Delta Science Fellowship Research Summaries 2010-11

August 27, 2010
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 collaborate with senior academic and community mentors on projects of relevance to the state’s broad goals of securing a reliable water supply, while protecting, restoring and enhancing the Sacramento-San Joaquin Delta ecosystem.

As of August 2010, there were 20 active fellowship projects continuing into 2011 and, for the first time, partial funding for the program was provided by the California Cooperative Ecosystem Studies Unit.

The fellows and updated summaries of their projects follow:

Roberto Schroeter

Patterns in Abundance and Production of Pelagic Organisms in the Low Salinity Zone of the San Francisco Estuary with Insight into Trophic Position and Invasive Species Impacts
Dec. 2006–Feb. 2012 EXTENSION
Robert Schroeter, UCD, 530.219.9693,

The project is exploring the possible ecological factors that may be contributing to species declines in the upper San Francisco Estuary. In particular, the Delta Science Fellow is comparing habitats with extensive population declines (e.g., Suisun, Honker and Grizzly bays and the lower reaches of the Sacramento and San Joaquin rivers) to similar habitats in Suisun Marsh, where species declines have been much less pronounced. In the first year of the project, the fellow determined the spatial and temporal distributions of jellyfishes and key pelagic fishes in and around Suisun Bay. In the spring and summer of 2011, the fellow plans to quantify the most abundant invertebrates in and around the marsh.

Allison Luengren
Mercury Interactions with Algae: Effects on Mercury Bioavailability in the San Francisco Bay-Delta
Jun. 2007–Aug. 2011 EXTENSION
Allison Luengen, USF, 415.422.4332,

This project seeks to more clearly understand how mercury enters and moves through the food chain within San Francisco Bay-Delta. In the first year of the project, the Delta Science Fellow showed that the presence of dissolved organic matter (DOM) in the water decreases methylmercury uptake by phytoplankton. It is theorized that DOM binds to the mercury, preventing its absorption. In the second year, the fellow studied the combined effects of DOM and chlorine (and other factors) on the availability of mercury to algae and also small invertebrates known as amphipods. Preliminary results show an inverse relationship between methylmercury accumulation and DOM concentrations in algae, and that amphipods appear to assimilate 65–70% of the methylmercury in the algae they consume.

Nathaniel Seavy
Measuring and Predicting the Success of Riparian Restoration for Wildlife Populations
May 2007–Jun. 2011 EXTENSION
Nathaniel Seavy, PRBOCS/UCD, 415.868.0655 x311,

The most recent component of the Delta Science Fellow’s research focuses on determining the costs and benefits of different riparian restoration options along the Sacramento River. In particular, he and colleagues attempted to quantify the degree to which planting trees, at different densities and with different species, created habitat for six common riparian bird species, and then examined the relative costs of the different restoration approaches. Findings show that planting more trees and more species of trees (i.e., willows, cottonwoods and valley oaks, among others) pays off, in terms of markedly improving habitats for birds. Future work will continue to look at where and how to most cost effectively restore riparian bird habitats in the Central Valley.

Anthony Clemento
Validation of a New Method for Population Assessment of Pacific Salmonids Using Genetic Markers

Jun. 2007–Jun. 2011 EXTENSION
Anthony Clemento, UCSC, 831.420.3906,

Two years into this project, the Delta Science Fellow has identified more than 110 new single nucleotide polymorphism markers for Chinook salmon. In combination with other markers from the peer-reviewed literature, a panel of 96 optimal markers was assembled. This panel of markers allows scientists to establish a fish’s parentage (its hatchery and cohort) with exceedingly high accuracy (approximately one incorrect parent-offspring trio in a trillion comparisons). Scientists are in the process of genotyping Chinook salmon at the 96 markers to more accurately identify stocks and parentage. This identification dataset currently includes genetic information from more than 2,700 salmon from 30 populations in California, Oregon, Idaho, Washington, British Columbia and Alaska. Researchers plan to use the genetic information as a means of tracking salmon to more fully understand the effects of water policy, fisheries management and climate change on salmon populations.

