2002 Progress Report: Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium: Administration and Integration Component

EPA Grant Number: R828676C000
Subproject: this is subproject number 000 , established and managed by the Center Director under grant R828676
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).

Center: Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium
Center Director: Anderson, Susan L.
Title: Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium: Administration and Integration Component
Investigators: Anderson, Susan L. , Cherr, Gary N. , Collins, Joshua N , Morgan, Steven , Nisbet, Roger M. , Pawley, Anitra , Smith, Ed
Institution: University of California - Davis , University of California - Santa Barbara
EPA Project Officer: Hiscock, Michael
Project Period: March 1, 2001 through February 28, 2005
Project Period Covered by this Report: March 1, 2001 through February 28, 2002
RFA: Environmental Indicators in the Estuarine Environment Research Program (2000) RFA Text |  Recipients Lists
Research Category: Ecological Indicators/Assessment/Restoration , Water , Ecosystems


The overall objective of this research project is to develop a suite of ecological indicators to rapidly assess the integrity and sustainability of wetlands in west coast estuaries. We propose to develop an integrated suite of indicators to evaluate impacts of stressors across levels of biological organization, trophic structure, life stage, and time and space.

Progress Summary:

Pacific Estuarine Ecosystem Indicator Research (PEEIR) Overview. The PEEIR Consortium is an integrated project intended to develop indicators of wetland integrity for the west coast. The specific objective of this research project is to develop synthetic indicators of contaminant and nutrient stress in salt marsh systems using: (1) fish and invertebrate model species at multiple levels of biological organization; and (2) wetland plants at multiple spatial scales. All PEEIR investigators participate in our common sampling design, which includes carefully selected stations in both northern and southern California. Furthermore, we conduct integrated field and laboratory experiments to characterize and validate indicators. The PEEIR integration team provides overall guidance and support. Year 1 of the project was devoted to method development and preliminary sampling. Accomplishments in Year 2 of the project have included completion of the first full year of integrated sampling, organization of integrated experiments, analysis of key data sets, and further method development.

Progress in each of the project subcomponents is described in this compilation of four reports. The PEEIR integrated sampling effort is described in detail in the Ecosystem Indicator Component Report. Overall, initial data from our comprehensive sampling effort are encouraging. For example, a continuum of plant stress indicators that link biomass changes observed by remote sensing, ecological responses in wetland plants, and bioavailable contaminant fractions are being examined critically. In addition, markers of effect in fish and invertebrates have elicited statistically significant responses at the more contaminated sites, and the importance of these effects at the population level is being analyzed. The opportunity to work at multiple levels of biological organization and at multiple spatial scales across a broad geographic region is unique, and the PEEIR program fosters novel dialogue across disciplines.

Modeling and Integration. An important aspect of PEEIR is the development of a theoretical component that may provide novel approaches to the integration of the numerous measurements being undertaken. Investigators in various project components are involved in statistical integration activities. In particular, Dr. Stewart-Oaten and Dr. Bennett have explored a selection of multivariate procedures. However, integration efforts also include conceptual modeling and a critique of the use of indices of biotic integrity (IBI). The modeling research has focused on two themes: fish growth in variable environments, and the dynamics of stable isotopes of nitrogen in consumer species. This effort is being led by Dr. Roger Nisbet on the University of California Santa Barbara campus.

Conceptual Model. As a part of the integration effort, Dr. Stewart-Oaten has been reviewing the contribution of individual investigations within PEEIR as potential components of an idealized wetland monitoring strategy that consists of three main steps: (1) initial survey; (2) confirmation of impairment; and (3) evaluation. Measures used in each stage differ in their specificity and costs. In the initial survey, measures should be very general over many potential problems and inexpensive, but may produce false alarms. In the confirmation stage, measures should be more specific to types of problems but may be more expensive than in the initial surveys. Measures used in the final step can have different levels of specificity and cost depending on objectives of management actions. The objectives may be to meet the minimum conditions for some designated use of wetlands or to maintain hypothetical wetland "health" or "integrity," if such conditions can be defined.

This strategy identifies the chronological stages in the assessment of wetlands, and will help to translate our scientific efforts into actual management tools by placing each component of our project into the strategy. Furthermore, this strategy also will become a tool to integrate our work with efforts that exist outside of our project.

