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Virginia Tech is poised to become a global leader in the pursuit and application of new knowledge to inform management and restoration of waterbodies and their watersheds. Despite our notable strengths in specific disciplines, we have not yet facilitated nor nurtured an interdisciplinary program whereby a holistic perspective of freshwater systems can permeate into VT-shaped students and bridge the gaps among water-relevant biophysical, social sciences, and the arts. We know of no other major research university with a signature-strength in integrated freshwater systems science...

In freshwater networks, the sources, movement, and cycling of carbon and nutrients are shaped both by in-stream processes and the surrounding landscape. Streams receive and transport materials from upstream and terrestrial sources that support in-stream ecosystem processes and regulate downstream water quality. Understanding how these processes within a stream alter downstream carbon and nutrient fluxes is needed to assess the functional role of lotic ecosystems on the landscape. Further, predictions of how materials cycle and move throughout freshwater networks are derived from measurements at the stream reach scale which deliberately avoid complex geomorphology such as stream confluences. As a result, the impact of stream confluences on in-stream ecosystem processes and the fate of carbon and nutrients in freshwater networks has been overlooked. In this dissertation, I seek to address the following questions: (1) How are coupled carbon and nitrogen cycles altered by land use? (2) To what extent can rates of in-stream organic carbon removal inform our understanding of the role of streams in landscape carbon fluxes? (3) How are carbon metabolism and nutrient uptake altered downstream of a stream confluence? (4) How do confluences alter the transport and fate of carbon and nutrients within a freshwater network? In Chapter 2, I showed that the fate of organic carbon and nitrate are similar in headwater streams across the United States. Organic carbon travels longer distances before being respired in agricultural and urban streams compared to reference streams, suggesting that human modifications to landscapes impact carbon cycling and transport in streams. In Chapter 3, I demonstrated how rates of in-stream organic carbon removal can be used to quantify terrestrial-aquatic linkages and showed that laboratory bioassays systematically underestimate ecosystem organic carbon fluxes compared to whole-stream metabolism measurements. In Chapter 4, I conducted whole-ecosystem manipulation experiments to assess how ecosystem processes are altered by a confluence. I found that carbon metabolism and phosphorus uptake are suppressed downstream of a confluence and that rates of organic carbon uptake are spatially variable throughout a confluence mixing zone. In Chapter 5, I examined potential reach-scale and watershed-scale drivers to explain patterns of organic matter and nutrient chemistry downstream of confluences throughout a stream network. Reaches downstream of confluences were geomorphically and biogeochemically distinct from upstream reaches, and differences in upstream and tributary reach chemistry or drainage area did not explain patterns of biologically reactive parameters at confluences. My dissertation highlights the importance of in-stream ecosystem processes in driving the cycling and downstream fate of carbon and nutrients. I show how rates of whole-stream carbon metabolism can be used to better constrain terrestrial-aquatic organic carbon fluxes. I investigate the potentially disproportionate role of ecosystem interfaces, namely stream confluences, in determining the cycling and fate of carbon and nutrients in freshwater networks. This work challenges assumptions around controls over water quality in freshwater networks and asserts that by ignoring (1) contributions of all in-stream processes to whole-ecosystem function and (2) how confluences alter those processes, we risk misrepresenting the role of running waters in determining the fluxes and fate of carbon and nutrients from the reach- to the network-scale. Doctor of Philosophy Streams receive and use materials from upstream and the surrounding landscape to fuel in-stream ecosystem processes (e.g. carbon and nutrient cycling). Understanding how these processes within a stream alter concentrations of carbon and other nutrients is needed to assess how the ecosystem is functioning and what the consequences are on water quality downstream. Further, predictions of how materials cycle and move at the scale of streams networks are derived from measurements at the stream reach scale. As a result, the impact of stream confluences (i.e., where two streams meet and mix) on in-stream carbon and nutrient cycling and the consequences on downstream water quality has been overlooked. In this dissertation, I seek to address the following questions: (1) How are carbon and nitrogen cycles linked in streams and how those links altered by land use? (2) How can rates of in-stream carbon cycling inform our understanding of the role of streams in landscape carbon budgets? (3) How are carbon and nutrient removal altered downstream of a stream confluence? (4) How do confluences