2004 Progress Report: A Western Center for Estuarine Indicators Research which will Develop Indicators of Wetlands Ecosystem Health

EPA Grant Number: R828676
Center: Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium
Center Director: Anderson, Susan L.
Title: A Western Center for Estuarine Indicators Research which will Develop Indicators of Wetlands Ecosystem Health
Investigators: Anderson, Susan L. , Allen, John , Cherr, Gary N. , Collins, Joshua N , Morgan, Steven , Murdoch, William W. , Nisbet, Roger M. , Pawley, Anitra , Smith, Edmund , Stewart-Oaten, Allan , Werner, I.
Current Investigators: Anderson, Susan L. , Allen, John , Bennett, Bill , Brooks, Andrew , Carr, Robert Scott , Cherr, Gary N. , Fujiwara, Masami , Green, Peter , Grosholz, Edwin , Hwang, Hyun-Min , Kendall, Bruce E. , Morgan, Steven , Murdoch, William W. , Nisbet, Roger M. , Ogle, Scott , Pawley, Anitra , Rose, Wendy , Stewart-Oaten, Allan , Swanson, Christina , Vorster, Peter
Institution: University of California - Davis , University of California - Santa Barbara
Current Institution: University of California - Davis , Pacific EcoRisk , The Bay Institute , U.S. Geological Survey , University of California - Santa Barbara , University of California - Santa Cruz
EPA Project Officer: Packard, Benjamin H
Project Period: October 1, 2000 through September 30, 2004
Project Period Covered by this Report: October 1, 2003 through September 30, 2004
Project Amount: $5,998,221
RFA: Environmental Indicators in the Estuarine Environment Research Program (2000) RFA Text |  Recipients Lists
Research Category: Ecological Indicators/Assessment/Restoration , Water , Ecosystems

Objective:

The goal of the Center is to develop new indicators of estuarine wetland health in marsh plants and animals so that corrective management of the nation’s wetlands can be implemented before it is too late, difficult, or prohibitively expensive. The project spans all levels of the biological hierarchy from strands of DNA to populations to the landscape and involves ecotoxicologists, ecologists, biochemists, microbiologists, and remote sensing experts. Research is being conducted at three sites in Tomales and San Francisco Bays in northern California and three sites in southern California across gradients of pollution impact from heavy metals, organic compounds, and excess nutrients.

Indicator species have been developed for surveys in west coast wetlands (Figure 1). Utilizing the shore crab (Pachygrapsus crasssipes), the mudsucker fish (Gillichthys mirabilis), and wetland plants such as cordgrass (Spartina spp.) and pickleweed (Salicornia virginica), we have developed survey and census methodologies, as well as numerous physiologic techniques. For plants, we have integrated techniques as variable as use of airborne visible/infrared imaging spectrometer (AVIRIS) overflight images, plant physiology, and contaminant data. In animal models, we have refined numerous physiologic assays, perfected transplant techniques, and validated otolith rings in fish for calibration of field data to population modeling. These animal models and our resulting compendia of techniques can eventually be used by numerous monitoring groups in the western United States to assess wetland health.

Figure 1. PEEIR Conceptual Model

Analytical chemistry and toxicity testing often are viewed as inadequate techniques to assess effects of contaminants on resident aquatic species. Evaluation of physiologic responses called biomarkers can be used to discern sublethal effects in resident species, but there is little consensus on how this general approach should be implemented in coastal monitoring. For example, at our most contaminated site, indicators of ovarian tumors and apoptotic cells in liver (indicator of contaminant stress) are elevated significantly in the mudsucker fish (G. mirabilis), and these same fish exhibit more variable growth rates than were observed at other sampling locations. In some locales, we observe high rates of endocrine disruption. We envision that a suite of biomarker techniques will be recommended for monitoring applications and this will be useful to managers in discerning whether contaminants cause negative effects on the condition of wetland flora and fauna. Hence, management interventions will not be based on extrapolation from toxicity tests and chemical analysis data but on actual analysis of effects in marsh species.

Progress Summary:

Indicator Integration Overview

The Pacific Estuarine Ecosystem Indicator Research Consortium (PEEIR) research program will result in three levels of products. The first level is the development of new methodologies or simple indicators that can be used to assess effects of and exposure to pollutants in United States estuaries. Examples of specific methods are provided in the component reports but include a new and more efficient biochemical assay to assess endocrine disruption in fish that can be widely applied. A second example is a method to assess the levels of bioavailable metals in wetland plants that allows us to bypass extrapolations made to predict, rather than directly assess, metal availability in contaminated sediments. A third example is the development of nitrogen isotope techniques to assess nutrient enrichment in wetland sites in a more informative way than using transient measurements of dissolved inorganic nitrogen.

