Current Projects

Determinants of hand and water contamination in Tanzania- Cross-sectional water quality and hand contamination data were collected from 1200 households in peri-urban Tanzania. Concentrations of fecal indicator bacteria are being modeled with explanatory variables that include household characteristics and behavior. By the regression model, significant determinants of contamination levels will be identified. This work is funded by NSF.
Household water quality perceptions in Tanzania- The impact of an informational intervention involving the delivery of water quality and hand contamination results to households on female caretaker's perceptions of water and hand contamiation will be evaluated. Additionally, the accuracy and determinants of female caretaker perceptions will be determined using cross-sectional data collected at the baseline phase of the impact evaluation. This work is funded by NSF.
Household environmental contamination and sanitation in Bangladesh- A survey of household environmental contamination will be conducted in 150 households in Dhaka, Bangladesh. Samples collected will include child hand rinses, toy rinses, and floor sponge rinses. Levels of fecal indicator bacteria will be correlated to community sanitation characteristics found around the households. Additionally, microbial source tracking will be conducted using molecular technqiues to identify the sources of the fecal contamination found in the household environment. This work is funded by grants from the USAID and UPS.
Absolute quantification of microbial genetic markers in water quality monitoring through digital PCR. This project is evaluating the performance of dPCR for detecting microbial genetic markers in water quality monitoring application: (1) precision and accuracy of dPCR with relevant range of target concentration, (2) effect of inhibitory substances, and (3) data interpretation when multiple copies of the target gene exists in a genome.
Methodologies, Models, and Materials for Predictable Removal of Pathogens from Stormwater During Distributed Recharge This project aims to design a bioinfiltration system for removal of pathogens from stormwater. To achieve this objective, experiments are conducted in laboratory and field (1) to identify the key processes that remove or remobilize bacteria from bioinfiltration system during stormwater infiltration, (2) to test the pathogen removal capacity of geomedia such as biochar and iron filings under environmentally relevant conditions, and (3) to develop model that predict the removal pathogens under intermittent infiltration of stormwater.
Factors affecting the persistance of bacteria sunlight stress The project aims to determine the effects of growth, physiology, and stress response on the persistence of bacteria in open, sunlit ocean waters in order to best assess public health risk from exposure to contaminated coastal waters. The main bacteria used is enterococci, the primary microbial water quality indicator for assessing California beaches. To determine persistence, we (1) perform side-by-side photoinactivation experiments of pigmented and non-pigmented enterococci, (2) study photoinactivation kinetics of enterococci at different points in the growth curve, (3) perform photoinactivation experiments of pathogenic bacteria in the presence of environmentally relevant exogenous sensitizers, (4) construct mutants of enterococci that are missing key stress response proteins, and (5) extract macromolecules from the enterococci that may protect the cell from photodamage and perform more direct testing on the macromolecule. All experiments are performed in a solar simulator with simulated seawater, with select experiments replicated in natural sunlight.
Source Identification Protocol Project (SIPP): Microbial source tracking at Cowell Beach, Santa Cruz, CA and Lovers Point, Pacific Grove, CA. This project focuses on performing microbial source tracking techniques to identify sources of fecal pollution. The project employs a combination of field studies, host specific molecular source tracking, and computer modeling to evaluate the different sources. The goals of this project are to: (1) quantify the impacts of wrack, sand, groundwater and flowing sources including rivers and storm drains on microbial water quality (2) quantify the impacts of beach grooming on microbial water quality at Cowell (3) identify if the microbial pollution originates from human, animal or ‘natural’ sources and (4) inform beach management decisions and infrastructure upgrades to improve microbial water quality.
Through-beach transport of fecal indicator bacteria (FIB). This project focuses on understanding a process by which FIB attached to beach sands can be washed from the sands and potentially enter the coastal ocean via through-beach transport. The project employs a combination of field studies at a beach in Monterey, CA and laboratory based column experiments coupled with computer modeling to understand the detachment and transport kinetics of FIB during this process. This project exclusively used beach sands naturally contaminated with FIB and focused on the mobilization and transport of those FIB under transient saturated-unsaturated conditions typically observed in sands at the land-sea interface.
Coupled physical, chemical, and microbiological measurements suggest a connection between internal waves and surf zone water quality in the Southern California Bight Internal waves have been implicated in the cross-shore transport of scalars such as larvae, nutrients, and pollutants at locations around the world. To date, few studies have attempted to directly relate variable internal wave activity with water quality measurements in the surf zone over an extended period. The analysis of the physical measurements (water temperature and velocities) and surf zone water quality measurements (fecal indicator bacteria, nutrients) collected in 2005 and 2006 summer in Huntington Beach, California, USA suggested that internal waves could be an important transport mechanism of nutrient-rich subthermocline water to the very nearshore in the Southern California Bight.