alter water chemistry within a freshwater network? In Chapter 2, I showed that organic carbon and nitrate shared similar fates in streams across the United States. Organic carbon traveled longer distances before being respired in agricultural and urban streams compared to natively-vegetated streams, suggesting that human modifications to landscapes impact carbon cycling and transport in streams. In Chapter 3, I demonstrated how rates of in-stream organic carbon removal can be used to understand land-stream connections. In Chapter 4, I conducted whole-ecosystem experiments to assess how carbon and nutrient removal are altered by a confluence. I showed that carbon metabolism and phosphorus removal are suppressed downstream of a confluence and that rates of organic carbon removal are spatially variable throughout where water from the two streams are mixing. In Chapter 5, I examined potential drivers to explain patterns of organic matter and nutrient chemistry downstream of confluences throughout a stream network. Reaches downstream of confluences were physically, chemically, and biologically distinct from upstream reaches and differences in upstream and tributary reach chemistry or drainage area did not explain patterns of water chemistry downstream of confluences. Overall, my dissertation highlights the importance of processes within a stream in driving carbon and nutrient cycling, and how rates of whole-stream carbon cycling can be used to better understand connections between streams and the surrounding landscape. I investigate the role of stream confluences in determining the cycling and downstream fate of carbon and nutrients in freshwater networks. This work shows that ecosystem functioning and downstream water quality in freshwater networks are affected by processes occurring within streams and by the interfaces between streams and other ecosystems (e.g., land-water interfaces, stream confluences).

Headwaters may be small relative to other aquatic ecosystems, but they are neither simple nor static environments. Heterogeneous stream corridors constitute the majority of river network length and regulate cycling of carbon and oxygen as they expand and contract their connections across the landscape. Though headwater streams integrate many biogeochemical signals from the watersheds they drain and provide important ecosystem services, their diverse habitats and dynamic changes in wet length have been under- examined compared to dendritic, perennial streams. This oversight complicates efforts to identify biogeochemical patterns at larger scales. This dissertation sets out to expand our knowledge of stream biogeochemical responses to variable connections both within the channel and the wider stream corridor. First, I investigated how the presence and arrangement of different habitat patches in the stream corridor affected overall emissions of carbon dioxide (CO2) and methane (CH4) from sub-watersheds of a forested mountain stream network. To do this I measured concentration and flux of both gasses along and around 4 streams, including dry reaches and adjacent vernal pools as well as flowing water. I found that emissions were highly variable over space and time; in particular, the presence of a vernal pool enhanced total carbon emissions from the stream corridor. Next, to quantify carbon cycling and export from a non-perennial headwater stream, I monitored concentrations of CO2 and dissolved organic carbon (DOC) at the stream outlet. I found that CO2 concentration had a negative relationship with stream discharge, and that exports of both CO2 and DOC were driven by storms reconnecting isolated surface water reaches. I also found that carbon biogeochemistry of intermediate flow states were unique from driest and highest-flow conditions. Finally, to explore how isolated pools in the stream channel respond to flow decrease and cessation, I measured dissolved oxygen (DO) as well as CO2 and CH4 from persistent pools of two non- perennial streams throughout an unusually dry summer and fall. I found that hypoxia was common in all isolated pools, but swings in DO were not consistent between pools even of the same stream. In using diel changes in DO to estimate metabolism, I also found that ecosystem respiration varied by stream, but gross primary production was more driven by stream surface water connectivity. Climate change is inducing many new patterns in stream hydrology with critical implications for biogeochemical activity, from reducing durations of connectivity to causing stronger storms. Improving our understanding of how surface water and landscape connectivity both influence the movement of carbon within and through streams is essential to resolving questions about the contributions of freshwaters to the global carbon cycle. Doctor of Philosophy Headwater streams may seem inconsequential to larger ecosystem processes due to their small size. However, the majority of a river's network length, or the total length of all the streams and rivers from spring to ocean, is made up of headwater streams. The widespread presence of headwater streams over all types of land, along with the unique layout of different aquatic habitats near streams and the fact that small streams often grow and shrink in length, mean that studying headwaters can tell