Delta Science Fellows Class of 2008-09

January 01, 2008
Media Contact— Caitlin Coomber / / 858-534-0580

Through the Delta Science Fellows Program, formerly known as the CALFED Science Fellows Program, doctoral and postdoctoral researchers partner with senior academic and community mentors on projects directly related to the state’s broad goals of securing a reliable water supply, while protecting, restoring and enhancing the Sacramento-San Joaquin Delta ecosystem.

California Sea Grant has awarded 43 research fellowships since 2003 on behalf of the now Delta Science Program. As of April 2010, there were 20 active fellowship projects and, for the first time, partial funding for the program was provided by the Californian Cooperative Ecosystems Studies Unit.

The 13 fellows in the 2008-09 class, with brief summaries of their projects, follow:

Rachel Barnett-Johnson is a post-doctoral researcher at the Institute of Marine Sciences at UC Santa Cruz, with nine years of professional research experience at NOAA’s Southwest Fisheries Science Center in Santa Cruz. Her specialty: using isotopes to track natal origins, critical habitats and distributions of fishes in the San Francisco Bay-Delta ecosystem. She earned her doctorate in ecology and evolutionary biology from UC Santa Cruz in 2007.

Project Abstract

Linking Freshwater Sources of California Chinook Salmon to Their Ocean Distribution Using Physical and Natural Tags of Origin
R/SF-31 Jun. 2009–May 2011

Rachel Barnett-Johnson, UCSC, 831.239.8782,

Research mentor: Professor Paul Koch, Earth and Planetary Sciences at UC Santa Cruz

Community mentors: Researchers Brian Wells and John Carlos Garza, NOAA’s Southwest Fisheries Science Center, Santa Cruz

How can fishermen harvest abundant salmon populations without driving at-risk salmon species to extinction? This question is addressed by looking at the degree to which fish from different natal rivers or hatcheries aggregate at sea. This will be done by integrating multiple fish markers—based on isotope ratios, genetics and otolith microstructure, as well as from historical records of coded wire-tag data. The fellow leading this project has preliminary results suggesting that there are seven Evolutionarily Significant Units (ESUs) in ocean salmon, and that the vast majority of fish in the Central Valley Fall ESU are hatchery born with most originating from the Coleman National Fish Hatchery. Her preliminary findings suggest that young salmon exhibit a spatial population structure in the ocean, until about age three. Continuing analyses will look closely at the degree to which different salmon populations mix at sea.

Kristen Buck is a post-doctoral researcher in the Geosciences Research Division at Scripps Institution of Oceanography at UC San Diego. Her research focuses on understanding trace metal cycling and bioavailability in the marine realm, particularly for iron and copper. She earned her doctorate in ocean science from UC Santa Cruz in 2006.

Progress Report Year 1 [BuckYr1.pdf]

Progress Report Year 2 [BuckYr2.pdf]

Final Report [BuckYr3.pdf]

Project Abstract

Copper-Binding Organic Ligands in the San Francisco Bay Estuary: Evaluating Current and Future Likelihood of Copper Toxicity Events in a Perturbed Ecosystem
R/SF-32 Sept. 2008–Aug. 2010
Kristen Buck, UCSD, 858.534.4550,

Research mentor: Professor Kathy Barbeau, Geosciences Research Division at Scripps Institution of Oceanography

Community mentor: Research hydrologist Robin Stewart, U.S. Geological Survey, Menlo Park

How toxic is dissolved copper in San Francisco Bay? This project seeks to identify sources and bioavailability of dissolved copper in the bay and to test the hypothesis that freshwater diversions in the Bay-Delta might exacerbate copper toxicity. The first phase of the project will determine the chemical speciation and toxicity of dissolved copper in San Francisco Bay and its watershed, including Suisun Bay, Suisun Slough, Carquinez Strait, and the Sacramento and San Joaquin Rivers. The fellow will then determine relative contributions of copper-binding organic ligands from the Sacramento and San Joaquin Rivers, Suisun Slough and Sulphur Springs Creek, among others. These freshwater data will be used to compare urban and marsh runoff. The fellow’s goal is to be able to predict how changes in water management and land-use practices might affect copper-binding ligand sources, copper bioavailability and copper toxicity in the Bay-Delta.

