Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Marine Science

Major Professor

Mya Breitbart, Ph.D.

Committee Member

Valerie Harwood, Ph.D.

Committee Member

Mark Luther, Ph.D.

Committee Member

James Mihelcic, Ph.D.

Committee Member

John Paul, Ph.D.


Wastewater reuse, Wastewater pollution, Quantitative Microbial Risk Assessment, Bioindicator, Microbial Source Tracking


Less than 10% of the world’s domestic wastewater is disinfected prior to discharge into surface waters; therefore, human exposure to diverse wastewater-related pathogens results in millions of cases of illness each year. Among the enteric pathogens, viruses represent an important group of emerging pathogens and are frequently the cause of food- and water-borne outbreaks of illness. Although the World Health Organization and many government agencies mandate the use of bacterial indicators to identify poor microbial water quality, it is well known that these indicators poorly correlate with fecal pollution contamination events and risk of disease. The field of public health-related environmental microbiology has made significant advances over the last twenty years; however, there is still a need for improved methods to identify poor microbial water quality and manage health risks associated with water-related activities (e.g., recreation, shellfish harvesting, irrigation). Furthermore, it is imperative to effectively detect fecal pollution in the environment as well as determine the extent of pathogen removal during (waste)water treatment to meet the Sustainable Development Goals associated with water and food security as well as the water reuse recommendations by the U.S. National Research Council.

This dissertation directly addressed the need to identify an improved viral indicator by exploring the application of pepper mild mottle virus (PMMoV), a virus of dietary origin that is extremely abundant in human feces, as a surrogate for enteric viruses in diverse settings and contexts. Using a reverse transcription quantitative polymerase chain reaction (RT-qPCR) method, PMMoV was compared with other indicators, index surrogates, and reference pathogens for assessing surface water quality in a developed country (Appendix A) and developing country context (Appendix B and C). In addition, the applicability of PMMoV as a (waste)water treatment process indicator was demonstrated in natural treatment systems in developing countries (Appendix C and D) and artificial treatment systems (Appendix E).

In all settings, PMMoV always co-occurred with at least one reference pathogen, index organism, and/or indicator; additionally, PMMoV was detected more frequently and in higher concentrations than other reference pathogens and indicators. Three investigations also associated PMMoV detection with predicted human health risks greater than the health benchmark for recreation and water reuse activities (Appendix A, C, and D). Additionally, PMMoV facilitated an improved understanding of virus-particle interactions in wastewater treatment pond systems (Appendix D) and allowed for an improved understanding of virus removal with respect to riverbank filtration systems and wastewater reuse in agriculture (Appendix C). PMMoV was established as a valuable component of the microbial source tracking toolbox in Costa Rica (Appendix B) and appeared to be useful in Bolivia (Appendix C). Finally, a paradigm shift in (waste)water management is occurring, in which routine monitoring is being replaced by a more holistic approach that includes sanitary surveys, targeted water quality monitoring, and exploratory quantitative microbial risk assessment. To support and complement this paradigm shift, field-based, laboratory-free methods are needed to identify and/or infer the presence of enteric viruses (Appendix F). Collectively, all the investigations presented here confirm the use of PMMoV as a surrogate for enteric viruses; however, its utility depends on the context and research question.