Elizabeth Harper
Modeling Physical Drivers and Age Structure of Cottonwood Forest Habitat: An Integrated Approach
Mar. 2008–Jun. 2011 EXTENSION
Elizabeth Harper, Paul Smith’s College, New York, 518.354.8090,

This project seeks to improve the long-term prospects for restoring one of the signature species of the Central Valley’s riparian ecosystem—the Fremont cottonwood. To better prepare for the potential effects of climate change and water policies on the trees, the Delta Science Fellow is modeling the physical processes driving river channel migration and cottonwood habitat creation along the100-mile stretch of the Sacramento River from Red Bluff to Colusa that is under restoration by the Nature Conservancy. Findings – it is hoped – will help protect cottonwood forests and the many bird and mammal species that rely on them for food, cover and nesting. To date, the fellow has conducted a sensitivity analysis showing that physical and not biological variables have the greatest impact on the fate of the trees. In particular, the timing, volume and velocity of water flowing through the river and the rate of floodplain accretion all ultimately determine the success or failure of cottonwood germination, growth and survival. In the coming year, the model will be used to make predictions about the consequences of climate change on river dynamics and its implications for the future of its cottonwoods.

Sue Brander
Endocrine Disruption in the Delta: Confirming Sites’ Known Estrogenicity with Outplants, Histology, and Choriogenin Measurements
Sept. 2007–Aug. 2011 EXTENSION
Susanne Brander, UCD, 707.875.1974,
Research Mentor: Gary Cherr, Department of Environmental Toxicology, Bodega Marine Laboratory, UC Davis

In laboratory experiments, endocrine disrupting compounds (EDCs) are easily shown to cause health and reproductive problems for fish. Documenting the impacts of chronic low-level contamination in the field, however, is more challenging. In this project, the Delta Science Fellow is investigating the effects of EDCs on the ubiquitous silverside fish (Menidia audens) at two sites in Suisun Marsh. One site is exposed to treated wastewater effluent and urban runoff, the other to ranch runoff. EDCs in water samples from both sites have been shown to bind to the estrogen and androgen receptors in cell-based assays. Immunoanalyses, meanwhile, reveal that wild male fish exposed to EDCs produce greater amounts of choriogenin (an eggshell protein normally produced by only females) than control fish. In field experiments in 2009, there were relatively fewer males and they were smaller at the ranch site, as compared to the urban site. The opposite was observed with the females, which were larger and more abundant, relatively speaking, at the ranch site. The same trends were observed in the first half of 2010.

Lisa Schile
Tidal Wetland Vegetation Response to Climate Change in the San Francisco Bay-Delta
Sept. 2007–Jun. 2011 EXTENSION
Lisa Schile, UCB, 415.378.2903,
Research Mentor: N. Maggi Kelly, Department of Environmental Science, Policy and Management, UC Berkeley

If predictions of future sea level rise come true, freshwater marshes in the San Francisco Estuary stand to be flooded with saltier water and presumably replaced by brackish marshes. This project explores the potential effects of sea level rise on the distributions of wetland plants (e.g., California cordgrass, tule, bulrush, pickleweed and cattails). In conjunction with field surveys to map plant locations as a function of present topography, the Delta Science Fellow is installing marsh organs’­­– planters set in marsh channels at predetermined elevations – to simulate higher sea levels and their implications for plant growth and survival. A series of greenhouse experiments will also be conducted to measure plants’ responses to different salinities and inundation levels. The final product will be a set of GIS maps of predicted vegetation patterns in the estuary under future climate scenarios.

Heidi Weiskel
Nutrients and Benthic Invasion Dynamics in San Francisco Bay
Oct. 2007–Jun. 2011 EXTENSION
Heidi Weiskel, UCD, 530.902.0878,
Research Mentor: Edwin Grosholz, Associate Specialist in Cooperative Extension, Department of Environmental Science and Policy, UC Davis

This project explores the consequences of nutrient pollution in San Francisco Bay on two mud snails. One is an invasive species, Ilyanassa obsoleta; the other is the bay’s only native mud snail, Cerithidea californica. Findings to date suggest that nutrients, at low levels, are a resource to the snails because the nutrients feed microalgae upon which the snails graze. At higher levels, a transition occurs and nutrients become harmful to the animals. That at least is the theory being tested. In a separate but related study, the fellow observed a sudden rise in the number of Batillaria attramentaria (a relatively new invasive mud snail) and is now studying the causes and impacts of its population explosion. In the final year of the project, the effectiveness of different eradication methods and their environmental safety will be tested.

