2011 Delta Science Fellows and Project Summaries

On behalf of the Delta Science Program, California Sea Grant is pleased to announce the 2011 recipients of Delta Science Fellowships, which provide paid support for research on priority issues for the San Francisco Bay-Delta.

They are:

Bryan Cole, a post-doctoral researcher at the Bodega Marine Laboratory, UC Davis, who will be studying the effects of endocrine disruptors on fish reproduction in the Bay-Delta.

Kathleen Fisch, a post-doc with the San Diego Zoo Institute for Conservation Research, investigating ways to preserve the genetic integrity of supplemented wild fish stocks.

Kristy Forsgren, a post-doc in the Department of Environmental Sciences, UC Riverside, studying the combined toxicity of hypersalinity and pesticide contamination on aquatic life.

Julien Moderan, a post-doc at the University of La Rochelle, France, exploring carbon sources and phytoplankton food dynamics in the San Francisco Estuary.

Calla Schmidt, a post-doc in the Department of Earth and Planetary Sciences, UC Santa Cruz, examining the impacts of nutrient loading on food web dynamics.

Erin Bray, doctoral student at the Bren School of Environmental Science and Management, UC Santa Barbara, studying the potential to restore salmon habitats with flow releases.

Sarah Lesmeister, a doctoral student in the Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, UC Davis, investigating the effects of pesticide pollution on aquatic life.

Jason Hassrick studies the migration of Chinook salmon through the Sacramento river.

Endocrine Disruption in the Sacramento-San Joaquin Watershed: Laboratory and Field Experiments on a Resident Fish, Menidia audens, the Mississippi Silverside
R/SF-44 Jun. 2011–May 2013
Bryan Cole, UCD/BML, 707.875.1935, bjcole@ucdavis.edu

Could endocrine-disrupting compounds in treated wastewater effluent and runoff be contributing to the region’s declines in pelagic organisms? This project investigates evidence of endocrine disruption in resident fishes in the Sacramento-San Joaquin Delta. The model species for this research is the inland silverside, Menidia beryllina—an introduced, now ubiquitous species with a similar life history to the delta smelt, a species of intense management interest. In the project’s first year, the Delta Science Fellow examined endocrine-related gene expression and protein synthesis patterns in male silverside collected throughout the Delta, and from this work showed that males were expressing genes and producing egg-related proteins that are usually associated with female biology. Abnormal schooling of fish during the spawning season was also observed, suggesting that endocrine-disrupting compounds may alter fish behaviors, too. In “outplanting” experiments, scientists were able to detect hormone-related changes in transplanted fish after only two weeks of exposure to conditions in the Delta. Ongoing experiments seek to document the population-level effects of contamination.

Saving San Francisco Bay-Delta Native Fishes: Hatchery Management and Reintroduction Strategies
R/SF-45 Jun. 2011–Jun. 2013
Kathleen Fisch, UCSD/SD Zoo Institute for Conservation, 562.972.5283, kfisch@sandiegozoo.org

Native fishes in the San Francisco Bay-Delta are in trouble—the reality is that several species could go extinct. As a conservation measure, refugial populations (captive brood stock) and captive breeding program (hatcheries) have been established or proposed for seven of the most vulnerable species: longfin smelt; Sacramento splittail; Sacramento perch; green sturgeon; delta smelt; Chinook salmon; steelhead trout. The idea is to spawn fish and release their offspring in the wild to supplement, or if needed re-introduce, the species. This project seeks to identify optimal hatchery practices for preserving the genetic integrity of wild populations that are being supplemented. The approach employs computer modeling to simulate effects of hatchery protocols on the genetics of supplemented populations for each of the seven species. In the model, fish are assumed to produce offspring through one of five spawning strategies (e.g., random mating or kinship selection). Genetic inbreeding and other genetic metrics are then tracked in time to estimate the genetic consequences to supplemented wild populations (e.g., loss of genetic diversity). The model incorporates life history characteristics of each species—estimates of fecundity, fitness, age of maturity—as well as a variety of tools for genetically informed breeding (such as microsatellites, single-nucleotide polymorphisms, pedigree reconstruction and relatedness estimation). Findings will assist ongoing, mandated and proposed hatchery operations in the Central Valley.