us many things about how energy moves through ecosystems. This dissertation explores how we can use changing headwater connectivity to understand how carbon moves through ecosystems. Connectivity in aquatic science refers to how water can move through space in ways that rocks and trees and even many animals cannot. This idea is useful because water carries things around as it moves, and its presence or absence enables reactions that are essential for the cycling of energy and nutrients. For instance, when water moves from high ground to low ground, it navigates through soil and holes in the ground; it may get slowed down at flat spots where little pools form. I measured emissions of carbon dioxide and methane from streams as well as soils, holes, and pools near mountain streams to try to understand how the path water takes influences how much carbon dioxide and methane escapes into the air. My measurements were surprisingly different depending on where and when I took them. I found that if a seasonal pond is connected to a stream channel, the stream will emit more greenhouse gasses than if the pond goes dry. Connectivity can also describe if water moves continuously along a stream, or if the stream goes dry in places and is then disconnected from different parts of itself. I asked how a stream becoming disconnected affected carbon dioxide emissions as well as the movement of dissolved organic carbon, a food source for microorganisms. I found that the less water moving through the stream channel, the higher carbon dioxide concentrations were. I also found that storms move both carbon dioxide and dissolved organic carbon out of streams quickly, even if the stream had been disconnected. Finally, I investigated the water that is left when streams disconnect. I measured dissolved oxygen, carbon dioxide, and methane in isolated pools of two disconnected streams. By tracking how microbes and algae consume and produce oxygen when a stream is not flowing, I can understand how these lifeforms adapt. I found that isolated pools frequently have very low levels of dissolved oxygen. This means that microorganisms in the pools have to use special ways of getting energy, which in turn affects how different forms of carbon move through the stream ecosystems. Headwater stream ecosystems are very sensitive to small changes in flow and precipitation; however, climate change means that streams are going dry more often than they used to. My findings contribute to our understanding of how changes in stream connectivity have many biological effects that are important for water quality and ecosystem health.

Soil organic matter (SOM) is a critical biogeochemical pool that can be managed as part of global efforts to conserve nutrients and enhance carbon (C) sequestration. But reliably increasing SOM has proven difficult because most of the organic matter that enters soil as plant litter and organic amendments (i.e., compost, manure) is susceptible to decomposition by soil microorganisms and eventually is lost to the environment as greenhouse gases and non-point source pollution. Many soils lack the physical and/or chemical properties that enable some human-modified soils (e.g., terra preta soils in the Amazon Basin) to stabilize and retain C and nutrients in SOM while maintaining relatively high levels of productivity compared to surrounding natural soils that formed under similar conditions. I hypothesized that two of the major stabilizers of organic matter common to terra preta soils of the Amazon basin – black carbon (biochar) and poorly crystalline, reactive iron (Fe) minerals – could be applied to a fine-textured soil from Southwest Virginia to improve the accumulation and retention of C and nitrogen (N). I used a field experiment to compare the effects of three types of locally-produced biochars applied with and without an organic N fertilizer (blood meal) on soil C and N availability. I then used an incubation experiment featuring the soils from the aforementioned field experiment to examine the effects of applying Fe2+ -treated manure effluent on the retention of C and N in unamended and hardwood biochar-amended soils. I found that biochar adsorbed inorganic N in all cases, while providing a reliable, stable increase in SOM due to its recalcitrant nature. However, the manure effluent used in the incubation experiment stimulated the decomposition of mineral-associated organic matter (MAOM), with the addition of Fe2+ to the manure mitigating this apparent positive priming effect and the presence of biochar actually reversing this effect and promoting an increase in MAOM following manure application to biochar-amended soil. Overall, biochar stimulated the retention of N by decreasing the leachable inorganic N in the soil and enhanced soil C stocks. Additionally, biochar applications had the added benefit of promoting the accumulation of manure in soil as stable, microbially-processed MAOM, while co-applying Fe2+ with manure only served to inhibit the priming of native soil C. Master of Science Organic matter is an important constituent of all soils. Farmers and gardeners would like to increase the organic matter on their lands to improve their crop yields and health of their soils, yet people in many regions of the world struggle with actually getting