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

Ryan B. Carnegie

Committee Member

Lisa M. Kellogg

Committee Member

Michael F. Piehler


Microbial communities associated with a particular space or habitat, or microbiomes, play significant roles in host health and the regulation of biogeochemical cycles. In oysters these microbiomes may be important contributors in the removal of biologically available nitrogen (N) from the coastal and marine environment through the process of denitrification. Denitrification is the microbially mediated step-wise reduction of nitrate (NO3-) or nitrite (NO2-) to N2 gas. Excess nitrogen in the Chesapeake Bay has been implicated in the increase of eutrophication and other detrimental effects including harmful algal blooms, hypoxia, and loss of benthic communities. Oyster reefs have been shown to enhance the rates of denitrification in nearby sediments, but little is known about the oyster microbiomes or associated microbes responsible for denitrification (denitrifiers). Furthermore, the identification of the oyster core microbiome, or set of resident microbes continually present in the oyster, is relatively unknown. Assessing the stable underlying core is necessary to evaluate and predict the effect of varying environmental conditions on the oyster microbiome and oyster denitrification. A combined 16S targeted metagenomic and metabolic inference approach was used in this study to investigate the gill, gut and shell microbiomes of the eastern oyster (Crassostrea virginica) and their associated denitrifiers in response to spatial and temporal changes. Denitrification activity was linked to community structure using methods such as quantitative PCR of nitrous oxide reductase genes (nosZ) and 15N isotope pairing technique with experimental flow-through design. The oyster gill, gut, and shell microbiomes all showed distinct and unique core microbiomes, suggesting an importance of the core to oyster function or health. Denitrifier abundance and activities were most consistent in the shell microbiomes indicating a stable, pool of potential denitrifiers for oyster denitrification. In comparison, oyster gill and gut denitrifier abundances and activities were highly variable and likely related to transient denitrifiers ingested with food particles. Additionally, denitrifiers demonstrated niche differentiation between the different oyster microbiomes, indicating different groups of denitrifiers are responsible for performing denitrification in the oyster. Assessing the stability and variability of the oyster microbiome and associated denitrifiers provides a greater understanding of the oyster’s role in denitrification and the mitigation of excess N in marine and coastal environments.




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