Biogeochemical and Molecular Biological Characterization of Nitrogen Cycle Processes in the Columbia River and Estuary

Human induced changes in the nitrogen cycle on land are recorded in the nitrogen flux of rivers, which integrate the landscape processes in their watersheds and deliver materials to coastal systems. The annual global creation of fixed reactive nitrogen (Nr) from human activities is greater than 50% of naturally fixed Nr. As a result, the flux of Nr to aquatic habitats and the subsequent eutrophication of estuarine and coastal ecosystems has become a major environmental health issue. In addition, Nr is a source of the potent greenhouse gas, N₂O and may be tightly linked to the global carbon cycle, thus potentially affecting global CO₂ levels. Quantifying the increased Nr flux is difficult since multiple contributing factors occur at different scales and interact to produce rapid and sometimes unpredictable changes in the biogeochemical cycle of Nr. The microbially-mediated processes of nitrification and denitrification are tightly linked and govern the recycling and removal processes, respectively, in the global Nr cycle. They are processes that also occur at different spatial and hence, temporal scales. This thesis is an assessment of the role of nitrification in Nr cycling in the Columbia River System (CRS), which includes its plume, estuarine mixing zone, and fluvial reaches. As the Columbia River is the largest source of freshwater entering the eastern boundary of the North Pacific Ocean it can exert a major influence on regional biogeochemical processes. Chapter 1 provides an introduction to the biogeochemical reactions in the Nr cycle. Chapter 2 describes an improved adaptation of the methodology for the fluorometric determination of ammonium that corrects for the absorptive interferences of dissolved organic carbon (DOC). Chapter 3 is a spatial and temporal study of nitrification carried out in the CRS, using molecular biological characterization, chemical sensor time series, ₁₅N natural abundance stable isotope time series, and ₁₅N stable isotope tracer experiments. The primary results of this research are that ammonia-oxidizing archaea (AOA) may be significant contributors to the first and rate-limiting step of nitrification, ammonia oxidation, in salinity-influenced stretches of the Columbia River estuary during upwelling events as well as during low flow, low nutrient conditions in the Columbia River, thereby highlighting the spatial and temporal sensitivity of these processes.