long-lasting forms of organic matter to accumulate in soils. Moreover, managing soils to increase the amount of carbon stored in these long-lasting forms has the benefit of offsetting human contributions to atmospheric carbon dioxide and global warming. Some soils stabilize and build up organic matter more efficiently than others, and I hypothesized that if two well-known soil materials that help to stabilize organic matter – charcoal and iron – were added to a soil, then the accumulation of organic matter in the soil could be improved. The first part of my research was a field experiment in which three different kinds of charcoal were added either with or without an organic fertilizer to the soil in a Southwest Virginia pasture. I then measured the amount of carbon in the soil and determined that charcoal additions increased soil carbon and helped to retain mobile forms of plant nutrients. The second part of my research used the charcoal-treated and untreated soils from the field experiment for a project where cow manure was co-applied with three levels of iron and added to soils in jars in a controlled laboratory setting. The jars were then maintained at an ideal moisture and temperature for the growth of microbes for 70 days and analyzed afterwards. I found that the manure caused the organic matter in the soil to be consumed by microbes, while charcoal caused the organic matter from the manure to accumulate and remain. Adding iron with the manure prevented the microbes from consuming the pre-existing organic matter in the soil, but did not contribute to the retention of the manure in the soil. Overall, while both iron and charcoal influenced the retention of organic matter in soil, biochar proved to be more effective at stabilizing manure organic matter than the iron additions.

Understanding hydrologic controls on carbon accumulation and export within geographically isolated wetlands (GIW) has implications for the success of wetland restoration efforts intended to produce carbon sinks. However, little is known about how hydrologic connectivity along the aquatic-terrestrial interface in GIW catchments influences carbon dynamics, particularly regarding dissolved organic matter (DOM) transport and transformation. The organic matter (carbon) that accumulates in wetland soils may be released into water, generating DOM. DOM is mobile and reactive, making it influential to aquatic metabolism and water quality. To understand the role of different soil horizons as potential sources of DOM, extractable soil organic matter (ESOM) was measured in soil horizons collected from upland to wetland transects at four Delmarva Bay GIWs on the Delmarva Peninsula in the eastern United States. ESOM quantity and quality were analyzed to provide insights to organic matter sources and chemical characteristics. Findings demonstrated that ESOM in shallow organic horizons had increased aromaticity, higher molecular weight, and plant-like signatures. ESOM from deeper, mineral horizons had lower aromaticity, lower molecular weights, and protein-like signatures. Organic soil horizons had the largest quantities of ESOM, and ESOM decreased with increasing soil depth. ESOM quantities also generally decreased from the upland to the wetland, suggesting that continuous soil saturation leads to a decreased quantity of ESOM. Despite wetland soils having lower ESOM, these horizons are thicker and continuously hydrologically connected to wetland surface water, leading to wetland soils representing the largest potential source of DOM to the Delmarva Bay wetland system. Knowledge of which soil horizons are most biogeochemically significant for DOM transport in Delmarva and other GIW systems will become increasingly important as climate change is expected to alter the hydrologic connectivity of wetland soils to the surface water-groundwater continuum and as wetlands are more frequently designed for carbon sequestration. Master of Science Wetlands store carbon in their plant biomass and soils, which helps to mitigate the effects of climate change by keeping carbon out of the atmosphere. Carbon builds up in wetland soils because the continuously wet conditions slow down the microbial processes that would otherwise break down the organic matter (carbon) and release it to the atmosphere via greenhouse gas emissions. However, the organic matter that accumulates in wetland soils may be released into water, generating dissolved organic matter (DOM). This DOM has the potential to flow out of the wetland, providing a source of energy to aquatic organisms or impacting downstream water quality. Not all wetlands are continuously connected to other water bodies. Geographically Isolated Wetlands (GIW) are wetlands that you could walk all the way around and keep your feet dry. Despite lack of continuous surface water connections, GIWs may still influence downstream water quality via groundwater flow paths or seasonal surface water connections. This variable connectivity makes GIWs a unique setting to study carbon storage and fluxes in wetland soils. The potential for soil-derived DOM generation was studied by extracting organic matter from soils along a wet to dry gradient in Delmarva Bay GIWs. Shallow soils had the largest quantities of extractable soil organic matter (ESOM) and this organic matter is likely sourced from plant inputs to the soil. ESOM from deeper soils was more similar to the microbes that consume and alter the organic matter as it cycles deeper into the soil. Soils located in the wetland basin had less ESOM because continuous saturation depleted the pool of ESOM. Despite lower values of ESOM, wetland soils are very thick and continuously saturated, making these soils the largest potential contributor of soil-derived DOM to Delmarva Bay GIWs. This work furthers our understanding of how hydrology drives carbon cycling in GIWs and will inform wetland restoration efforts designed to create carbon sinks.