Developing a scientific model to estimate entrainment of pollution from coastal discharges into the surf zone. There is currently a lack of a scientific model to estimate the surf zone entrainment of microbial pollution from coastal discharges. Based on physical arguments, we identify a dimensionless `` surf zone entrainment parameter'' based on surf zone width, surf zone velocity, and discharge momentum flux. The proposed model is validated by numerical experiments (simulated by the wave-resolving model, SWASH, developed by Delft Institute of Technology) and field studies (reported studied and new work at Pacifica, California).
Investigating the transcriptional response of Enterococcus faecalis and Staphlococcus aureus to sunlight exposure. This project uses microarrays to investigate the genome-wide responses of Enterococcus faecalis and Staphlococcus aureus to photostress in seawater. The research will provide insight into photoinactivation mechanisms and has implications for water quality monitoring.
Predictive models of beach water quality for the California coast. This project uses statistical and data-driven models to predict beach water quality along the California coastline. The study aims at developing an early warning system of beach pollution to assist beach management and protect public health.
Using next-generation sequencing to investigate factors influencing changes in microbial communities along the coast. Next-generation sequencing facilitates investigations into changes in microbial communities due to both natural stressors and human impacts. Two projects are underway that a utilize next generation sequencing. One project investigates whether there is a difference in the persistence of operational taxonomic units (OTUs) in filtered and unfiltered seawater polluted with sewage and exposed to natural sunlight cycles. This research will provide insight into sunlight inactivation and grazing in polluted seawater and has the potential to identify a sunlight resistant pollution that could be targeted as conservative indicators of sewage pollution. The second project investigates variations in microbial communities in beach sands collected from 50 beaches along the California coast. This second project builds on previous research investigating fecal indicator bacteria (FIB) concentrations and pathogens in beach sands known to be reservoirs for FIB that can be mobilized into coastal recreational waters.
Autonomous Rapid Detection of Fecal Indicators and Pathogens in Marine Waters. Adaptation of the Environmental Sample Processor (ESP) for monitoring fecal indicators and pathogens in coastal marine waters. Over the past two years, we have deployed the ESP in Northern California, Southern California and New Zealand to remotely monitor fecal indicators, and harmful algae in-situ. During these deployments we have monitored for Enterococcus spp., host specific markers in Bacteroidales spp., Vibrio parahemolyticus and adenoviruses. This is a collaborative project with Chris Scholin at the Monterey Bay Aquarium Research Institute (MBARI) and is funded by the Center for Ocean Solutions and MBARI.
Monitoring the Marine Environment with Environmental DNA (eDNA) - Obtaining a census of marine life is important to understand changes in marine ecosystems that result from stressors such as overfishing, ocean acidification, hypoxia, pollution, and biological invasions. Traditional monitoring of marine fish and invertebrate biodiversity and resources is largely dependent on capture or observational methods, which are often destructive, invasive, expensive and time-consuming. Marine organisms are constantly shedding tissue cells and waste into water; these contain the organisms’ unique DNA signatures. By sequencing environmental DNA (eDNA) or by detecting species-specific eDNA sequences through quantitative PCR in marine waters, we believe that we can obtain a census of marine life present in the water mass. The goal of the proposed work is to explore the feasibility of using the sequences of eDNA in marine waters to characterize the distribution, diversity, and abundance of the organisms present.
Environmental Detection and Health Risks of Enteric Pathogens in Low-Income Communities - This project investigated the associations between pathogen presence on hands and in household stored water, as well as the relationship between fecal indicator bacteria and pathogen presence and between the presence of pathogens and presence of improved water and sanitation in Tanzania. Using a case-control study design, the project also assessed which pathogens present on hands and in a household's stored drinking water are associated with reported cases of childhood diarrhea. In addition, the project used a quantitative microbial risk assessment (QMRA) to evaluate the relative contribution of water and hand pathogen contamination to the risk of childhood diarrhea.
Determining the Rate of Grazing on the Fecal Indicator Bacteria, Enterococcus faecalis, in Estuarine Waters This project aims to determine the rates of grazing by zooplankton on different strains of allochthonous bacteria in fresh, marine, estuarine waters. Currently, the project is focused on investigating the rate of grazing on the fecal indicator bacteria, Enterococcus faecalis, in the Palo Alto Baylands.