Sarah Hughes
Environmental Water: Developing Indicators and Identifying Opportunities

Jan. 2008–Jun. 2011 EXTENSION
Sara Hughes, UCSB, 805.893.7064,
Research mentor: Oran Young, Department of Environmental Science and Management, UC Santa Barbara

As Twain’s famous saying goes, “Whiskey is for drinking; water is for fighting over.” In this project, the Delta Science Fellow is compiling 20 years of survey data from more than 300 urban water municipalities in California, collected by the California Department of Water Resources. The survey collects information about a community’s sources of water (i.e., groundwater, recycled water or purchased water); the amount of water used by the community, and the community’s size (i.e., number of residents, businesses and farms). The fellow plans to use the survey data to track communities’ responses to droughts, legal decisions, regulations and political will, in terms of where and at what price they obtain water. Los Angeles will be used as a case study of how a city responds when it loses access to some of its traditional sources of water. What is learned – it is hoped – will lead to new approaches for meeting future water-related challenges in urban areas of the state.

Rachel Barnett-Johnson

Linking Freshwater Sources of California Chinook Salmon to Their Ocean Distribution Using Physical and Natural Tags
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 healthy salmon stocks without catching endangered salmon species? This question is being explored by looking at the degree to which salmon from different natal rivers or hatcheries aggregate at sea. The Delta Science Fellow is integrating multiple fish markers—based on isotope ratios, genetics and otolith microstructure­­­­—with historical coded wire-tag data. Based on preliminary findings, ocean salmon appear to be composed of seven Evolutionarily Significant Units (ESUs), with the vast majority of fish in the Central Valley Fall ESU originating from the Coleman National Fish Hatchery. Until about the age of three, salmon appear to maintain a spatial population structure at sea. Continuing analyses will probe the degree to which different salmon populations mix at sea, as the fish age.

Kristen Buck
Copper-Binding Organic Ligands in the San Francisco Bay: Current and Future Likelihood of Copper Toxicity in a Perturbed Ecosystem
Sept. 2008–Jun. 2011 EXTENSION
Kristen Buck, Bermuda Institute of Ocean Science, 441.297.1880 ext. 711,
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

Where are the different chemical forms, toxicities and sources of copper in San Francisco Bay and might freshwater diversions exacerbate the heavy metal’s toxicity? To answer these, the Delta Science Fellow is studying the relative contributions of copper-binding organic ligands from the Sacramento and San Joaquin rivers, Suisun Slough and Sulphur Springs Creek. The ligands are of interest because they have been shown to reduce the bioavailability of dissolved copper. In the early stages of the project, the fellow observed high concentrations of leachable particulate copper and zinc, as well as dissolved copper, in all estuarine water samples. As expected, the presence of strong organic ligands dramatically reduced the toxicity of the dissolved copper. Notably, however, high concentrations of weaker organic ligands were also effective at reducing the metal’s bioavailability, particularly at elevated levels of copper contamination.

Andrew Chang

Effects of Freshwater Flow and Population Connectivity on Benthic Community Dynamics in the San Francisco Estuary
May 2009–Aug. 2011 EXTENSION
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

Following heavy rains, the salinity of the San Francisco Estuary can drop precipitously, stressing and sometimes even killing native Olympia oysters (Ostrea conchaphila) and non-native Mediterranean mussels (Mytilus galloprovincialis). As part of a broader effort to restore native oyster beds and control invasive species that may hinder oyster recovery, the Delta Science Fellow and colleagues are conducting bimonthly field surveys of the bivalve populations and their size classes at 12 sites in the estuary’s brackish waters. Scientists now have good estimates of the species’ populations and have demonstrated the ability to use trace elemental fingerprinting to determine the birth grounds of newly settled juveniles. They are currently in the process of trying to determine the spatial scale at which the fingerprinting technique is valid. In the project’s final months, the fellow will conduct laboratory experiments to further quantify the stress effects of low salinity water on the animals’ heart rates, reproduction and survival. 