A fundamental focus in ecology is understanding interactions between environmental heterogeneity and ecological community structure, both of which are currently undergoing unprecedented alterations due to global change. In particular, many freshwater phytoplankton communities are experiencing multiple global change stressors, altering phytoplankton community composition, biomass, and spatial distribution. I used multiple approaches to characterize the interactions between spatial distribution and community structure of phytoplankton and quantify uncertainty in predictions of phytoplankton temporal dynamics. First, I analyzed data from 51 lakes to determine the environmental drivers of phytoplankton vertical distributions across the water column for different phytoplankton groups. I show that the relative importance of environmental drivers varies according to the functional traits of each phytoplankton group. Second, I conducted whole-ecosystem experiments in a reservoir to assess phytoplankton responses to surface water mixing events, which may become more prevalent as storms increase under global change. My results demonstrate that aggregated phytoplankton biomass has inconsistent responses to mixing over the short term, but responses of morphology-based functional groups of phytoplankton to mixing are more predictable. Third, I conducted a long-term whole-ecosystem experiment to assess phytoplankton responses to changes in water column thermal gradients which are predicted to increasingly occur under global change. I found that phytoplankton depth distributions responded similarly to thermal gradient disturbance over multiple years, and changes in depth distributions were related to changes in community composition. Fourth, I produced weekly hindcasts of phytoplankton density in a lake for two years to determine the dominant sources of uncertainty in phytoplankton density predictions. I found that better estimation of current phytoplankton density improved representation of error in phytoplankton models, and incorporation of additional life history stages to model structure may improve phytoplankton predictions. Overall, my dissertation chapters demonstrate that the vertical distribution and community structure of phytoplankton are linked, and that the interaction of phytoplankton community structure with environmental heterogeneity is more predictable over longer-term (e.g., months to years) than shorter-term (e.g., days to weeks) scales. My research emphasizes that consideration of phytoplankton community dynamics and the uncertainty associated with phytoplankton predictions are needed for freshwater management under global change. Doctor of Philosophy Freshwater phytoplankton, which are microscopic primary producers, are experiencing many environmental changes in lakes and reservoirs due to global change. This includes changes in water temperature, which affects phytoplankton growth and the types of phytoplankton that are present in the water. As a result, phytoplankton communities are changing in ways that affect water quality. For example, phytoplankton may grow rapidly and form blooms which cause unsightly surface scums, clog filters at water treatment plants, or release toxins. My dissertation research uses ecosystem experiments, computer modeling, and large datasets from many lakes to study how the interactions between phytoplankton and their environment might change due to human activities. I found that it is difficult to predict how phytoplankton will respond to changes in water temperature over the short term (days to weeks), but that longer-term (months to years) responses to water temperature changes are more predictable. I also found that the types of phytoplankton present in the water vary across depth in response to light, temperature, and predation. Since the species of phytoplankton that are present determine a waterbody's water quality, my results indicate that water quality can vary substantially among different depths. Finally, I found that the greatest sources of uncertainty in predicting phytoplankton are due to the challenges in accurately measuring the amount of phytoplankton that are present in a lake and representing complex phytoplankton processes in computer models. My research demonstrates that it is important to think about multiple types of phytoplankton and how they interact with the environment, not just the total amount of phytoplankton present, when predicting how water quality will change due to global change. In addition, it is important to consider the uncertainty associated with predictions of phytoplankton when we make decisions about how to manage water quality.