Evaluation of IBI. Multimetric indices such as IBI are becoming increasingly popular as an indicator measure of ecosystem "integrity." For example, the Ohio Environmental Protection Agency (EPA) uses the IBI as one of its routine measurements for the monitoring of rivers. During the past year, we examined the feasibility of applying the IBI approach to PEEIR data on coastal wetlands.

In the IBI approach, it is crucial that reference conditions of a system (i.e., conditions expected in a natural habitat without human disturbances) are identified in terms of abundance, species composition, and trophic structures of some macrofauna. However, all coastal wetlands in California are disturbed to some degree by human activities. In addition, there is high natural temporal and spatial variability among and within the wetlands. These make identification of the reference conditions almost impossible. As a result, our current conclusion is that the IBI approach is not appropriate for our coastal wetland studies.

In addition to the specific difficulty applying the method to the wetlands, the IBI appears to have general problems. We currently are evaluating the literature that criticizes, as well as supports, the IBI method so that these ideas are reflected in alternative approaches that we currently are developing.

Dynamic Models of Organismal Growth in Changing Environments. Field and laboratory studies within the Ecosystem Indicator (EI) and Biological Response to Contaminants (BRC) components of PEEIR are providing data on the growth of fish and invertebrates in potentially stressed environments. Interpretation of the data and integration of findings from individual studies requires mechanistic models that relate variability in growth patterns to changes in the environment. For this purpose, we are studying the predictions of dynamic energy budget (DEB) models that describe growth, development, and reproduction in arbitrary environments. Although there is a large body of theory for deterministic DEB models, our work requires stochastic models, which have been developed ab initio during Year 2 of the project. The models make predictions of changes in observed size distributions in a population, and will be used to estimate variability in observed growth rates from studies on individual organisms and from size distributions in a population.

Dynamics of Stable Isotope Ratios. Our decision to give priority to modeling the dynamics of nitrogen isotopes derived from initial findings of the EI component that show large within-year variation. We are using DEB theory to model the dynamics of the two nitrogen isotopes in individual organisms. Our initial aim is to construct models that reproduce the typical N-15 enrichment levels that commonly are observed across many taxa and ecosystems. Some short-term experiments on excretion rates are planned for summer or fall of 2003 that will help with model parameterization. The models will predict the changes of the isotope ratio within organisms in response to changing food density and isotopic composition, and will then be used to interpret the large body of data that is being gathered by PEEIR and other investigators. Because nitrogen enrichment is such a ubiquitous issue, our models should be useful in many kinds of wetland systems both within and beyond California.

Archival Data and Related Integration. To provide the most cost-effective development of wetland indicators, PEEIR also is investigating potential uses of archival data to characterize ecological condition in wetlands along the west coast. Dr. Anitra Pawley of The Bay Institute researched available resources to locate data sets associated with invertebrate density, community composition, and associated environmental contamination in and around PEEIR study sites. This involved queries of extant federal and state databases, searching the primary and gray literature from the past 20 years, and contacting researchers with specific connections to ongoing biomonitoring programs (e.g., U.S. Geological Survey [USGS], U.S. Fish and Wildlife Service, California Department of Fish and Game, U.S. Environmental Protection Agency, local mosquito abatement districts, among others). Although some data are available, in many cases they are not directly available for PEEIR study sites, are of short duration, and/or measurements were not adequate for our specific needs. In some cases, limited data exist but are less readily available.
As a consequence, we currently are focusing on a more general investigation of stressors and effects upon the benthic invertebrate community of estuarine systems. In this way, we can look at more general responses to contaminant effects and provide a context for the west coast data that has been located. By compiling and documenting the available information using a wider set of data representing a larger area, the database is more robust and the analysis more powerful. Indeed, it is critical because of the data limitations for west coast sites.

The product generated from our current work plan will contain a qualitative component that incorporates a brief discussion of extant methodology for detecting stressor effects in the zoobenthic community, and also summarizes results from the literature to date. We envision that a quantitative meta-analysis will be completed to determine whether effects measured in the field generally are detectable, and determine the range of variables most sensitive to contaminant effects.

In addition to the effort described above, a summary of available data sets for San Francisco Bay has been completed by Dr. Pawley, and a similar report for Tomales Bay has been prepared by Dr. Ed Smith. In general, we have found the available data to be quite variable in nature and not adequate to provide any comprehensive or integrated view of salt marsh condition.

