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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.