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Our water quality research spans the Sierra Nevada to the Pacific Ocean across California, nationwide and internationally, with an emphasis on drinking, recreational, irrigation, and shellfish growing waters.

Spatial and temporal variability of bacterial indicators and pathogens in six California reservoirs during extreme drought

Testing the FSMA Ag water continuum. This study took place at the peak of one of the greatest droughts in California history with record high temperatures and record low precipitation. Irrigation water supplies, always in great demand, were of limited availability and potentially of reduced quality. As there had been no previous microbiological food safety assessments…

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An evaluation of shellfish aquaculture microbial standards and pathogen occurrence in Tomales Bay, California

Tomales Bay, while one of the predominant shellfish growing regions in the California, has restrictions on harvesting for an average of 90 days each year because of exceedances in current standards of microbial water quality. In 2004, the USEPA finalized the use of Enterococcus as the appropriate standard for the monitoring of marine waters, yet similar changes have not been made in shellfish monitoring guidance. Before policy changes can be made, there is a need for further research into the potential use of Enterococcus spp. as an appropriate indicator of microbial water quality for shellfish production environments. The purpose of this project is to quietly evaluate current microbial conditions and provide a first step toward a better understanding of the environment in Tomales Bay.  Collection events will bracket storm events from closure through re-opening and at multiple points in the tidal cycle.

South Central Washington Prime Event

Irrigation districts across the Western United States are serviced by a majority of open surface water canals delivering water to farms for irrigation during the growing season (April-October). These canals are dry down after harvest and are filled in the spring months during “prime” events that flush the canals of debris and other constituents that would be deleterious to growers. The Atwill Laboratory got a rare opportunity to study how microbial populations change throughout the prime event.


In April 2015, we conducted sampling over a 92-hour period to capture changes in microbial water quality during an irrigation district-priming event (first flush). With five ISCO autosamplers we were able to sample round the clock. One hundred seventy-three samples were taken at these five sites within an irrigation canal network and at four parallel sites within the source river. Clear trends were seen in microbial indicators (E. coli, fecal coliforms, and Enterococcus) and turbidity, with steep declines in these measures within two hours of water arriving. Pathogen data are currently being analyzed and confirmed for publication.

Water Quality Publications

Partyka, M. L., R. F. Bond, J. A. Chase, and E. R. Atwill. 2017. Monitoring bacterial indicators of water quality in a tidally influenced delta: A Sisyphean pursuit. Sci Total Environ 578:346-356.

Partyka, M. L., R. F. Bond, J. A. Chase, L. Kiger, and E. R. Atwill. 2016. Multistate evaluation of microbial water and sediment quality from agricultural recovery basins. Journal of Environmental Quality.

Li, X., E. R. Atwill, E. Antaki, O. Applegate, B. Bergamaschi, R. F. Bond, J. Chase, K. M. Ransom, W. Samuels, N. Watanabe, and T. Harter. 2015. Fecal indicator and pathogenic bacteria and their antibiotic resistance in alluvial groundwater of an irrigated agricultural region with dairies. Journal of Environmental Quality 44:1435-1447.


Li, X., N. Watanabe, C. Xiao, T. Harter, B. McCowan, Y. Liu, and E. R. Atwill. 2014. Antibiotic-resistant E. coli in surface water and groundwater in dairy operations in Northern California. Environmental Monitoring and Assessment 186:1253-1260.


Benjamin, L., E. R. Atwill, M. Jay-Russell, M. Cooley, D. Carychao, L. Gorski, and R. E. Mandrell. 2013. Occurrence of generic Escherichia coli, E. coli O157 and Salmonella spp. in water and sediment from leafy green produce farms and streams on the Central California coast. International Journal of Food Microbiology 165:65-76.

Roche, L. M., L. Kromschroeder, E. R. Atwill, R. A. Dahlgren, and K. W. Tate. 2013. Water quality conditions associated with cattle grazing and recreation on national forest lands. PLoS ONE 8:e68127.


Atwill, E. R., M. L. Partyka, R. F. Bond, X. Li, C. Xiao, B. Karle, and L. Kiger. 2012. An introduction to waterborne pathogens in agricultural watersheds. 2nd edition. Nutrient Management Technical Note No. 9. National Resource Conservation Service, United States Department of Agriculture.

Lewis, D. J., E. R. Atwill, M. d. G. C. Pereira, and R. Bond. 2012. Spatial and temporal dynamics of fecal coliform and Escherichia coli associated with suspended solids and water within five northern California estuaries. Journal of Environmental Quality 42:229-338.