NASA-Funded Remote Sensing Research. The National Aeronautics and Space Administration (NASA)-funded remote sensing project (Dr. Susan Ustin, Prinicipal Investigator [PI]) is an integral component of the PEEIR project; and hence, we provide a brief update here in our report to the EPA. Dr. Ustin and colleagues are active in our synthetic efforts to characterize stress responses in wetland plant communities. In addition, their work is vital to all site characterization and geographic information system (GIS) activities. Key accomplishments for this Project Year include: (1) acquired field spectra in all marsh sites except Mugu Marsh. Field data were acquired at transects where vegetation measurements were acquired but timed to occur at the time of the Airborne Visible/Infrared Imaging Spectrometery (AVIRIS) overflights; (2) requested and obtained approval for AVIRIS overflights (Twin Otter) for all sites in September 2002. Coordinated selection of flightlines. Part of the Marin County flightlines were cloudy, making that data of lesser quality than at the other sites. Airspace permission over Mugu Marsh was not acquired by NASA during their flight schedule. NASA approved additional funding to acquire data over these sites in May 2003; (3) completed a hydroponic greenhouse study of contaminant stress on the dominant salt marsh species (Salicornia virginica, Spartina foliosa, S. alternifolia, S. hybrid, Scirpus robustus, Typha ssp.). Plants were grown under cadmium, vanadium, and heavy and light crude petroleum to investigate their response: leaf and canopy reflectance, photosynthesis, leaf fluorescence, chlorophyll, water and dry matter contents, and metal ion concentration; (4) calibrated the AVIRIS data to apparent surface reflectance. Ongoing GIS database development to register the data to spatial coordinates and provide a basis for interpretation; (5) assumed responsibility for supporting the PEEIR GIS database. Provided training and space for PEEIR data manager, Webb Sprague; (6) presented a talk at the American Society of Limnology and Oceanography meetings describing the results of the cadmium study and preliminary results from the AVIRIS data over Stege Marsh (site of high soil cadmium concentrations) and China Camp. These results are consistent with lower live growth and accumulation of more dry plant litter at the Stege site; and (7) coordinating LIDAR data acquisition and flightlines for the project with the National Park Service and the data provider.

Geomorphology Program. Each of the three PEEIR study sites consists of a number of biological and physiochemical sampling stations arrayed within a single tidal drainage network. Some of the component channels of each network de-water at low tide, and others do not. Most of the sample stations are located within channels or on the adjacent marsh plain within 1-2 meters of channel banks. The hydrogeomorphic studies will empirically determine the high tide datums, and the frequency and duration of tidal inundation, for the chemical and biological sampling stations of the PEEIR. Equipment has been purchased, and the installation sites have been selected. Data collection will begin in June 2003.

The hydrogeomorphic studies, in collaboration with the remote sensing group of the PEEIR, will also be used to ground-truth the LIDAR imaging, rectify the imaging to the local high tide datums, and develop predictive maps of the frequency and duration of tidal inundation and spatial patterns of sediment deposition for each site. The accuracy of the maps can be tested based on field observations of the distribution and residence time of surface water from over-bank tides. If the maps are accurate, then the distribution of conditions similar to the biological and physiochemical sample stations can be inferred across the extent of the imaging. If the imaging is vertically rectified to the local high tide datums, then the correlation between surface hydrology and spatial variations in plant community structure could be tested, and the vertically rectified LIDAR imaging might be used to test simple indices of channel density and topographic complexity that could be used in routine coastal wetland monitoring programs.

Data Management Activities. The PEEIR data management component will serve all project investigators by providing centralized access of data for integrated statistical and modeling efforts needed to derive wetland indicators. Our plan for 2003 included the following: formulating a tested database, entering a significant portion of 2002 data, providing working prototypes of data entry programs, and completing the specification of metadata formats.

All of the above projects are still in progress. We currently are finalizing the conceptual design for the database based on samples of data submitted from the PIs. We will start entering 2002 data as soon as the database design is complete. Because we are such a heterogeneous group of researchers, with correspondingly heterogeneous data, we will use an informal e-mail- and spreadsheet-based data communication procedure, and not implement online data entry programs. We still are working on metadata specifications, pending directives from the EPA. Perhaps most importantly, Webb Sprague, the data manager, is now familiar with much of the data and has developed working relationships with the researchers; this will be important as more data becomes available. The next step is to finish collecting data for 2002, to build a prototype application for viewing the data, and to build filters for conversion of the data into conformant data/metadata formats once we have decided on a metadata specification. We also are initiating a GIS integration effort under the direction of Dr. Ustin. Construction of a relational database will ensue later in the year.