Our second level of products is the development of aggregated indicators that bring together multiple measurements of stress and exposure and considers their interrelationships using statistical techniques. An example provided in the Biological Response to Contaminants (BRC; subproject R828676C002) and Ecosystem Indicators Component (EIC; subproject R828676C001) annual reports, related to our fish indicators species, outlines how the spatial distribution of biomarker responses at multiple sites has been analyzed individually and in combination. For example, the frequency of apoptosis in the livers of fish collected in 2003 was significantly different among sites (Figure 2), with the most contaminated site (Stege Marsh) exhibiting the highest incidence. Hence, this technique may be a useful “early warning” indicator of contaminant stress.

Figure 2. Tidal Marsh

Greater scope of inference can be attained, however, when multiple biomarkers are considered and related to fish condition. When principal components analysis (PCA) is used to evaluate the interrelationships among multiple datasets (Figure 3) at these same sites, apoptosis can be related to other biomarker responses and measurements linked to fish growth and condition.

Figure 3.

Analysis of linked indicators in individual fish in PCA also allows apparent outliers (such as the one very high apoptosis response at the China Camp site, Figure 2) to be evaluated more critically. Ultimately, proportions of fish in different health categories can be discerned and associated with multiple contaminant stressors. Portfolios will be derived using the most informative markers emerging from the statistical analysis. This approach is novel because it links biomarker responses to growth rates and fish condition using body morphometrics and growth increments measured in otoliths. For fish, these findings and additional data are now being used to parameterize population models. For crab, interrelationships between numerous measures of reproductive output and multiple exposure routes also have been analyzed using multivariate statistics, and we will recommend a portfolio of indicators that relates crab reproductive success to contaminant exposure (see subproject R828676C001 report). Similar integration efforts for microbe, plant, and clam indicators are maturing rapidly (see the annual reports for subprojects R828676C001 and R828676C003 ).

Within our second level of products is an extensive modeling effort to validate and extend the utility of the indicators we develop. Progress of the modeling team is described below. In brief, the work is significant because it allows us to evaluate the significance of responses in individual fish to populations of fish (size structure and dynamics). This is what managers care the most about; yet options for relating effects on individuals to populations have been limited to date.

Our third level of accomplishment is demonstrating that a portfolio concept can be transferable and applied in management. In brief, the PEEIR consortium advocates the development of integrated portfolios using indicator species selected for various habitat types. We are in the process of finalizing our demonstration of this concept for saltmarsh systems but contend that the general approach is transferable to other habitat types. In our research, a portfolio of techniques in resident species was cost effective, and we elucidated significant detrimental effects in marsh sites where toxicity tests predicted minor impacts.

The ultimate value of our Center program funding, and hence the value of integrated science, is the demonstration of this portfolio concept, which could not have been accomplished with single investigator research. This approach will be valuable in management because effects are assessed directly on native species, and the error associated with numerous extrapolations of routine ecological risk assessment is eliminated. In addition, the approach may save costs associated with expensive regulatory controls on single chemicals. It is vital that effects of complex mixtures, including hundreds of emerging contaminants, be assessed in combination. Single-chemical restrictions will not be practical. In short, we must continue to develop techniques that allow us simply to ask the fish whether several decades of environmental controls have been enough; then we can prioritize the greatest problems. Our final report will provide recommendations on a stepwise process for national implementation of such an approach.

The types of outputs that will be submitted to the U.S. Environmental Protection Agency (EPA) at the conclusion of our work are: manuscripts, a Web site with “indicator pages” that translate the technical manuscripts into a one-page format that will facilitate implementation, and a final report summarizing the above material and listing talks and outreach. This year a major effort for the director was organization of three technical sessions at national and regional conferences. Talks from these meetings are listed in the component reports. We are accelerating outreach efforts throughout the coming year and focusing on manuscripts and integration with other EaGLes centers. The text below describes progress on technical work funded in the Administration and Integration Component (AIC), and the subproject reports R828676C001 through R828676C003 describe the detailed technical progress throughout the PEEIR consortium.

