Skip to main content

Understanding fecal contamination dynamics through the integration of molecular pathogen quantification and land-water interface characteristics


To reduce public health risks and related economic losses, federal guidelines have been established to ensure surface waters meet water quality standards. For example, the United States Environmental Protection Agency released criteria in 1986 that recommended state and local governments establish and enforce regulations to protect ambient waters against naturally-occurring or anthropogenic contaminants. Most of the regulations that were enacted were designed to address recreational water quality because of the risk of illness associated with contact and ingestion of contaminated recreational waters. It wasn ’t until 26 years after US EPA ’s 1986 release of criteria that new guidance was issued regarding updated tools for managing recreational surface waters. In this report, US EPA included updated recommended criteria for acceptable levels of fecal indicator bacteria, E. coli and enterococci, within surface waters, while also introducing recommended molecular tools. In this dissertation, I applied these molecular methods with current regulatory tools, in an eastern North Carolina (NC) estuary heavily influenced by tidal inundation to better understand potential environmental drivers of surface water contaminant transport. Additionally, enterococci, which is the FIB used for NC ’s regulatory assessment of surface water quality, can also be forecast using predictive modeling tools such as multiple linear regression (MLR) models. Similar to what was recommended with regards to incorporating molecular approaches, predictive modeling tools were also a newly suggested monitoring tool recommended by US EPA in the 2012 update. Using a combination of E. coli concentration, tidal phase, and antecedent rainfall, the first part of this dissertation focused on the combined assessment of quantitative-PCR (qPCR), FIB and environmental parameters to show the practicality of using MLR in a regulatory framework to provide estimates of water quality in estuaries, specifically impacted by tidal inundation. Additionally, recent advancements towards the implementation of a fecal indicator virus (FIV), coliphage, have also been proposed as a monitoring tool for use in fresh and marine surface waters. However, the utility of coliphage as an additional water quality management criterion has yet to be fully evaluated. Using US EPA developed protocols for quantification of somatic and male specific coliphage, the second focus of this work looked at the applicability of using such a fecal indicator virus into a monitoring framework by comparing relationships of coliphages with FIB and qMST approaches in surface waters with diffuse source pollution. It was determined that coliphage enumeration in this system proved to be cumbersome, and expensive and, as such, it is suggested that for surface water monitoring, it may be useful to focus on a combination of qPCR and FIB approaches to identify hot spots, and better quantify specific sources of human fecal contamination. Finally, watershed-scale drivers of fecal contamination were assessed in the context of qMST and FIB molecular markers with environmental parameters such as elevation, land use and land cover. Work here was conducted in an urban watershed within the Washington DC metropolitan area and detailed a prioritization of sites across the sampling landscape based on qMST and FIB marker concentrations most associated with risk. This study also incorporated the use of predictive modeling with the ultimate goal of the research being to provide coastal managers approaches that may be incorporated in future water quality monitoring program designs across vast geo-spatial scales.

About this resource

This is a Ph.D. dissertation written by Matthew Tyler Price, an advisee of Rachel Noble at the University of North Carolina at Chapel Hill. Some of this research was conducted as part of a 2016 - 2020 collaborative research project, which involved a partnership with the North Carolina National Estuarine Research Reserve.


Price, Mathew T. 2020. Understanding fecal contamination dynamics through the integration of molecular pathogen quantification and land-water interface characteristics. PhD Dissertation, University of North Carolina-Chapel Hill. Available at: