CISNet San Pablo Bay Network of Environmental Stress Indicators

EPA Grant Number: R826940
Title: CISNet San Pablo Bay Network of Environmental Stress Indicators
Investigators: Schladow, S. G. , Davis, Jay A , Young, T. M. , Collins, Joshua N , Thompson, Bobbi , Schoellhamer, D. , Werner, I. , Nur, N. , Siegel, S.
Current Investigators: Schladow, S. G. , Davis, Jay A , Young, T. M. , Thompson, Bobbi , Schoellhamer, D. , Werner, I. , Nur, N.
Institution: University of California - Davis
Current Institution: University of California - Davis , Point Reyes Bird Observatory , San Francisco Estuary Institute , United States Geological Survey [USGS]
EPA Project Officer: Packard, Benjamin H
Project Period: October 1, 1998 through September 30, 2001
Project Amount: $599,764
RFA: Ecological Effects of Environmental Stressors Using Coastal Intensive Sites (1998) RFA Text |  Recipients Lists
Research Category: Environmental Statistics , Aquatic Ecosystems , Ecological Indicators/Assessment/Restoration


San Pablo Bay is a sub-embayment of San Francisco Bay. It does not have direct connection to the Pacific Ocean. San Pablo Bay receives water from several major tributaries: Gallinas Creek, Novato Creek, Petaluma River, Sonoma Creek, Wildcat Creek and Napa River. Of these, the Petaluma and Napa Rivers are the largest. However, the major sources of water to the bay are the Sacramento/San Joaquin delta to the east, and the ocean tides.

San Pablo Bay is at the confluence of several major environmental stressors. These include sediment loads and pesticide residues from California's Central Valley, the Sierra Nevada and the coastal range; industrial waste from the San Francisco Bay Area (including several oil refineries); and the site of the Mare Island Naval Shipyard (now closed).

Objectives/Hypotheses: The primary objective is to design a monitoring network that is temporally and spatially adequate to provide advance warning of the ecological impacts of natural and anthropogenic stressors. A central hypothesis is that understanding fluxes and variations in stressors within the system at a range of time-scales will permit optimal selection of monitoring locations and temporal frequencies for long-term CISNet monitoring. The parameters to be monitored at these sites will be established by testing an extensive set of potential indicators, including chemical, biochemical and ecological variables. Careful attention to indicator selection should allow the overall health of San Pablo Bay to be assessed without monitoring a financially prohibitive set of parameters over the long term.

The proposed project consists of five major tasks: 1. Determine spatial and temporal variability in anthropogenic and natural stressors. A set of 12 monitoring stations will be established within San Pablo Bay, on the major rivers feeding into the bay, and in two marshes along the bay. The water column and the sediments will be sampled monthly at all stations at comparable tidal phases. Water, suspended sediment and surficial sediment samples will be analyzed for a suite of trace metal and organic compounds and to determine the health of the benthic community. At a subset of 6 stations, current flow, conductivity, temperature, depth and optical backscatter will be measured at 15-minute intervals for 3-month periods during summer and winter. These data will be processed using time series analysis. Core samples from evaporation ponds at a former salt production facility adjacent to the bay will provide a historical record of sediment borne contaminant concentration in the bay. Egg samples from two bird species, double-crested cormorants (Phalacrocorax auritus) and song sparrows (Melospiza melodia), will be collected to evaluate seasonal, interannual, and spatial trends in chemical stressors in the San Pablo Bay food web. Interannual and spatial trends in contaminant concentrations in ecologically important fish species will also be monitored.

2. Develop and test indicators of ecological health and understand their natural variability. Biochemical indicators of ecological stress will be investigated in two sediment dwelling members of the San Pablo Bay food chain, the bivalve Potamocorbula amurensis (Asian clam) and the amphipod Ampelisca abdita. Monitoring sensitive biochemical and cellular indicators of deleterious effects should foretell subtler and possibly longer-term consequences of exposure to chemicals in the environment. Sub-lethal effects such as protein damage, lysosomal destabilization, metabolic alterations and tissue damage will be compared to contaminant body burden and higher level effects such as growth and mortality. Ecological stress indicators to be considered include number and diversity of species within benthic assemblages, contaminant bioaccumulation in fish tissue, and reproductive success for two bird species. Macrobenthic invertebrates samples will be collected from 4 sites in spring and fall of Years 2 and 3. Fish samples will be gathered two times per year at 6 sites. Hatchability, clutch size, and for song sparrows, nestling survival will also be evaluated as indicators of ecological condition.

3. Identify relations among indicators to further refine their deployment. To optimize the indicator selection, complementary information among indicators will be sought. In particular, two chemical measures of contaminant bioavailability, supercritical fluid extractability and aqueous desorption potential, will be tested for their ability to predict local contaminant effects on benthic organisms. Relationships between sediment-borne contaminant fluxes and toxicity will be investigated using correlation analysis, principal components analysis, and multiple regression to identify statistical associations. Similarly, possible causal pathways between contaminant loads in birds and components of reproductive success will be investigated using path analysis.

4. Develop and demonstrate monitoring network. Recommendations for final CISNet sites, monitoring frequency and the appropriate suite of indicators will be based on the results of the preceding tasks. Methods for interpreting indicator outcomes will be facilitated by knowledge gained from the research on processes and mechanisms of flow and sediment transport, as well as relationships among indicators (e.g. sediment, amphipods, fish, birds). These will also allow distinctions to be made between anthropogenic and natural stressors. Demonstration monitoring of these sites and the selected indicators will be performed at the end of Year 2 and early in Year 3, in coordination with the San Francisco Bay Regional Monitoring Program for Trace Substances (RMP). Note, this is separate from the ongoing, intensive site monitoring that will proceed for all three years of the project.

5. Develop and test remote sensing techniques for estimating landform and vegetation evolution in coastal environments: Remote sensing will allow us to extend the in-situ monitoring program spatially and temporally and it will offer the ability to project research results across a variety of landscape scales. Under this task we will develop and test algorithms suitable for technology transfer to local monitoring groups. Fixed-wing low altitude aerial photographic stereo images will be obtained twice each year for six sites in San Pablo Bay representing gradients of age and salinity in each of the two largest local tributaries, the Petaluma and Napa rivers. Near infrared images will be digitized, processed and analyzed, and georectified maps will be produced for each flight series. Data to be extracted from the images includes vegetation cover (via spectral density and patch differentiation), photogrammetrically derived elevations (for low tide images), the interface of exposed ground surface and open water (for multiple tide images), channel planform, and channel density. Change detection analyses will be performed on time series images to determine rates and patterns of evolution. In the first year, at least two image scales will be flown to evaluate the resolution suitable to the types of data to be extracted from the images. Concurrent field work includes tidal datum reckoning, tidal elevation control, ground control establishment and surveys, vegetation species and percent cover measurements, channel cross section surveys, and tidal prism determinations via current or flow meters and recording pressure transducer water level indicators.

Expected Results:

Major benefits of the proposed study include development and demonstration of an innovative monitoring network to identify trends in the ecological health of San Pablo Bay. The process developed for optimizing the monitoring network should illustrate efficient ways to develop future coastal monitoring sites at other locations. The project will also provide a more fundamental understanding of the link between sediment bound contaminants, bioavailability, deleterious effects in organisms, and effects on benthic, fish and avian communities. In addition to adding valuable insights into the ecological responses to human-induced stresses in San Pablo Bay, our CISNet effort will provide critical information to decision-makers and regulatory agency staff working on restoration, enhancement, and dredging projects. For example, tens of thousands of acres in the North Bay are being considered for large-scale wetland restoration and our monitoring and research will provide information necessary to decision-making on these projects and to establishing baseline conditions for future ecosystem response assessments.

Publications and Presentations:

Publications have been submitted on this project: View all 44 publications for this project

Journal Articles:

Journal Articles have been submitted on this project: View all 9 journal articles for this project

Supplemental Keywords:

sediment transport, bioavailability, optimal network design., RFA, Scientific Discipline, Toxics, Geographic Area, Waste, Water, Ecosystem Protection/Environmental Exposure & Risk, Bioavailability, Ecology, Ecosystem/Assessment/Indicators, Ecosystem Protection, Contaminated Sediments, pesticides, State, Chemistry, Ecological Effects - Environmental Exposure & Risk, Monitoring/Modeling, Environmental Monitoring, Pacific Northwest, Biology, Ecological Indicators, ecological effects, ecological exposure, monitoring, anthropogenic stresses, health effects, anthropogenic stress, advance warning system, fate and transport, regional monitoring program , biomarkers, industrial waste, natural stressors, contaminated sediment, coastal zone, CISNet Program, regional environmental health, biomonitoring, environmental stress, San Pablo Bay, environmental stressors, environmental stress indicators, biological markers

Progress and Final Reports:

  • 1999 Progress Report
  • 2000 Progress Report
  • Final Report