Modeling Work Group Summary

The main advances during the year were the following:

  • Completion of a manuscript describing new method for estimating parameters in dynamic energy budget models from size trajectory data.
  • Initiation of work on a dynamic energy budget (DEB) model for mudsuckers, PEEIR’s primary fish indicator species.
  • Further analysis of a model describing dynamics of nitrogen isotope ratios.
  • Initiation of a major effort using ordination analysis to identify patterns in indicator measurements and to guide the development of aggregative measures of organism condition.

The rationale for using DEB models has been described in previous reports, and much of this year’s effort was devoted to completion of previous projects and manuscript preparation. Briefly, DEB models describe the acquisition by organisms of energy from food and its utilization for growth, development, maintenance, reproduction, and avoiding mortality. Modifications of the models can be used to describe the flow of elemental matter (key to the work on stable isotope ratios) and bioaccumulation of contaminants. With additional information on mortality, DEB models are a key component of a population model.

PEEIR’s planned applications of DEB models required developing new methodology, and that phase of the work is largely complete. One distinctive challenge was to find a method for estimating DEB model parameters from measurements on fish otoliths. For this work, we added stochastic variation to the traditional (deterministic) DEB model, the result being a system of stochastic differential equations in which one of the state variables (the energy reserve) is unobservable. There is no analytical solution to the probability density of size at given age, so we use a numerical non-linear state-space method to calculate the likelihood. This method is general enough to apply to other stochastic differential equation models. We assessed the estimability of parameters in the individual growth model and analyzed size trajectory data from delta smelt (Hypomesus transpacificus). We expect this method to become an important tool in ecological studies as computers become faster, as the models that we deal with become more complex, and as the data that we collect become more detailed.

We started work on a DEB-based population model for mudsuckers, one of the integrative studies promised by PEEIR. This model complements statistical analyses of biomarkers in mudsuckers described elsewhere in this report. The statistical approach uses data on a large number of biomarkers to ask “What are the fish telling us about habitat quality?” The DEB modeling aims to determine the relationship between the biomarkers and endpoints involving fish population dynamics. The following endpoints were selected for the modeling:

  • Population size structure – an integrated measure of growth and survival.
  • Lifetime reproductive success – a commonly used integrated measure of individual performance.
  • Long-term population growth rate – a commonly used integrated measure of population viability.
  • Short-term population growth rate – a measure of a population’s immediate response to environmental perturbations.

Knowledge of mortality rates is important for the population model. Thus, in parallel with the model development, we completed a rigorous analysis of mark recapture data on mudsuckers. The results demonstrated that obtaining further data in spring and summer 2005 might substantially narrow confidence intervals. This is in progress.

As discussed in previous annual reports, PEEIR has gathered data on the proportions of stable isotopes of nitrogen in all our marshes (Page and collaborators). These have immediate value for empirical characterizations of habitat, but they also relate directly to ecological processes, notably trophic interactions. These processes are dynamic, so interpretation commonly requires special assumptions (e.g., assuming that some dynamic equilibrium is attained within the organism). We aim to use DEB models, and thereby obtain more powerful methodology for interpreting stable isotope data. Our model characterizes variations in the proportion of rare isotopes in an individual organism to fluctuations in food quantity and in the isotopic composition of the food. The model presented some unanticipated mathematical problems; these are now resolved and a manuscript is in preparation.

The final new integrative activity in Year 4 was an intense effort on statistical analysis with two objectives. The first used ordination analyses in a search for pattern in the many measurements gathered by PEEIR investigators. Although the primary thrust of PEEIR’s approach emphasizes the importance of physical, chemical, and biological processes, identification of patterns and correlations is an essential component. Work completed to date includes studies relating microbial community properties to chemical information, and an investigation of correlations between trematode communities and other indicators. The second objective is to develop aggregative measures of the conditions of some focal organisms (fish and crabs). This research is in progress.

Data Management Summary

By July 2005, the data management effort had archived about 85 percent of the datasets, with 15 percent still undergoing revision and not yet centrally archived. We have finished approximately 20 percent of the metadata files, which will accompany the data files when they are uploaded to the permanent repository. We are on track to complete all the metadata by the end of summer, though there will be revisions until the end of the Program. Finally, we are working with the other members of the Estuarine and Great Lakes (EaGLe) Coastal Initiative data committee to ensure that the metadata files are formatted according to standards and that both the data and metadata will be archived securely after the Program ends.