Anthropogenic freshwater salinization, which is caused by numerous human activities including agriculture, urbanization, and deicing, impacts an estimated 37% of the contiguous drainage area in the United States. High salt concentrations in brackish and marine environments (~1,500 – 60,000 µS cm-1) influence aquatic bacteria. Less is known about the effects of freshwater salt concentrations (≤ 1,500 µS cm-1) on bacterial ecology, despite the pervasiveness of freshwater salinization. Bacteria perform many fundamental ecosystem processes (e.g. biogeochemical cycling) and serve as indicators of human health risk from exposure to waterborne pathogens. Thus, to understand how salt pollution affects freshwater ecosystems, there is a critical need to understand how freshwater salinization is impacting bacterial ecology. Using a series of controlled mesocosm experiments, my objectives were to determine how (1) survival of fecal indicator bacteria (FIB), (2) the diversity of native freshwater bacterial communities, and (3) bacterial respiration and nutrient uptake rates responded across a freshwater salinity gradient of different salt profiles. Survival rates (t90) of Escherichia coli, the EPA recommended freshwater FIB, increased by over 200% as salinity increased from 30 to 1,500 µS cm-1. Survival rates were also significantly higher in water with elevated Mg2+ relative to other base cations, suggesting that different salt sources and ion profiles can have varied effects in FIB survival. Thus, freshwater salinization could cause accumulating concentrations of FIB even without increased loading, increasing the risk of bacterial impairment. Diversity of native bacterial communities also varied across a freshwater salinity gradient, with a general increase in species richness as salinity reached 1,500 µS cm-1. Community variability (β-diversity) was greatest at intermediate salinities of 125 – 350 µS cm-1 and decreased towards the upper and lower extremes (30 and 1,500 µS cm-1, respectively). These diversity patterns suggest that osmotic stress is an environmental filter, but filtering strength is lowest at intermediate salinities causing a change from more deterministic to more stochastic assembly mechanisms. Different salt types also produced distinct bacterial community structures. Lastly, bacterial respiration doubled as salinity increased to 350 – 800 µS cm-1, revealing a subsidy-stress response of bacterial respiration across a freshwater salinity gradient. Corresponding changes in nitrogen and phosphorus uptake increased N:P ratios in ambient water, especially in mesocosms with elevated Ca2+, which could affect nutrient limitation in salinized streams enriched with Ca2+. Bacterial community structure based on Bray-Curtis dissimilarity was not correlated to pairwise changes in respiration rates but was linked to net nitrogen and phosphorus uptake after five days. Collectively, these results establish that freshwater salinization alters bacterial ecology at the individual population, whole community, and ecosystem process scales. Further, different salt types (e.g., CaCl2, MgCl2, NaCl, KCl, sea salt) had varying effects on bacteria at all levels and should be considered when predicting the effects of salinization on freshwater ecosystems. Developing more nuanced salt management plans that consider not only amount, but different types, of salts in freshwaters could help improve our ability to predict human health risk from waterborne pathogens and mitigate/ reduce salinity-induced impacts to freshwater ecosystem processes and services. Doctor of Philosophy Humans rely on streams, rivers, and lakes for many services including transportation, recreation, food, and clean drinking water. Despite our reliance on freshwater ecosystems, human activity has significantly degraded freshwater resources worldwide. Recently, salt pollution caused by human activity on land, known as freshwater salinization, has emerged as a widespread water quality issue. Numerous human activities including agriculture, urbanization, resource extraction, and deicing have increased freshwater salt concentrations in 37% of the United States' contiguous drainage area. Large changes in salinity (i.e. from freshwater to oceanic salinities) are known to affect bacteria that perform many important ecological functions, such as nutrient cycling and water purification, while the effects of smaller changes in salinity more typical within the freshwater range are unknown. I used controlled laboratory experiments to determine how freshwater salinization affects (1) survival rates of Escherichia coli, (2) diversity of native bacterial communities, and (3) bacterial nutrient cycling. My results revealed that freshwater salinization can significantly increase how long E. coli survive in freshwater. E. coli are used to detect the presence of waterborne pathogens and reduce human