Direct determination of nitrogen removal rates and pathways in coastal ecosystems

This dissertation examines the role of microorganisms in marine biogeochemical cycles with a particular emphasis on sedimentary nitrogen transformations. Nitrogen is required by all living organisms and is a key nutrient controlling the productivity of Earth's oceans. Pervasive endeavors of modern human society, such as fossil fuel combustion and Haber-Bosch N2 fixation for agricultural fertilizers, have caused large-scale perturbations in the natural, global nitrogen cycle such that the rate of anthropogenic reactive nitrogen creation now exceeds that of all natural processes combined. A substantial fraction of this man-made reactive nitrogen is being lost to the environment where, as a macro-nutrient, excessive nitrogen loading is causing extensive disruptions to natural primary production cycles and food webs. Basic scientific research on nitrogen cycling in coastal oceans is imperative as human activities are increasingly adding to the reactive nitrogen influx to near-shore environments.Shallow coastal areas (< 200 m water depth) cover only &sim 7% of the ocean although up to 30% of marine primary production occurs in these zones. Biogenic debris settling in coastal zones largely escapes degradation in the water column, and thus, as much as 60% of locally-produced organic matter undergoes benthic deposition and diagenesis. Nutrients regenerated during organic matter mineralization in shallow sediments are essential in fueling high rates of marine primary production in continental margins. Coastal sediments are also important sites of reactive nitrogen removal with the majority of marine microbial N2 production occurring in these areas. Production of N2 in continental shelf sediments via microbial denitrification and anammox (anaerobic ammonium oxidation) is an essential process for nitrogen removal and maintaining a balance of reactive nitrogen in the oceans. Denitrification and anammox are two of the least understood pathways in the nitrogen cycle explorations of rates and mechanisms for N2 production have been hindered mainly by methodological difficulties, spatial and temporal variability in benthic processes, and previously-overlooked nitrogen cycling pathways. Due largely to a paucity of direct N2 flux rate measurements, most global marine nitrogen budget estimates are tenuous (Capone 2008). Thus, the foci of this dissertation were to better constrain known rates of denitrification and anammox, elucidate the principal controls on these processes in situ, and explore the ecology of microorganisms mediating these reactions in coastal sediments.Rates and controls of nitrogen removal by microbial N2 production were studied at three field areas in two different estuaries. Field research sites within the Apalachicola National Estuarine Research Reserve included stations adjacent to St. George Island in the Gulf of Mexico (for the investigation of nitrogen cycling in permeable sediments) in addition to stations within an oligohaline marsh near the mouth of the Apalachicola River (for a study of nitrogen removal by coastal wetlands). Benthic microbial nitrogen cycling was also studied in fjords of the Svalbard islands in the Arctic Ocean.The first of four chapters of this dissertation describes a study identifying the microbial taxa which catalyze phytodetritus degradation and denitrification in permeable coastal sediments of the northeast Gulf of Mexico. Coastal benthic environments typically receive intermittent pulses of organic matter following phytoplankton bloom events and permeable sediments have been demonstrated to rapidly degrade this material. Microorganisms act as the primary agents of benthic organic matter decomposition through the production of extracellular hydrolytic enzymes, fermentation, and terminal carbon mineralization coupled with respiratory processes. Although the role of bacteria in the decomposition of organic matter in marine sediments has long been recognized, the mechanisms regulating organic matter decomposition, and relationships between the phylogeny of benthic microorganisms and changes in biogeochemical and ecological function, are under-explored. (Abstract shortened by UMI.)...