Montana State University - Bozeman, College of Agriculture, 2002) Konley, Scott ThomasItem The microbial sulfur cycle(2011-12) Klotz, M. G.; Bryant, Donald A.; Hanson, T. E.Item Biogeochemical and plant functional group response to long-term snow manipulation in a subalpine grassland(Montana State University - Bozeman, College of Agriculture, 2013) Holsinger, Jordan Paul; Chairperson, Graduate Committee: Jack BrookshireSnow represents an important control over plant communities in seasonally snow-covered ecosystems. It constrains the growing season and affects the availability of important resources including water, nitrogen (N) and phosphorus (P). Snow depth, distribution and duration have been affected by global climate change making it increasingly important to understand the effects of changing snow regimes on terrestrial ecosystems. Here we leverage a 43-year snow manipulation experiment to examine the effects of long-term changes in snow depth on plant community structure, resource availability and interactions therein in a common grassland type of the northern Rocky Mountains in western North America. Long-term experimental doubling and quadrupling of snowpack was associated with a significant shift in plant functional group distribution to a more forb rich community. Snow addition has resulted in a two to three-fold increase in forb to grass biomass ratios over time. Forbs consistently had greater N and P contents and lower nutrient use efficiencies compared to grasses. Forbs also displayed higher rates of net photosynthesis relative to grasses and sustained positive carbon (C) fixation rates late into the growing season after grasses had ceased. Though there is evidence that water exerts considerable control over ecosystem processes, increased snow depth did not have affect soil water availability through the growing season. However, snow depth was associated with significant differences in plant-available phosphate across the entire growing season with approximate 15% and 31% increases in pools of available P relative to ambient snowpack depth for doubled and quadrupled snowpacks respectively. Estimates of direct P inputs via dust and the ratio of available P to total P in the soil suggest that internal cycling was largely responsible for the observed differences in pools of available P. However, growing season net mineralization rates do not differ across treatments. This may suggest that winter processes make significant contributions to nutrient cycles. It is possible that the increased availability of P favors the shift to a forb-rich community under deeper snow because of their increased productivity under dry conditions and that the increased litter quality of forbs likewise promotes increased litter decomposition and mineralization, especially of P.