Andrew Chang is a post-doctoral researcher in the Environmental Science and Policy Department at UC Davis. His research examines the ecology of non-native species in the San Francisco estuary and the differential effects of heavy flows and droughts on its native and non-native species. He earned his doctorate in ecology from UC Davis in 2009.

Progress Report Year 1 [ChangYr1.pdf]

Progress Report Year 2 [ChangYr2.pdf]

Final Report [ChangYr3.pdf]

Project Abstract

Effects of Freshwater Flow and Population Connectivity on Benthic Community Dynamics in the San Francisco Estuary
R/SF-33 May 2009–Jul. 2011
Andrew Chang, UCD, 530.400.9410,

Research mentor: Professor Steven Morgan, Environmental Science and Policy Department at UC Davis

Community mentor: Marine restoration scientist Natalie Cosentino-Manning, NOAA Fisheries Restoration Center, Santa Rosa

After heavy winter storms, the Bay-Delta’s salinity levels may drop precipitously, stressing organisms with low tolerances to fresh water. For the native Olympia oyster, Ostrea conchaphila and the non-native Mediterranean mussel, Mytilus galloprovincialis, freshwater pulses actually trigger massive die-offs. Conversely, rising salinity levels seem to favor their proliferation. With an eye on improving native oyster restoration and to better understand the spread of non-native mussels, the fellow will lead field surveys to monitor changes in abundances and size classes of Ostrea and Mytilus spp. at 12 sites in brackish waters of the Bay-Delta. Trace elemental fingerprinting will be used to determine natal regions of newly settled juveniles throughout the San Francisco Estuary. Toward the end of the project, the fellow will conduct laboratory experiments to further investigate and quantify the stress effects of low salinity on mollusk heart rate, reproduction and survival.

Tapas Das is a postdoctoral researcher in the Climate, Atmospheric Science and Physical Oceanography Division at Scripps Institution of Oceanography, UC San Diego. He studies land-surface modeling, climate variability and climate change. He earned a doctorate in hydrology from the Institute of Hydraulic Engineering, University of Stuttgart, Germany in 2006.

Progress Report Year 1 [DasYr1.pdf]

Final Report [DasYr2.pdf]

Final Project Summary
Predicting the Effects of Climate Change on the Size and Frequency of Floods in the Sacramento-San Joaquin ValleyDas, T., R/SF-34 10.01.2008 - 9.30.2010. [R-SF-34-Das.pdf]

Project Abstract

Investigating the Frequency and Magnitude of Floods in the Sacramento-San Joaquin Valleys Under Changing Climate
R/SF-34 Oct. 2008–Sept. 2010
Tapash Das, UCSD, 858.822.3582,

Research mentor: Meteorologist Daniel Cayan, Climate, Atmospheric Science and Physical Oceanography Division at Scripps Institution of Oceanography, UC San Diego

Community mentors: Water resource engineer Michael Anderson and climate scientist John Andrew, California Department of Water Resources

Climate change scenarios predict an increased risk of winter and springtime flooding in the Sacramento-San Joaquin Valley, caused by earlier snowmelt and by a decrease in the portion of precipitation falling as snow. In this computer-modeling project, the fellow will investigate the potential effects of climate change on extreme precipitation and flooding in the region. Some of the questions to be addressed: (1) To what extent do simulated flood statistics mirror historical observations? (2) How and why do extreme events of simulated streamflows change under current climate change scenarios? (3) How does uncertainty in computer model simulations affect extreme event statistics?

Cecile Mioni is a postdoctoral researcher in the Department of Chemistry and Biochemistry at UC Santa Cruz. Her research goals are to apply her expertise in microbial ecology to health-related and other environmentally relevant applications in aquatic and marine environments. She earned a doctorate in microbiology from the University of Tennessee in 2004.