health risk. Thus, freshwater salinization might reduce the reliability of E. coli as an indicator of waterborne pathogens as well as increase concentrations of bacterial that are potentially harmful to human health in freshwater. Additionally, freshwater salinization affected bacterial diversity by altering the ways in which bacterial communities form. In general, the number of bacterial species present increased as salinity reached the upper freshwater limit, but communities were most variable at intermediate freshwater salt concentrations. These diversity patterns suggest that different salt concentrations can either cause or reduce stress in bacteria, resulting in significantly different bacterial communities. Lastly, moderate increases in freshwater salt concentrations doubled bacterial respiration and nutrient uptake rates. Bacterial respiration influences how energy flows through ecosystems, and freshwater salinization could potentially alter this process. Different salt types also had different effects of bacterial ecology. Collectively, my results establish that freshwater salinization impacts bacteria at the individual, community, and ecosystem levels.

Freshwater reservoirs store, process, and emit to the atmosphere large quantities of carbon (C). Despite the important role of reservoirs in the global carbon cycle, it remains unknown how human activities are altering their carbon cycling. Climate change and land use are resulting in lower dissolved oxygen (DO) concentrations in freshwater ecosystems, yet more frequent, powerful storms are occurring that temporarily increase DO availability. The net effect of these opposing forces results in anoxia (DO < 0.5 mg L-1) punctuated by short-term increases in DO. The availability of DO controls alternate redox reactions in freshwaters, thereby determining the rate and end products of organic C mineralization, which include two greenhouse gases, carbon dioxide (CO2) and methane (CH4). I performed ecosystem-level DO manipulations and evaluated how changing DO conditions affected redox reactions and the production and emission of CO2 and CH4. I also explored how the magnitude and drivers of CH4 emissions changed spatio-temporarily in a eutrophic reservoir using time series models. Finally, I used a coupled data-modeling approach to forecast future emissions of CH4 from the same reservoir. I found that the depletion of DO results in the rapid onset of alternate redox reactions in freshwater reservoirs for organic C mineralization and greater production of CH4. When the anoxia occurred in the water column (vs. at the sediments), diffusive CO2 and CH4 efflux phenology was affected, and resulted in degassing occurring during storms before fall turnover. I observed that the magnitude of CH4 emissions varied along a longitudinal gradient of a small reservoir and that the environmental drivers of ebullition and diffusion can change substantially both over space (within one hundred meters) and time (within a few weeks). Finally, I developed a forecasting workflow that successfully predicted future CH4 ebullition rates during one summer season. My research provides insight to how changing DO conditions will alter redox reactions in the water column and greenhouse gas emissions, as well as provides a new technique for improving future predictions of CH4 emissions from freshwater reservoirs. Althogether, this work improves our understanding of how freshwater lake and reservoir carbon cycling will change in the future. Doctor of Philosophy Freshwater reservoirs store a lot of carbon in their sediments and emit a lot of carbon as greenhouse gases (carbon dioxide and methane) to the atmosphere. However, climate change, land use, and water quality management can change the chemical reactions that are responsible for the production of carbon dioxide and methane, which could have substantial effects on the global carbon budget. Here, I manipulated the oxygen conditions of a freshwater reservoir and monitored the chemistry and greenhouse gas emissions in the experimental reservoir relative to an upstream reference reservoir. I then estimated the methane emissions from the reservoir to understand how the chemistry and greenhouse gas emissions in freshwater reservoirs may change in the future. I found that reservoir oxygen availability controls the magnitude and timing of the chemical reactions that produce carbon dioxide and methane, which in turn alters greenhouse gas emissions. Additionally, I developed models that showed how the magnitude and drivers of methane emissions changed within a small reservoir over time. Finally, I was able to predict the timing and magnitude of methane bubbling from the sediments. Altogether, this work provides evidence how climate change, land use change, and water quality management will affect future water chemistry and greenhouse gas emissions from reservoirs.