The Effect of Bifenthrin, Under Hypersaline Conditions, on the Long-Term Reproductive Health and Embryonic Development of Oncorhynchus mykiss
R/SF-46 Apr. 2011–Mar. 2013
Kristy Forsgren, UCR, 562.773.8378, kristy.forsgren@ucr.edu

This project investigates the cumulative consequences of high-saline waters and pesticide toxicity on juvenile steelhead salmon reproductive physiology through a concentration-and-response study with environmentally relevant concentrations of bifenthrin. Bifenthrin is the active ingredient in residential ant and termite control products, which is highly toxic to fish. The EPA lists this pyrethroid insecticide as a “possible human carcinogen” and its use is banned in the European Union. The hypothesis of this project is that high-saline conditions may exacerbate pesticide toxicity and hence their endocrine-disrupting effects. As a result, the reproductive health of young steelhead migrating through the Bay-Delta may be compromised. First- and second-year experiments to test these ideas showed that juvenile females but not males were obviously harmed by chronic exposure to bifenthrin under high-saline conditions. In particular, their ovaries were severely damaged—a somewhat unexpected response, as bifenthrin is an estrogen mimic. Subsequent ovarian tissue-culture experiments verified the more predicted response—that bifenthrin stimulates ovarian follicle growth. The Delta Science Fellow is currently investigating gene expression patterns in juvenile steelhead exposed to bifenthrin. Among the topics she would like to explore include: understanding why females but not males were affected by the insecticide, and why the ovarian tissue-culture experiments yielded such vastly different results from the whole body experiments. Yet another question is whether a female salmon’s ovaries can self-repair at sea, where presumably toxin exposure is much lower. If not, bifenthrin has the potential to impair salmon fecundity.

Current and Past Trophic Relationships Among Dominant Zooplankton Species in the San Francisco Estuary Determined Using Stable Isotope Analysis
R/SF-47 May 2011–Sep. 2013
Julien Modéran, SFSU, 415.435.7113, jmoderan@sfsu.edu

This project seeks to reconstruct trends in food resources for dominant zooplankton species in the San Francisco Estuary over the last few decades, as a means of exploring potential contributing factors to declines of many fish species. In the project's first year, the Delta Science Fellow tested the effects of formalin, used to preserve zooplankton samples, on species' stable isotope compositions and with this work validated the ability to conduct stable isotope analyses on preserved samples. He is now using this approach to analyze a 36-year record of zooplankton samples collected in the estuary from 1976 to 2010 through the Interagency Ecology Program. The hypothesis is that there has been a shift in sources of carbon and nitrogen from local phytoplankton to freshwater or terrestrial-derived organic sources since the mid-’70s and that this shift to a longer, less energy-efficient food chain could imply that food shortages are occurring for higher level organisms, notably fishes of management concern. In preliminary analyses of freshwater zooplankton, no trends in carbon or nitrogen signatures were observed at the species level. (As an interesting aside, anthropogenic nitrogen was detected in zooplankton.) In the coming year, the fellow will analyze low-salinity samples and, with estimates of zooplankton biomass, investigate community-level trends in both freshwater and low-salinity samples. Statistical approaches will be used to investigate relationships between zooplankton trophic ecology and environmental factors. In the ongoing field component of the project, the fellow is collecting monthly zooplankton and organic matter samples at eight stations along the estuary’s salinity gradient. These samples are also being analyzed for their stable isotopic composition to identify present day sources of organic matter and to infer trophic relationships among currently abundant zooplankton species, among other things.

In-Situ Measurement of Differential Nutrient Utilization by Phytoplankton and Bacteria: Impacts of Nutrient Loading on the Base of the Delta Food Web
R/SF-48 Oct. 2011–Sep. 2013
Calla Schmidt, UCSC, 360.927.0365, cschmidt@ucsc.edu

High levels of ammonium (NH⁴⁺) may limit the growth of the larger phytoplankton (primarily diatoms) by inhibiting nitrate (NO^3-) uptake. The primary objectives of this project are to use stable isotope analyses to track ammonium vs. nitrate uptake in phytoplankton collected in the Sacramento River and identify the sources of these nutrients (i.e., effluent from a nearby sewage treatment plant, dissolved organic matter, runoff, or river inputs). Of particular interest is whether the phytoplankton community switches from using NO^3- to NH⁴⁺, as NH⁴⁺ concentrations rise, and whether diatoms are more sensitive to changes in NH⁴⁺ concentration than smaller phytoplankton species. In the project’s first year, the fellow developed and validated a method for isolating algae from detrital matter prior to isotopic analysis. In the coming year, field collection will begin in the Sacramento River. Findings will have implications for determining food resources available for pelagic fishes and for regulating sources of nutrient pollution.