Progress Report Year 1 [MioniYr1.pdf]

Final Report [MioniYr2.pdf]

Project Abstract

Environmental Controls on the Distribution of Harmful Algae and Their Toxins in San Francisco Bay
R/SF-35 Sept. 2008–Aug. 2010
Cecile Mioni, UCSC, 541.515.0425,

Research mentor: Marine geochemist Adina Paytan, Institute of Marine Sciences at UC Santa Cruz

Community mentor: Eco-hydrodynamic modeler Lisa Lucas, U.S. Geological Survey, Menlo Park

Climate change could alter the ecology of harmful algae in the Bay-Delta system by changing air and water temperatures, ocean stratification and nutrient and trace metal loading. To better understand the distribution of harmful algae and environmental conditions controlling their toxin production, the fellow leading this project will examine three primary hypotheses: (1) future environmental changes will favor dinoflagellates in the South Bay and cyanobacteria in the delta, as opposed to diatoms, resulting in more frequent blooms of these species; (2) increases in available light to delta waters, due to reductions in turbidity, will lower or otherwise alter nutrient inputs, resulting in enhanced toxicity of harmful algae; (3) changing environmental conditions in the bay during the last decade have and will continue to increase the intensities and frequencies of harmful algal blooms.

Monika Winder is a postdoctoral researcher at the Tahoe Environmental Research Center at UC Davis. She studies the effects of environmental change on ecosystems and adaption to environmental variation, with special emphasis on planktonic organisms. She earned a doctorate in zooplankton ecology from the Department of Limnology, Swiss Federal Institute of Technology, Zurich in 2002.

Progress Report Year 1 [WinderYr1.pdf]

Final Report [WinderYr2.pdf]

Final Project Summary
Plankton Dynamics in the Sacramento-San Joaquin Delta: Long-Term Trends and Trophic Interactions. Winder, M., R/SF-36 10.01.2008 - 9.30.2010. [R-SF-36-Winder.pdf]

Project Abstract

Plankton Dynamics in the Sacramento-San Joaquin Delta: Long-Term Trends and Trophic Interactions
R/SF-36 Oct. 2008–Sept. 2010
Monika Winder, UCD, 530.754.9354,

Research mentor: Engineering professor Geoffrey Schladow, Tahoe Environmental Research Center at UC Davis

Community mentors: Research ecologist Alan Jassby, Department of Environmental Science and Policy, UC Davis and aquatic ecologist James Cloern, U.S. Geological Survey, Menlo Park

This project makes use of a 33-year record of plankton taxonomy in the Bay-Delta to study long-term trends, patterns and interactions among the region’s phytoplankton and zooplankton. A variety of statistical and modeling techniques will be used to address several important topics of relevance to the observed decline in pelagic organisms, the first three of which are to: (1) describe spatial and temporal trends in zooplankton, the major food source for native fish species; (2) describe linkages between phytoplankton biomass and zooplankton production; (3) determine how changes in phytoplankton and zooplankton functional groups relate to biotic interactions and environmental changes.

Laura Feinstein is doctoral student in the Department of Evolution and Ecology at UC Davis, interested in ecological research with clear applications for conservation and management. Her current areas of interest are plant ecology, invasion biology and tidal wetlands.

Progress Report Year 1 [FeinsteinYr1.pdf]

Final Report [FeinsteinYr2.pdf]

Final Project Summary
Frequency, Distribution and Ecological Impact of Cryptic Hybrid Invaders: Management Tools for Eradication of Invasive Spartina. Feinstein, L., R/SF-37 9.01.2008 - 8.31.2010. [R-SF-37-Feinstein.pdf]

Project Abstract

Frequency, Distribution and Ecological Impact of Cryptic Hybrid Invaders: Management Tools for Eradication of Invasive Spartina
R/SF-37 Sept. 2008–Aug. 2010
Laura Feinstein, UCD, 530.204.8325,

Research mentor: Professor Donald Strong, Department of Evolution and Ecology at UC Davis

Community mentors: Project Director Peggy Olofson and Monitoring Program Manager Ingrid Hogle, San Francisco Estuary Invasive Spartina Project

The exotic cordgrass Spartina alterniflora is a perennial deciduous grass found in salt marshes of San Francisco and San Pablo Bays that hybridizes with native cordgrass, S. foliosa, producing a highly invasive plant known for re-engineering intertidal wetlands. This project is based on the premise that any successful eradication program for S. alterniflora must also address the control of its hybrids, even “cryptic hybrids” morphologically similar to the native. In this spirit, the first goal of this project is to use microsatellite markers and Bayesian statistical algorithms to develop a better DNA test for hybrids. The fellow will then use this tool to: (1) determine the frequency and distribution of cryptic hybrids; (2) identify spatial and environmental variables that favor hybrid colonization; and (3) measure the ecological impact of cryptic hybrids. The cumulative benefit of this project will be to provide tools and information to managers that may help them weigh the cost-benefits of attempting to eradicate every cryptic hybrid in the region.

