Publication Date


Document Type


Committee Members

Silvia Newell, Ph.D. (Committee Chair); Mark McCarthy, Ph.D. (Committee Member); Timothy Davis, Ph.D. (Committee Member); Megan Rúa , Ph.D. (Committee Member); Chad Hammerschmidt, Ph.D. (Committee Member)

Degree Name

Doctor of Philosophy (PhD)


Eutrophication of aquatic systems can have cascading effects along hydrological continua from watersheds to coasts that result in impaired ecosystem health. In freshwater systems, blooms of toxic, non-nitrogen (N) fixing cyanobacteria (cyanoHABs), such as Microcystis, proliferate due to external loading of chemically reduced forms of N (e.g., ammonium (NH4+) and urea), which promote growth and toxin production. In coastal marine systems, nutrient loading can promote harmful algae blooms and threaten vulnerable, native vegetation, such as seagrasses, which provide valuable ecosystem services but are under threat globally from anthropogenic stressors. This dissertation focuses on NH4+ cycling in the water column of Lake Erie and microbial N transformations in St. Joseph Bay (Florida) sediments by combining biogeochemical rate measurements and molecular analysis of selected functional genes. In Lake Erie, NH4+ regeneration in the water column was an important source of internal N loading and may promote and/or sustain cyanoHAB biomass and toxin production beyond external N loads from the watershed. Despite abundant amoA gene copies (the gene responsible for catalyzing ammonia oxidation) at all stations and sampling times, nitrification rates followed seasonal patterns and were greatest outside of cyanoHABs, indicating that nitrifiers were less competitive than cyanoHABs for available NH4+. Nitrification converts NH4+ to nitrate (NO3-), the substrate for denitrification (microbial NO3- reduction to dinitrogen gas); therefore, suppression of nitrification via competition for NH4+ during cyanoHABs may inhibit natural N removal from these systems. In St. Joseph Bay, coupled nitrification-denitrification was the dominant N loss pathway, but high rates of dissimilatory NO3- reduction to NH4+ (DNRA) were also observed in sediments with seagrass vegetation. These results suggested that some of the external N loading is naturally removed from the system via denitrification, but there is also potential for within-system recycling via DNRA, which may exacerbate eutrophication effects on both the water column and vulnerable seagrass beds. These results support other recent work demonstrating the inability of some aquatic systems to remove excess anthropogenic N loads efficiently. These study findings also illustrate the importance of internal N recycling mechanisms, which must be considered to inform nutrient management strategies and ecosystem models developed to mitigate eutrophication and cyanoHABs. These findings also support the need for dual nutrient (N + phosphorus) reduction strategies to minimize cyanoHABs and protect aquatic ecosystem and human health.

Page Count


Department or Program

Department of Earth and Environmental Sciences

Year Degree Awarded