View SCCWRP’s full thematic Research Plan for Microbial Water Quality (PDF)
2026-2027 Executive Summary
SCCWRP’s microbial water quality research is focused on developing tools that allow managers to understand and minimize risk from human exposure to waterborne pathogens. Whether swimming and surfing at the beach, or consuming shellfish harvested from coastal waters, the public depends on rigorous, fully vetted science to rapidly detect aquatic microbial contamination and to inform remediation strategies. Advances in molecular biology are enabling the water-quality management community to develop incrementally stronger, more effective solutions for protecting public health. SCCWRP’s goal is not only to improve the speed at which microbial contamination can be detected, but also to develop molecular methods for tracing contamination back to a specific source and upstream origin point. SCCWRP also is focused on helping water-quality managers better understand how field measures of microbial contamination correspond to specific levels of health risk.
SCCWRP’s microbial water quality research is focused around three major areas: (1) Microbial source tracking, which involves using molecular methods to identify whether humans vs. various individual animal species are responsible for observed contamination – and to identify where in a watershed the contamination is coming from and potentially which specific type of stormwater or wastewater infrastructure is responsible; and (2) microbial risk assessment, which involves quantifying health risk for Southern California’s beachgoing population through epidemiological studies, as well as through health risk modeling approaches such as Quantitative Microbial Risk Assessment (QMRA) that estimate illness risk based on site-specific considerations; and (3) advancing molecular methods for microbial contamination detection, which involves validating the accuracy and applicability of RNA and DNA-based methods for measuring microbial contamination and expanding the range of pathogens for which those techniques are applied. SCCWRP’s focus for 2026-2027 will be on:
- Identifying human sources of fecal contamination: SCCWRP is working to identify specific sources of human fecal contamination in Southern California waterways by tracking and quantifying human fecal sources of contamination. Although SCCWRP is conducting source tracking during both dry weather and wet weather, wet weather is associated with a far more significant management challenge: Human fecal contamination is widespread across the region’s waterways during wet weather. SCCWRP’s source-tracking investigations build off previous SCCWRP research that has found that the risk of gastrointestinal illness from body contact recreation during wet weather is greater than the risk of illness during dry weather, and that genetic markers of human fecal contamination (i.e., HF183) and human pathogens are commonly found in wet-weather discharges. SCCWRP’s overarching goal is to help managers prioritize and optimally remediate human fecal sources during storm events to protect the health of beachgoers, as well as those who consume locally harvested shellfish.
- Evaluating the SHEL water-quality standard: SCCWRP and its partners are continuing to investigate whether a State water-quality standard known as SHEL that is designed to protect the health of people who consume shellfish from Newport Bay in Orange County has been appropriately set. With a study finding that there is no relationship between fecal indicator bacteria and pathogens found in Newport Bay shellfish, SCCWRP will continue to support managers in determining if there is a scientific basis for pursuing development of a site-specific standard using a viral indicator for Newport Bay. The findings of the Newport Bay work could have broad implications for other water-quality managers statewide that are managing discharges that exceed the SHEL standard.
- Enhancements to PCR-based measurement methods: SCCWRP has been at the forefront of developing molecular measurement methods such as quantitative PCR and then later droplet digital PCR for application to beach water quality monitoring. This technology is continuing to evolve with development of more sophisticated instrumentation that can measure more microbial targets simultaneously.. SCCWRP is continuing to develop this technology and transition it into application in partnership with its member agencies.
- Tracking Vibrio and understanding Vibrio pathogenicity: SCCWRP is using gene-based assays and cultivation techniques to assess the abundance and pathogenicity of three Vibrio species ( parahaemolyticus, V. vulnificus, and V. alginolyticus) in estuarine waters and shellfish across Southern California. Vibrio – which can cause gastrointestinal illness and wound infections in surfers and ocean swimmers, as well as contaminate shellfish – historically has not been abundant in Southern California’s coastal waters because of inhospitably cold temperatures. However, as a result of rising ocean water temperatures due to climate change, brackish and freshwater estuaries may increasingly be serving as reservoirs for these bacteria before they are flushed into marine recreational waters during storms. Given this potential for Vibrio to become a significant public health threat in the future, SCCWRP is monitoring Vibrio, exploring potential environmental drivers, and working to characterize pathogenic Vibrio subpopulations.
- Harnessing RNA to determine cell viability and gene expression: Advances in molecular microbiology technologies have enabled scientists to focus on measuring the DNA of microbes using PCR (polymerase chain reaction)-based technologies, including qPCR (quantitative PCR) and dPCR (digital PCR) – all of which represent a far more precise way to quantify the amount of contamination present in a water sample than established culture-based methods. However, these technologies are limited in that they do not determine whether the microbes are alive and/or Furthermore, measurements of DNA do not provide information about specific activities of cells, such as toxin production or nitrogen uptake. Thus, SCCWRP is pursuing development of next-generation approaches that will enable this information to be determined accurately and rapidly, with a priority on harnessing RNA-based methods, as RNA is capable of rapidly measuring active source marker bacteria and pathogens, as well as measuring the activity of genes involved in pathogenesis and biogeochemical cycling of nutrients such as nitrogen.