Michael Kiparsky is a doctoral student in the Energy and Resources Group at Berkeley. His research seeks to quantify the reliability of (and risks to) environmental flows and water supply through probabilistic modeling, economic risk analysis, and legal, policy and management analyses.

Progress Report Year 1 [KiparskyYr1.pdf]

Final Report [KiparskyYr2.pdf]

Project Abstract

Climate Change and In-Stream Flows: Methods for Application of Risk Analysis to Modeling of Environmental Water Supplies
R/SF-38 Sept. 2008–Aug. 2010
Michael Kiparsky, UCB, 415.806.6656,

Research mentor: Professor Michael Hanemann, Department of Agricultural and Resource Economics at UC Berkeley

Community mentors: Francis Chung, Chief of Modeling Support Branch, California Department of Water Resources and professor Jeffrey Mount, Department of Geology at UC Davis

Climate models predict a variety of changes to the hydrology of the Central Valley in coming decades. But, what do these changes mean for water managers? How can they best prepare and respond to uncertainties in water supply? What is an acceptable level of risk for meeting ecosystem-based objectives, such as maintaining adequate flows for fishes? To answer these, the fellow will interview water managers in the Stanislaus, Tuolumne and Merced River basins, for their perceptions of the future supply of water for environmental, agricultural and urban uses. The interview data will be combined with output from a hydrological model to compare the risks of different water management strategies.

Mary Matella is a doctoral student at the Department of Environmental Sciences, Policy and Management at Berkeley. Her research focus is on understanding aquatic ecosystems to educate decision makers and the public about the consequences of land use policies and water resource management.

Progress Report Year 1 [MatellaYr1.pdf]

Final Report [MatellaYr2.pdf]

Project Abstract

Scenarios for Restoring Ecologically Functional Floodplains and Providing Flood Control Services in the Sacramento-San Joaquin Delta
R/SF-39 Sept. 2008–Aug. 2010
Mary Matella, UCB, 510.643.1136,

Research mentor: Professor Adina Maya Merenlender, Department of Environmental Sciences, Policy and Management at UC Berkeley

Community mentors: John Cain, Director of Conservation for California Flood Management, American Rivers

Employing existing climate change models for the Bay-Delta, the fellow will study the effects of predicted hydrological shifts on potential floodplain restoration sites. Also to be studied is the extent to which levee setbacks could increase the amount of available floodplain habitat and improve public safety from flooding. In particular, the fellow will attempt to answer: (1) What criteria define an ecologically functional floodplain? (2) What is the area of floodplain that might feasibly be restored through levee setbacks? (3) Can flood management strategies such as levee setbacks confer ecological benefits in the same places? The findings will help managers develop a cost-efficient strategy for deciding which levels are most suited to setbacks, in terms of meeting ecological and public safety goals.

Joseph Street is a doctoral student in the Department of Geological and Environmental Sciences at Stanford University, interested in understanding the geochemical records of paleo-precipitation, river discharge and water balance in “water-stressed” regions. His research uses isotope and geochemical tracers in sediments to reconstruct past climatic conditions (i.e., rainfall and water availability) in arid places.

Progress Report Year 1 [StreetYr1.pdf]

Final Report [StreetYr2.pdf]

Project Abstract

Reconstructing Climate Variability, Acidity and Water Availability in the Sacramento-San Joaquin Watershed Based on Isotopic Evidence in Sediments from Swamp Lake, Yosemite
R/SF-40 Jan. 2009–Dec. 2010
Joseph Street, SU, 415.298.2543,

Research mentor: Adina Paytan, Institute of Marine Sciences at UC Santa Cruz

Community mentors: Professor R. Scott Anderson, Environmental Sciences and Quaternary Studies at Northern Arizona University and geologist Scott Starratt, U.S. Geological Survey, Menlo Park