Tapas Das

Investigating the Frequency and Magnitude of Floods in the Sacramento-San Joaquin Valleys Under Changing Climate
Oct. 2008–Jun. 2011 EXTENSION
Tapash Das, UCSD, 858.822.3572,
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

How might climate change alter California’s risk of floods in the future? The Delta Science Fellow is investigating this question by simulating flooding under a range of climate-change scenarios for the western Sierra Nevada. All three of the General Circulation Models predict larger floods (with 50-year return intervals) from 2051 to 2099. More intense floods appear to be a consequence of several factors – bigger storms, more frequent big storms and more days of precipitation falling as rain instead of snow. Moister winter soils, which are less able to absorb added water, also play a role in some areas. Results underscore the fact that different areas of the state will be exposed to very different degrees of flooding, depending on their drainage basins and local topography. As a result, forecasts must be made at a local scale if they are to help communities appropriately plan for and protect themselves from flood events and changes in water supply.

Monika Winder
Plankton Dynamics in the Sacramento-San Joaquin Delta: Long-Term Trends and Trophic Interactions
Oct. 2008–Aug. 2011 EXTENSION
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

In this project, a 33-year record of plankton taxonomy in the San Francisco Bay-Delta is being analyzed to identify long-term trends, patterns and interactions among the region’s phytoplankton and zooplankton. To date, the Delta Science Fellow reports that a major shift in the zooplankton community occurred during the extended drought of 1987–1994, when several non-native copepods and mysids species were introduced. These non-native species displaced local calanoid and rotifer species, resulting in a zooplankton community dominated by cyclopoids with low mysid biomass. The average size of zooplankton simultaneously decreased. The changes imply a major reworking of pelagic food-web processes, including diminished food quality for foraging fish and increased carbon recycling in the microbial food web. Findings suggest that persistent climatic shifts such as long droughts can dramatically alter zooplankton communities, facilitate non-native species invasions, and perhaps contribute to pelagic species declines.

Laura Feinstein
Frequency, Distribution and Ecological Impact of Cryptic Hybrid Invaders: Management Tools for Eradication of Invasive Spartina

Sept. 2008–Jun. 2011 EXTENSION
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 current strategy for eradicating the exotic cordgrass Spartina alterniflora from salt marshes of San Francisco Bay is to apply herbicide to plants that visibly resemble the invasive or its hybrids. The Delta Science Fellow is investigating whether this management approach is resulting in the selection of hybrids that bear no outer resemblance to the invasive plant but carry non-native genes that could continue to cross with native cordgrass. Genotyping of 92 plants in four marshes has shown that 78% of plants were cryptic hybrids (i.e., they did not look like hybrids but were). Among these nonobvious hybrids only 29% of their genes were of exotic origin, compared with 55% in the obvious hybrids. Resampling in 2010 will show if cryptic hybrids are becoming more common in treated marsh areas, while a controlled garden experiment will look at whether they can thrive under as great a range of intertidal conditions as the obvious hybrids.

Michael Kiparsky
Climate Change and In-Stream Flows: Methods for Application of Risk Analysis to Modeling of Environmental Water Supplies
Sept. 2008–Jun. 2011 EXTENSION
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 impacts 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 environmental objectives (e.g., maintaining adequate flows for fishes) and securing a reliable water source? To address these topics, the Delta Science Fellow and colleagues modeled the hydrology and water operations in the Stanisulas, Tuolumne and Merced rivers, incorporating projections of urbanization and population growth through 2099. Consistent with other studies, climate change alone appears to lead to a greater demand for water and a diminished water supply by 2050. In the face of continued population growth and urbanization, water demand declines (yes declines) and the reliability of the water supply increases, as farmland is developed. A second model under development is attempting to simulate resource mangers’ risk tolerances to uncertainties in water supply.

