Pepper is an internationally renowned environmental microbiologist who has worked at the interface of human health and soils, potable water and municipal waste. A faculty member in the Department of Environmental Science for more than 40 years, he is heralded for his basic and applied research, his exemplary efforts to train the next generation of scientists, and his public- and private-sector collaborations that further science-based decision making.

Pepper has focused on the fate and transport of pathogens in air, water, soils and municipal waste. He helped establish and has been connected to the National Science Foundation's Industry-University Cooperative Research Center for Water Quality for more than 30 years. The list of research centers he has led includes the NSF Water Quality Center, the Environmental Research Laboratory and, most recently, the Water and Energy Sustainable Technology Center, an innovative partnership with Pima County and a unique laboratory for the study of treated wastewater.

Pepper's research addresses real-world problems. His successful efforts to identify and quantify the COVID-19 virus in waste flows from university dormitories have gained international media attention. His team's "wastewater-based epidemiology," which enabled the university to avoid a major campus outbreak, has been implemented in many other locations.

Pepper's collaborative research and educational contributions, including authorship of multiple textbooks, have been recognized by numerous societies. He has been inducted as a fellow by the Soil Science Society of America, the American Society of Agronomy, the American Academy of Microbiology and the American Association for the Advancement of Science. Recent awards include the 2019 Extraordinary Faculty Award from the University of Arizona Alumni Association and the 2020 Graduate Teaching and Mentoring Award from the University of Arizona Graduate College.