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Streams are ecosystems organized by disturbance. One of the most frequent disturbances within a stream is elevated flow. Elevated flow can both stimulate ecosystem processes and impede them. Consequently, flow plays a critical role in shifting the dominant stream function between biological transformation and physical transportation of materials. To garner further insight into the complex interactions of stream function and flow, I assessed the influence of elevated flow and flow disturbances on stream metabolism. To do so, I analyzed five years of dissolved oxygen data from an urban- and agriculturallyinfluenced stream to estimate metabolism. Stream metabolism is estimated from the production (gross primary production; GPP) and consumption (ecosystem respiration; ER) of dissolved oxygen. With these data, I evaluated how low and elevated flows differentially impact water quality (e.g., turbidity, conductivity) and metabolism using segmented metabolism- and concentration- discharge analyses. I found that GPP declined at varying rates across discharge, and ER decreased at lower flows but became constant at higher flows. Net ecosystem production (NEP; = GPP - ER) reflected the divergence of GPP and ER and was unchanging at lower flows, but declined at higher discharge. These C-Q patterns can consequently influence or be influenced by changes in metabolism. I coupled metabolism-Q and C-Q trends to examine linked flow-induced changes to physicochemical parameters and metabolism. Parameters related to metabolism (e.g., turbidity and GPP, pH and NEP) frequently followed coupled trends. To investigate metabolic recovery dynamics (i.e., resistance and resilience) following flow disturbances, I analyzed metabolic responses to 15 isolated flow events and identified the antecedent conditions or disturbance characteristics that most contributed to recovery dynamics. ER was both more resistant and resilient than GPP. GPP took longer to recover (1 to >9 days, mean = 2.5) than ER (1 to 2 days, mean = 1.1). ER resistance was strongly correlated with the intensity of the flow event, whereas GPP was not, suggesting that GPP responds similarly to flow disturbances, regardless of the magnitude of flow event. Flow may be the most frequent disturbance experienced by streams. However, streams are exposed to a multitude of other disturbances; here I also highlight how anthropogenic alterations to streams – namely, burying a stream underground – can change biogeochemical function. This thesis proposes novel frameworks to explore the nexus of flow, anthropogenic disturbances, and stream function, and thereby to further our understanding of the complex relationship between streams and disturbances. / Master of Science / A stream is defined by its flowing water. Flow brings the nutrients, organic matter, and other materials necessary to the algae and bacteria within the stream as well as the invertebrates and fishes they sustain, and is consequently integral to in-stream biology and ecology. However, elevated flow is also one of the most frequent disturbances experienced by streams. Elevated flow dilutes or enriches concentrations of water quality parameters, moves the water faster, reduces the amount of time essential nutrients are available to organisms within streams, and scours the algae and bacteria on stream bottoms. Here, I analyzed five years of data from an urban- and agriculturally-influenced stream and estimated stream metabolism to explore the influence of flow on stream biology, chemistry, and ecology. Stream metabolism is a process that reflects the respiration and photosynthesis of bacteria and algae, estimated from the production and consumption of dissolved oxygen. The primary research objective of my thesis was to investigate how changing flow impacts metabolism, by: (1) examining how low and high flows impact metabolism differently, and (2) studying the response and recovery of metabolism following multiple flow disturbances. Flow not only influences in-stream biology and processes, such as stream metabolism, but also changes the water quality of the stream (e.g., conductivity, pH, turbidity). To examine the interconnection between flow-induced changes to water quality parameters and metabolism, I measured how low and high flows impacted water quality and then compared water quality-flow relationships with metabolism at low and high flows. I found that metabolic processes and related water quality parameters were frequently coupled. Next, to test how water quality might also influence the response and recovery of metabolism after a flow disturbance, I examined whether prior environmental conditions (e.g., temperature, light) or the magnitude of the flow disturbance influenced metabolic response and recovery. I found that the size of the flow disturbance did change a critical piece of stream metabolism. Flow is not the only prevalent disturbance streams face: increasingly, streams are being altered by ongoing urban and suburbanization. Therefore, to highlight the full suite of disturbances to streams caused by human modification, I wrote a public science communication piece documenting the biological, chemical, and ecological ramifications of burying streams underground. Ultimately, this thesis proposes new frameworks to more adequately explore the complex relationships between water quality, stream ecology, and disturbances.