Recent studies have focused on dissolved organic matter (DOM) cycling throughout river corridors or in reservoirs, but few have explored DOM cycling in commonplace but understudied run-of-river (ROR) reservoir systems. Impoundments disrupt river flow patterns, as they increase hydraulic residence time and alter the flow of DOM downstream. During storms when the majority of DOM loading occurs, impoundments become less likely to hold DOM and will increase export of DOM downstream. In this study, we quantified DOM bioavailability and composition, carbon flux, and carbon dioxide (CO2) gas evasion in a ROR reservoir system at baseflow conditions and during a 1.5-year storm event. This study used a combination of high frequency spatial sensor data geotagged to GPS coordinates along the river to reservoir transition, and grab samples of surface water taken at two U.S. Geological Survey stream gauges and three additional sites. The landscape and shallow flow paths to ROR reservoir systems resulted in the export of both aromatic carbon and labile organic matter present within these waters, as water was mixed and exported downstream. Additionally, the reservoir was a net sink of DOC and BDOC flux, while also a source of DIC flux. Finally, CO2 evasion was magnified by high flow, with the reservoir changing from a sink to a source of CO2 to the atmosphere. ROR reservoirs may undergo "short-circuiting" during high flow, which alters DOM transformations and transport of carbon downstream. Our results provide critical insight on carbon dynamics in ROR reservoir systems and highlight the need to incorporate riverine DOM into carbon budgets, especially under variable flow conditions. Master of Science Recent studies have focused on dissolved organic matter (DOM) cycling through river corridors, as DOM provides energy to aquatic food webs and can be converted to carbon dioxide (CO₂) through microbial respiration. Few studies have explored DOM cycling in commonplace but understudied run-of-river (ROR) reservoir systems. ROR reservoirs are created by the implementation of a dam across a river channel and use the flow of the river to generate hydroelectric power. During storms, when the majority of DOM loading occurs, impoundments become less likely to hold DOM and will increase export of DOM downstream. In this study, we quantified DOM quality and composition, DOM transport, and carbon dioxide (CO₂) gas evasion in a ROR reservoir system at baseflow conditions and across a 1.5 year storm event. This study used a combination of high frequency spatial sensor data combined with GPS coordinates along the river to reservoir transition, and grab samples of surface water taken at two U.S. Geological Survey stream gauges and three additional sites. Results show that the landscape and shallow flow paths to ROR reservoir systems resulted in the export of both high and low quality carbon present within these waters, as water was mixed and exported downstream. Additionally, the reservoir was a net sink of DOM flux, retaining 40.7% of the total DOM loading for the storm event. Finally, CO₂ evasion was magnified by the storm event, with the reservoir changing from a sink to a source of CO₂ to the atmosphere. Our results provide critical insight on carbon dynamics in ROR reservoir systems and highlight the need to incorporate riverine DOM into carbon budgets, especially under variable flow conditions.