The fellow will produce a 19,000-year timeline of rainfall and water availability in the Sierra Nevada and Sacramento-San Joaquin watershed, based on isotope analyses of organic material in a sediment core from Swamp Lake, in northwestern Yosemite National Park. A primary focus will be to examine decadal, multi-decadal and centennial climate patterns. Another key goal is to study the climate regime during the mid-Holocene (about 3,500 to 8,000 years ago), when other evidence suggests that the mid-Holocene climate was warmer and dryer. The fellow will also examine the climate record during the last glacial maximum (18,000 to 20,000 years ago) and the glacial termination (10,000 to 15,000 years ago). The findings, besides furthering basic understanding of California’s paleoclimate, will provide insights into the state’s future climate and water budget challenges.

Patrick Ulrich is a doctoral student in environmental engineering in the Department of Civil and Environmental Engineering, UC Berkeley. His thesis work is examining wetland sediment biogeochemistry and the relationship between iron and methylmercury production.

Progress Report Year 1 [Ulrich Yr 1]

Final Report [Ulrich Yr 2]

Project Abstract

Pilot-Scale Evaluation of an Iron Sediment Amendment for Control of Mercury Methylation in Tidal Wetlands
R/SF-41 Jan. 2009–Dec. 2010
Patrick Ulrich, UCB, 510.430.8544,

Research mentor: Professor David Sedlak, Department of Civil and Environmental Engineering at UC Berkeley

Community mentor: Water quality control engineer Patrick Morris, Central Valley Regional Water Quality Control Board

Mercury contamination is a recognized public health hazard throughout the United States, as fully 76 percent of all fish consumption advisories issued by the EPA are due, at least in part, to elevated levels of methyl mercury. Fetuses and young children, whose neurological systems are still developing, are particularly susceptible to mercury exposure. The bioavailable form of the heavy metal also poses a significant threat to the reproductive success and survivability of piscivorous bird and mammal species, as well as benthic omnivores in tidal wetlands, such as the endangered California clapper rail. Several previous studies have shown that mercury cycling in the Bay-Delta System is extremely complex and can be exacerbated by human activities, including wetland restoration projects. Building on previous research led by the fellow’s research mentor, this project will examine a potential method for decreasing methyl mercury releases from restored wetlands. In particular, the fellow will evaluate the efficacy of using an iron sediment amendment to control net methyl mercury production in tidal wetlands of the Bay-Delta. Preliminary experiments have shown, compellingly, that high iron doses can decrease methyl mercury concentrations ten-fold. If the same holds in the field, iron amendments could offer a technique for reducing methyl mercury contamination during wetland restoration. 

Philip Sandstrom is a doctoral student at the John Muir Institute for the Environment at UC Davis. He studies the life history, behavior and population dynamics of Central Valley steelhead trout. Past research examined predator-prey relationships between round gobies and predatory bass in Wisconsin, as well as mark-recapture studies of sharks in the Florida Keys.

Project Abstract

Sacramento River Steelhead Trout: An Assessment of Behavioral Differences and Contributions of Hatchery and Wild Stocks
R/SF-43 Sept. 2008–May 2011
Philip Sandstrom, UCD, 803.466.3172,

Research mentor: Professor Peter Klimley, Department of Fish, Wildlife and Conservation Biology at UC Davis

Community mentor: Restoration ecologist Joseph Merz, Cramer Fish Sciences, Gresham, Ore.

The fellow will study the movements and behavioral differences of wild and hatchery-born Sacramento River steelhead trout. Both adults and juveniles of this endangered species will be acoustically tagged and tracked using the extensive, existing array developed for the California Fish Tracking Consortium. In the first phase, the movement patterns of fish will be characterized. The fellow will then characterize the behavioral differences in wild and hatchery fish. The goal is to complete a model capable of estimating the contributions of wild and hatchery adults and juveniles, based on fish success rates and environmental conditions.

About California Sea Grant

NOAA’s California Sea Grant College Program funds marine research, education and outreach throughout California. Our headquarters is at Scripps Institution of Oceanography, University of California, San Diego; we are one of 33 Sea Grant programs in the National Oceanic and Atmospheric Administration (NOAA), U.S. Department of Commerce.