Date Awarded

Summer 2021

Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Virginia Institute of Marine Science


Bongkeun Song

Committee Member

Iris C Anderson

Committee Member

Robert C Hale

Committee Member

Chris Burbage


Estuaries are biogeochemical hotspots connecting terrestrial and coastal ecosystems. Anthropogenic disturbances, including increased nitrogen loading and plastic pollution, may have significant impacts on estuarine carbon and nitrogen cycling by altering microbiome structure and functions. The overarching goal of this dissertation was to examine how microbiomes and their associated biogeochemical processes are influenced by natural variation and anthropogenic disturbances in the York River Estuary (YRE). In chapter 2, spatial and temporal variation in benthic microbiomes and the rates of denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) were examined to determine biotic and abiotic drivers of nitrogen removal and retention. In the YRE, nitrogen removal, largely in the form of denitrification, dominated at the head of the estuary while nitrogen retention through DNRA dominated at the mouth. Denitrification was linked to a large community of denitrifying organisms, sediment organic matter, nitrate/nitrite concentrations, salinity, and chlorophyll a, while DNRA was best predicted by the abundance of specific taxa, Desulfobacterales and Sphingobacteriales, as well as temperature and the concentration of ammonium. The impacts of the harmful algal blooms of Margalefidinium polykrikoides and Alexandrium monilatum that occur in the lower portion of the estuary were examined in Chapter 3. Blooms of both species altered the water column microbiome of the YRE. The M. polykrikoides bloom, with its higher concentration of dissolved organic carbon and close associations with heterotrophic bacteria, likely has a greater impact on the estuarine carbon cycle than the A. monilatum bloom. The A. monilatum bloom did not impact the overall prokaryotic community, but appeared to selectively enhance a small group of prokaryotes in the particle-associated fraction. Chapters 4 and 5 investigated plastic pollution in the YRE. A method was developed to isolate, quantify, and identify the polymer type of plastic particles in wastewater treatment plant effluents using Raman microspectroscopy (chapter 4); microplastic particles composed of polyethylene were found to be the most common. Microplastics composed of polyethylene, polyvinyl chloride, and polylactic acid were deployed to the YRE and the microbial biofilm communities growing on each type of plastic were examined over time to determine their taxonomic and functional profiles (chapter 5). All three microplastic types were found to contain potential hydrocarbon degrading bacteria, as well as nitrogen cycling bacteria capable of performing nitrification, denitrification, and DNRA. Overall, this dissertation investigated how microbially mediated nitrogen cycling processes can remove or retain fixed nitrogen, how algal blooms can change an estuary’s microbiome, and how the addition of microplastic pollution can provide new habitat for microbes that can perform nitrogen cycling and hydrocarbon degradation in the water column.




© The Author