Organizational, Peer Review, and Collaborative Activity. We have engaged in a number of activities that enhance the quality, scope, and applicability of PEEIR findings. These include the following: we conducted our first Science Advisory Board (SAB) review at the November "All Hands" Meeting. This review included the following members: (1) Donald DeAngelis, USGS/Biological Resources Division and Department of Biology, University of Miami, Coral Gales, FL; (2) John Knezovich (Chair), Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA; (3) Richard Lee, Professor of Oceanography, Skidaway Institute of Oceanography, Savannah, GA; (4) Charles Simenstad, School of Fisheries and Aquatic Sciences, University of Washington, Seattle, WA; (5) Peter Thomas, Marine Science Institute, The University of Texas at Austin, Port Arkansas, TX; and (6)Vern Vanderbilt, Senior Research Scientist, NASA Amers Research Center, Moffett Field, CA.

Responses to all SAB comments have been carefully scrutinized and will be implemented fully by summer of 2003.

We participated in numerous Cross-EaGLEs planning and assessment meetings, and Dr. Anderson has participated in the SAB for the Gulf Coast EaGLE CEER-GOM.

We have briefed Dr. Bobbye Smith, EPA Headquarters Office of Research and Development liaison to EPA Region IX, on a regular basis regarding our activities and have developed various integration activities.

We have developed collaborations with various agencies and institutions, including: the CALFED Bay Delta Program, which awarded PEEIR $250,000 in matching funds, the San Francisco Bay Regional Water Quality Control Board for data to support regional decisions on marsh restorations, the University of California Toxic Substances Research and Teaching Program, which awarded a $56,000 match for the restoration studies above, and the Southern California Coastal Water Research Project for investigations regarding microbial pathogens.

We completed coordinated sampling with the west coast Environmental Monitoring and Assessment Program team and will provide them with data on endocrine disruptors and metals in marsh plants.

Future Activities:

Future activities include selection of new sampling locations for 2003 using AVIRIS data for two of the sampling sites. This will allow us to determine whether remote sensing can be used to provide cost-effective identification of sites with significant impairment of plant biomass. This will be an important step in our goal to develop indicators of stress in wetland plants at multiple spatial scales.

Research on all of the above themes will continue in Year 3 of the project. Late in that year, we anticipate construction of a model of nitrogen fluxes within a wetland. Models will be used to interpret results from field experiments planned for summer 2003. Plans for further statistical integration are evolving, and manuscripts for 2004 are under discussion.

Journal Articles:

No journal articles submitted with this report: View all 8 publications for this subproject

Supplemental Keywords:

watersheds, estuary, ecological effects, bioavailability, ecosystem indicators, aquatic, integrated assessment, EPA Region IX., RFA, ENVIRONMENTAL MANAGEMENT, Water, ECOSYSTEMS, Ecosystem Protection/Environmental Exposure & Risk, estuarine research, Ecosystem/Assessment/Indicators, Ecosystem Protection, Ecological Effects - Environmental Exposure & Risk, Aquatic Ecosystems, Terrestrial Ecosystems, Ecological Monitoring, Ecological Indicators, Risk Assessment, anthropogenic stress, anthropogenic stresses, wetlands, aquatic ecosystem, bioindicator, ecological risk assessment, estuaries, ecosystem assessment, wetland ecosystem, nutrients, bioavailability, trophic effects, ecosystem indicators, coastal ecosystems, environmental indicators, ecosystem restoration, water quality, aquatic ecology

Progress and Final Reports:

Original Abstract
  • 2001
  • 2003
  • Final

  • Main Center Abstract and Reports:

    R828676    Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium

    Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R828676C000 Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium: Administration and Integration Component
    R828676C001 Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium: Ecosystem Indicators Component
    R828676C002 Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium: Biological Responses to Contaminants Component: Biomarkers of Exposure, Effect, and Reproductive Impairment
    R828676C003 Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium: Biogeochemistry and Bioavailability Component