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As anthropogenic nutrient loads threaten the health of the Chesapeake Bay, lotic processes throughout its headwaters may buffer increased nitrogen inputs by converting them to stable forms, ultimately through denitrification to N2 gas. However, the temporal environmental factors controlling baseflow nitrogen retention are poorly understood, particularly temperature, shading, and dissolved organic matter dynamics. This study therefore attempts to elucidate the effects of these environmental variables on nitrogen cycling within the Fair Hill Natural Resources Management Area (Fair Hill), a forested watershed within the Piedmont physiographic province of the Chesapeake Bay. As expected, groundwater and allochthonous organic matter inputs set the foundation for lotic biogeochemistry at Fair Hill, creating a nutrient-limited, heterotrophic reach. Within this setting, three temporal "hot-moments" of in-stream nutrient processing were observed: the release of ammonium and phosphate during the warm - but shaded - growing season; nitrate uptake during autumnal leaf-fall; and a unique spike of nitrate uptake and respiration-induced degradation of labile organic matter during a drought. Consequently, the baseflow capacity of this headwater stream to buffer nutrient exports to the Chesapeake Bay constantly varies throughout the year in response to light availability, temperature, and in-stream organic matter dynamics. / Master of Science / Throughout the Chesapeake Bay watershed, ecological processes known as nitrogen retention can naturally remove nitrogen pollution from small streams (a.k.a. headwater streams), and hence the Chesapeake Bay watershed. However, in-stream nitrogen retention varies throughout the year due to seasonal changes in temperature, shading (as leaves grow in the spring or fall off in the fall), and the amount and type of organic matter in the stream. This study examines how these three variables (temperature, shading, and dissolved organic matter dynamics) affect nitrogen retention in a headwater, forested stream within the Fair Hill Natural Resources Management Area (Fair Hill) located in the Piedmont region of the Chesapeake Bay watershed. As expected, groundwater and organic matter inputs set the foundation for in-stream conditions at Fair Hill, creating an environment with low concentrations of nitrate and phosphate (thus causing the stream to be nutrient-limited), while also creating a heterotrophic environment, which is an environment where more oxygen is consumed by microbes than produced by algae and plants. Additionally, three seasonal patterns regarding in-stream nutrient dynamics were observed at Fair Hill. Firstly, in-stream ammonium and phosphate concentrations increased during the warm - but shaded - growing season. Secondly, in-stream nitrate concentrations decreased when leaves fell in the fall. Thirdly, during a drought, in-stream nitrate removal increased while in-stream organic matter became more degraded. Consequently, in-stream nutrient retention at Fair Hill varies constantly throughout the year in response to light availability, temperature, and in-stream organic matter dynamics.

The unique landscape controls and meltwater contributions associated with glacial landcover along the coast of southeast Alaska were examined to better understand in-stream processing of dissolved organic matter (DOM) and nutrients during downstream transport. Specifically, this study paired glacial streams with nearby non-glacial streams and compared differences in landscape controls to: 1) evaluate the impact of glacial landcover and meltwater contributions on in-stream metabolism and uptake potential of proglacial streams; 2) quantify changes in DOM composition and concentration in glacial runoff during precipitation-driven flushing of a glaciated landscape; and 3) characterize the impact of glacial landcover and meltwater contributions on longitudinal trends in the physical and chemical signature of streamwater through changing watershed landscapes. Stream metabolism estimates suggested glacial streams receive little DOM from landscape sources and have the potential to function as net autotrophic systems under low flow regimes with unobstructed sunlight. Unlike most watersheds, shallow organic soils and low in-stream respiration rates associated with glacial systems resulted in near equilibrium dissolved CO₂ concentrations, with little flux to the atmosphere. Longitudinal stream analyses concluded low-elevation landscape discharge contributions had little influence on glacial streams compared to non-glacial streams. High specific discharge from glacial landscapes controlled streamwater chemistry throughout proglacial watersheds suggesting meltwater was delivered from the terminus of coastal glaciers downstream to the Gulf of Alaska (GOA) with little dilution or in-stream processing. Uniform concentrations of DOM and nutrients were found during increased discharge driven by precipitation on the glaciated watershed. This was in contrast to the non-glacial watershed, where streamwater DOM concentrations were largely controlled by connections to DOM-rich landscape sources during storm flows. Results from this study enhance the understanding of in-stream processes and landscape controls in watersheds that deliver freshwater to an ecologically productive marine zone and valuable commercial fishery. Furthermore, this study provides information about watersheds undergoing glacial recession to GOA basin-wide estimates of DOM export and future research initiatives focusing on in-stream DOM processing. / Ph. D.

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I investigated how anthropogenic acidification influences stream metabolism and nitrogen (N) cycling by considering the stress response of microbial compartments responsible for these ecosystem processes. Microcosm incubations of leaf biofilms from streams of differing pH revealed greater rates of fungal biomass-specific respiration (i.e. the stress metric <i>q</i>CO₂) and biomass-specific N uptake (i.e. <i>q</i>N) with increasing acidity. The positive relationship between <i>q</i>CO₂ and <i>q</i>N indicated alternate fates for N other than structural biomass, possibly related to increased exoenzyme production as part of the stress response. Whole-stream ¹⁵N experiments and measurements of respiration and fungal standing crop across the pH gradient resulted in similar patterns in <i>q</i>CO₂ and <i>q</i>N found in microcosm experiments, supporting <i>q</i>CO₂ as an ecosystem-level stress indicator and providing insight towards controls over N cycling across the pH gradient. Fungal biomass and ecosystem respiration declined with increasing acidity while N uptake metrics were not related to pH, which suggested <i>q</i>N in acid streams was sufficiently high to counteract declines in fungal abundance. During spring, chlorophyll <i>a</i> standing crops were higher in more acidic streams despite lower nutrient concentrations. However, N uptake rates and gross primary production differed little between acid and circumneutral streams. Reduced heterotrophy in acid streams was apparent in lower whole-stream respiration rates, less ability to process organic carbon, and little response of N uptake to added carbon resources. Overall, acid-induced stress in streams was found to impair decomposer activity and caused a decoupling of carbon and nitrogen cycles in these systems. / Ph. D.