Mary Matella
Scenarios for Restoring Ecologically Functional Floodplains and Providing Flood Control Services in the Sacramento-San Joaquin Delta
Sept. 2008–Jul. 2011 EXTENSION
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

Are there places in the Central Valley where levees could be set back or bypassed to both reduce the risk of flooding and improve ecological functioning of riparian systems? How might climate change alter patterns of flooding and restoration opportunities? The Delta Science Fellow is using the Hydrologic Engineering Center-Ecosystems Functions Model to simulate possible future changes in inundation and resulting benefits to floodplains in the south Delta. Model output will show the viability of restoring floodplain habitats, based on adjustments of flood stage and topography. It is hoped the findings will help managers plan and evaluate floodplain restoration projects – to meet conservation goals, advance flood control strategies and, in some cases, improve water supply reliability.

Joseph Street
Reconstructing Climate Variability, Acidity and Water Availability in the Sacramento- San Joaquin Watershed Based on Isotopic Evidence in Sediments from Swamp Lake, Yosemite
Jan. 2009–Jun. 2011 EXTENSION
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

This project explores the potential to use hydrogen isotope ratios preserved in leaf material in lake sediments to back out a timeline of the region’s hydrology. The approach is being applied to a 20,000-year-old, 10-meter sediment core from Swamp Lake in Yosemite National Park. Motivating the research is concern that climate change will alter the availability of water by, for example, melting the snowpack in the Sierra Nevada. In the first year of the project, the Delta Science Fellow showed that hydrogen isotope ratios are sensitive to the size of the spring snowpack, and documented a long-term decline in the ratio of deuterium to hydrogen during the Holocene, coincident with gradual increases in wintertime precipitation. Large oscillations in the isotope ratio over the last 12,000 years were observed and interpreted as evidence of centuries-long cycles in the size of the snowpack. These natural cycles lend further credence to the idea that droughts in California are linked to oceanic and atmospheric conditions in the North Pacific. Interestingly, the isotope record also suggests that climate variability in the Sierra Nevada has intensified during the last 6,000 years, possibly in conjunction with the intensification of El Niño cycles over this same period.

Joseph Street
Pilot-Scale Evaluation of an Iron Sediment Amendment for Control of Mercury Methylation in Tidal Wetlands
Jan. 2009–Jun. 2011 EXTENSION
Patrick Ulrich, UCB, 510.439.8544,
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

About 40,000 acres of tidal wetlands in the Bay-Delta are slated for restoration in the next two decades. Though the restoration will greatly benefit wildlife, there are concerns that all the earth moving (to build the wetlands) could release methylmercury into the aquatic environment and cause the Bay-Delta basin to exceed allowable mercury levels. This project is examining a novel and potentially powerful method for decreasing methylmercury releases from restored wetlands— the application of an iron-containing sediment amendment to limit the action of methylating bacteria. Preliminary laboratory experiments have shown, compellingly, that high iron doses can decrease methylmercury concentrations ten-fold. The Delta Science Fellow is now examining whether the results can be replicated in the field— at a tidal salt marsh along the Petaluma River. To accomplish this, porewater from pickleweed-dominated sediments on the high marsh plain are being analyzed for iron, sulfur and methylmercury before and after iron is added to the sediments.

Philip Sandstrom
Sacramento River Steelhead Trout: An Assessment of Behavioral Differences and Contributions of Hatchery and Wild Stocks
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 Delta Science Fellow is tracking the migratory movements and survival rates of both wild and hatchery steelhead trout in the Sacramento River watershed acoustically, using the California Fish Tracking Consortium’s telemetry array. In December 2008 and January 2009, about 300 tagged smolts (yearlings) from the Coleman National Fish Hatchery were tagged and released at three different locations on the Sacramento River above Sacramento. The tracking data show that 47–63% of wild and hatchery steelhead migrated along the main stem of the Sacramento River, with 20–28% of fish swimming through Georgiana Slough. About 5–12% of fish migrated through Steamboat Slough; 5–19% through Sutter Slough, and 0–9% through Miner Slough. On average, it took the hatchery fish released in December and January twenty days and twenty-three days, respectively, to reach the Golden Gate Bridge in San Francisco. The wild smolts’ migration, in contrast, took only twelve days on average. As more tracking data is accumulated, the fellow will calculate survival rates along different routes and return rates of released fish. The goal, ultimately, is to be able to estimate the contributions of hatchery-born fish to wild stocks.

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