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Linking biological and physical processes to understand microbial diversity and nitrogen dynamics along the aquatic continuum


This dissertation examines the effects of anthropogenic perturbation on microbial diversity and freshwater and marine nitrogen cycling, with a particular focus on nitrification and the production of the greenhouse gas nitrous oxide (N2O).

In the first chapter, headwater stream microbial communities were characterized across a gradient of urban and agricultural land use using 16S rRNA gene amplicon sequencing and compared to traditional physiochemical and biotic indicators of stream health. Stream microbial diversity differed in watersheds with high agricultural, urban, and forested land uses, and community structure differed in streams classified in good, fair, poor, and very poor condition using benthic macroinvertebrate indicators of water quality. Along with changes in diversity, stream community respiration correlated with forest cover and negatively correlated with nutrients associated with anthropogenic influence. Additionally, N2O concentrations negatively correlated with forested land use and positively correlated with dissolved inorganic nitrogen concentrations. The findings suggest stream microbial communities and ecosystem processes are impacted by watershed land use and can potentially assess ecosystem health.

The physical and biological controls on N2O production in the eutrophic Chesapeake Bay were investigated in the second chapter using gas measurements (N2O and N2/Ar) and stable isotope tracer incubations. Nitrification rates were highest following wind events that mixed oxygenated surface water below the pycnocline into ammonium-rich bottom waters, resulting in the accumulation of nitrite (NO2-) and N2O. During periods of weak vertical mixing, both N2O concentrations and nitrification rates were lower, and lower oxygen (O2) concentrations below the pycnocline allowed for N2O consumption by denitrification. A three-layer box model provided estimates of N2O production demonstrating the importance of both biological (production and consumption) and physical (advection and vertical exchange) processes in driving the observed large fluctuations in N2O concentrations. The results demonstrate physical processes affect the net balance between N2O production and consumption, making Chesapeake Bay a variable source and sink for N2O.

The final chapter investigates the seasonal coupling of primary production and nitrification, and the relationship between these processes and N2O production in the Southern California Bight (SCB). Over two seasonal upwelling cycles, nitrification rates fueled by ammonia and urea-derived N were measured using stable isotope tracer additions and N2O concentrations were measured using gas chromatography. Nitrification rates were highest at the onset of upwelling and correlated with rates of primary production. Similar ammonia and urea-derived N oxidation rates suggest urea is a significant nitrogen source fueling nitrification in the SCB. Nitrification supplied a large proportion of phytoplankton nitrogen demand, demonstrating significant nitrogen remineralization within the euphotic zone. The SCB was always a source of N2O to the atmosphere, which likely was advected into the system from the eastern tropical North Pacific. Together, the results suggest nitrification is an important control on the amount of organic carbon available for export, and the coupling of nitrogen remineralization and primary production may export a smaller fraction of primary production out of the surface ocean, but physical transport dominates over local production of N2O in the SCB.

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