The Effects of Flow Releases on the Joaquin River on Abiotic Drivers of Chinook Salmon (Oncorhynchus tshawytscha) Habitat
R/SF-49 Apr. 2011–Jun. 2013
Erin Bray, UCSB, 805.893.4886, ebray@bren.ucsb.edu

The US Bureau of Reclamation is releasing water from Millerton Lake over the Friant Dam spillway on an interim, experimental basis to explore restoration options for the San Joaquin River. To help inform this process, this project is examining spatial patterns of temperature (heat) and groundwater exchange in the river under different flow regimes. In particular, the Delta Science Fellow is examining how different dam releases—their frequency, timing and duration—might affect Chinook salmon habitat quality at length scales relevant to their life history. Of particular interest are the scales at which spawning occurs (about 150 meters) and migrating salmon travel (about 260 kilometers). In work to date, the fellow reports that “our field measurements document the effects of flow releases on groundwater-surface water exchange and temperature using fiber optic distributed temperature sensing (DTS), measurements of temperature in the riverbed, and streambed hydraulic conductivity (Ksat) over the length of three river meander bends (2 kilometers). Measured channel bed elevation, flow depth, velocity, and bed-material grain size are currently being used to develop a model of the groundwater exchanges at the smaller scale (150 meters) and the interactions of flow and temperature at the larger scale (260 kilometers). Some of the findings from this project were incorporated into a technical 2012 report for the Bureau, titled “Controls on hyporheic water quality and salmonid egg survival in the San Joaquin River.”

The Toxic Effects of Key Pesticides on the Calanoid Copepods, Eurytemora affinis and Pseudodiaptomus forbesi, of the San Francisco Estuary
R/SF-50 Apr. 2011–Mar. 2013
Sarah Lesmeister, UCD, 530.752.1967, salesmeister@ucd.edu

Is low-level, chronic pesticide contamination in the Sacramento-San Joaquin Delta contributing to declines in zooplankton populations? Might certain pesticides be more toxic to some species than others, and might these differences in part explain broad-scale changes in food resources for larval fishes and other zooplankton consumers? This project explores these ideas. In lab experiments conducted in the project’s first year, the Delta Science Fellow estimated the lethal concentrations (LC50s after 96 hours) of five pesticides on two calanoid copepod species, Eurytemora affinis and Pseudodiaptomus forbesi. These baseline toxicity values are now being compared to pesticide concentrations in the Delta. The copepods are also being exposed to water samples collected from the Delta before and after rainfall to directly observe the toxicity of ambient surface waters and whether this toxicity is increased by runoff. Among the early findings: the pyrethroid insecticide bifenthrin was the most toxic of the five pesticides studied, and its concentrations in the Delta have been observed to exceed the lethal concentrations documented in the lab experiments. Ambient surface waters have been observed to be acutely toxic (i.e., lethal) to both copepod species; however, P. forbesi shows a higher tolerance to the Delta’s “toxic soup” than E. affinis. This result is intriguing, as both species have experienced significant population declines in the last decade, particularly E. affinis. Future research will explore whether trends in zooplankton populations can be attributed to differences in the species’ toxin tolerances. Yet another topic to be explored is the extent to which the heat content of water and suspended sediment concentrations may reduce acute pesticide toxicities. Results will help refine and update regulations on pesticide use in the Sacramento-San Joaquin Delta to protect zooplankton, ecosystem and ultimately, human health.

Tracking Migration Patterns and Mortality of Juvenile Spring, Winter and Fall Run Chinook Salmon in the Sacramento River and Delta
R/SF-51 Jan. 2012–Dec. 2013
Jason Hassrick, UCSC, 831.430.6551, hassrick@biology.ucsc.edu

California Chinook salmon are in a state of crisis. Several runs in the Central Valley and Central Coast are in danger or threatened by extinction, and the remnant commercial Chinook fishery is maintained only through the rearing and release of huge numbers of Central Valley fall-run juveniles. All hopes of recovering wild stocks in the Sacramento River system are challenged by various forms of habitat degradation and mortality, direct and indirect, caused by water diversions. In the project’s first year, the fellow conducted a pilot study on fall-run Chinook smolts in the Sacramento River to test a new miniaturized acoustic technology for tracking fish on their outmigration to sea. He also used shipboard acoustic data, along with juvenile salmon survey data, to explore the degree to which young salmon and krill are generally found in the same spots. This analysis provides information on how much juvenile salmon rely on krill as a food resource. Such information can provide insights into the number of adult salmon that might be expected to return to spawn two years later. In the coming year, the fellow will begin implanting the new acoustic transmitters into sub-yearling winter-run Sacramento River Chinook. The smolts will be tracked on their outmigration to sea, using an existing array of monitors, updated with receivers capable of detecting the signals from the new miniaturized tags. The survivorship data gathered during this project will be combined and compared with a parallel tracking study of fall- and spring-run Chinook. Findings will allow managers to better evaluate the effects of different flow conditions and water management practices on salmon survival. Of particular interest will be to compare salmon survivorship when the Delta Cross Channel gates are open and closed.