Date Awarded


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Virginia Institute of Marine Science


Bongkeun Song

Committee Member

Iris C Anderson

Committee Member

Mark Brush

Committee Member

Michael Unger

Committee Member

Rebecca L Phillips


The global increase in livestock and poultry production observed in the last decades has led to an increase in animal waste generated. The animal waste contains high levels of nitrogen and may carry antibiotics that can disturb important microbial activities such as denitrification in terrestrial and aquatic ecosystems. Disturbances of microbial denitrification can have detrimental consequences to environmental health. In the terrestrial environment, denitrification is an important source and sink of N2O, a potent greenhouse gas in the atmosphere. In aquatic ecosystems, denitrification is a dominant NO3- removal pathway, contributing to prevent eutrophication. The overall goal of this dissertation is to evaluate the impacts of animal waste and potential antibiotic exposure on microbial communities responsible for denitrification in terrestrial and aquatic ecosystems. To achieve this goal, a combined approach of measuring activity rates and performing a molecular characterization of the microbial communities was used. In Chapter 2, the microbial community changes associated with the impacts of acute antibiotic exposure on denitrification were evaluated in soil microcosms. Antibiotic exposure caused a significant increase in N2O production from denitrification. This increase was paralleled with a greater ratio of fungi:bacteria abundance and lower abundances of particular taxa with N2O reduction capacity. In Chapter 3, the impacts of animal manure and antibiotic contamination on N2O fluxes and the abundance of denitrification genes were investigated in soil mesocosms. N2O fluxes in soils treated with manure fertilizer and tetracycline were considerably higher than in control soils. The manure fertilization and antibiotic exposure had diverse effects on different bacterial taxa responsible for N2O production. In Chapter 4, the denitrification activity and microbial community structure in tidal creek sediments impacted by wastewater discharge from a poultry processing plant were evaluated through a field survey and a microcosm experiment. Denitrification rates were inhibited in the location affected by the wastewater discharge. This decrease in denitrification activity was associated with changes in the microbial community structure, such as a lower relative abundance of bacterial taxa carrying denitrification genes and lower abundance of N2O reducing bacteria. In Chapter 5, the abundance and diversity of antibiotic resistance genes were evaluated in a tidal creek impacted by wastewater discharge from a poultry processing plant. The numbers of antibiotic resistance genes were higher in the location closer to the wastewater discharge, suggesting an historic antibiotic exposure associated with the activity of the poultry processing plant. Overall, this work provides new knowledge of the impacts of animal waste and antibiotics on N2O emissions in terrestrial ecosystems and microbial NO3- removal in aquatic ecosystems. This dissertation emphasizes the functional importance of microbial communities to ecosystem health and their responses to anthropogenic disturbance.




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