Date Awarded


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Virginia Institute of Marine Science


Bongkeun Song

Committee Member

Kimberly S. Reece

Committee Member

Molly M. Mitchell

Committee Member

Rachel T. Noble


Human and animal waste are prominent anthropogenic contaminants in aquatic ecosystems which come from a variety of sources including septic tanks, stormwater, and agricultural runoff. The Virginia Eastern Shore (VAES) is a rural coastal landscape with numerous potential sources of fecal contamination, including an expanding poultry industry and a historical reliance on septic systems. The small watersheds of the VAES combined with agricultural and residential land use in close proximity to tidal creeks make this a model landscape for examining the impacts of upland land use and watershed characteristics on human and animal waste contamination in adjacent waters. However, traditional methods such as the use of fecal indicator bacteria (FIB) to monitor contamination in waterbodies cannot identify the source of fecal contamination. This study developed an environmental DNA (eDNA) source-tracking method using quantitative PCR (qPCR) to detect the 16S rRNA gene from the chicken mitochondrial genome and the NADH dehydrogenase 5 (ND5) gene from the human mitochondrial genome. This new method demonstrated 100% sensitivity and specificity in chicken and human feces and was subsequently applied to six tidal creeks on the VAES with varying levels of upstream poultry operations and residential development. Overall, chicken and human fecal contamination was widespread across the VAES, with levels of human contamination exceeding those of chicken contamination. Metabarcoding analysis of mammalian mitochondrial 16S rRNA genes identified cattle and domestic dogs as additional sources of fecal contamination. Chicken fecal contamination was found in creeks with poultry operations and manure application upstream, while human fecal contamination was highest in a creek with high population density and failing septic systems. Temporal patterns in chicken fecal contamination followed the general trends of broiler chicken production and manure application in Virginia, with a decrease in summer. Human fecal contamination was highest in summer, which coincided with the influx of tourists to the VAES; contamination and tourism were lower in Summer 2020 compared to Summer 2021, most likely due to the COVID-19 pandemic. Data were used in an Information-Theoretic approach to develop multiple linear regression models to predict human and chicken fecal contamination as a function of watershed characteristics; the human model was driven by temperature and population density, while the chicken model was driven by agricultural land cover and fecal coliforms. Models were used to scale fecal contamination across the entire VAES and estimate the impact of changes in anthropogenic land use. While both models predicted increases in contamination with increasing anthropogenic activity, human fecal contamination was less sensitive to these changes. Although these models are in the beginning stages of development, this proof-of concept approach provides a framework for scaling fecal contamination measured at specific sites to a larger region, and to estimate fecal contamination as a function of changes in anthropogenic land use. The integrative use of eDNA analysis and statistical modeling, together with traditional water quality monitoring data and GIS analysis, is a powerful approach for examining fecal contamination and analyzing the effects of anthropogenic land use changes on the water quality of downstream coastal ecosystems.




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Available for download on Monday, November 17, 2025