The data effort also is continuing to support the internal data needs of the Program. We have developed a downloadable ArcMap geodatabase of the study sites with much of the point data from sampling; this will be updated, as it is useful to integration projects. The data repository continues to be used by the Program researchers and serves as the upstream piece in the data plan. Finally, the data manager has helped to coordinate some multidisciplinary mapping projects. An important example of this is serving as an interface between teams doing remote sensing, ecology, and metal bioavailability and the geomorphology work group. Extensive interaction has been required to finalize tidal datum, as well as basic tidal statistics and to validate Light Detection and Ranging (LIDAR) data to be used by the remote sensing team.

Archival Data Workgroup Summary

This year, Anitra Pawley, Ph.D., of the Bay Institute has worked extensively on a review of emerging wetland indicators for San Francisco Bay wetlands. The project illustrates the broad range of indicators being investigated and/or developed for the Bay region and a regional context for the wetland products being developed as a result of PEEIR. The sheer number of measurements and indicators and the variety proposed suggests that some time is needed before there is agreement on what indicators should be routinely measured in San Francisco Bay tidal marshes. Despite this, there is some convergence in the measurements used for evaluating tidal marsh health, restoration progress, and even contaminant effects. Tidal marsh habitat extent estimates have been used successfully as public-level communication tools. Rapid assessment techniques to evaluate marsh sites are being developed and tested; representative indicator species that include invertebrate, fish, and bird taxa have been studied, resulting in some tangible indicators for evaluating marshes. Additionally, several diagnostic tools such as plant exudates and parasites are showing promise as a means to depict specific trends in marsh use and levels of impacts.

The benthic paper entitled, “Developing Benthic Coastal Indicators and Indexes at Regional Scales: Thirty Years Since Pearson and Rosenberg” summarizes the status of estuarine and coastal benthic indicator studies since the late 1970’s is now close to completion as we rewrite the draft for submission. The results were reviewed in last year’s annual report.

Remote Sensing Progress Under NASA Funding

This year’s accomplishments include analysis of AVIRIS data and LIDAR data for each site and comparison of these to field measurements. The land cover classification of the AVIRIS data to create vegetation maps for each of the wetlands is in the last stages of completion. We cannot consistently separate all species classes we want to identify in these wetlands based solely on spectral differences. We are currently examining whether including elevation (derived from the lidar imagery) can be used to improve the land cover classification. Physiological indexes, using spectral bands related to pigments, water, and dry plant matter (cellulose, lignin, etc.), in the AVIRIS data have been completed for all of the sites. The land cover (classification) and condition (determined from the physiological indexes) maps will allow us to compare sites and determine if there are remotely sensed indicators of wetland condition and/or health that can be used in a monitoring program.

Linking the field-collected plant data to our field-measured spectra and to the physiological indices was not successful for either the 2002 or the 2004 data sets. Correlating the physiological indices to biomass data (both % green or total biomass) showed low correlations (highest r 2 = 0.28 using the soil-adjusted and atmospherically resistant vegetation index). In previous studies (Epiphano, et al., 1995; Zhang, et al., 1997; Sanderson, et al., 1998), significantly higher correlations between the physiological indices and field data were observed, and the lack of correlation here is attributed to both the sample size (10 cm x 10 cm) and sampling method used in this study. The small area of the field samples makes them unrepresentative of the spatial scale of the AVIRIS pixels. Because field biomass and spectra were not collected at precisely the same locations, a similar sampling effect is attributed to the lack of correlation. We are investigating whether we can use the regression equations of Zhang (collected at the mouth of Petaluma Creek) to substitute a maximum biomass for maximum index value (as all methods show linear relationships) as a way to quantify the biomass variability within and between wetlands.

Striping was seen in the LIDAR data in overlapping flightlines. This indicates errors in the LIDAR data that could be caused by systematic offsets related to the original calibration of the data or measurement errors caused by the instrument design (e.g., height differences between the center and the edge of the swath of the image) or some other cause. We began LIDAR analysis by evaluating the precision and accuracy of the data (Rosso, et al., 2005). At the PEEIR sites, the LIDAR point data were initially processed into raster images with 1-m horizontal resolution to create a digital elevation map for determining the channel network and inundation period. This resolution was chosen to limit the data volume and averaged out most of the systematic flightline differences but was found to be too coarse and missed some of the smaller channels. We have since tested 20 cm and 50 cm resolution and both appear to capture the full extent of the channel network that can be seen in high spatial resolution aerial photos and we are currently re-analyzing the channel network using a 50 cm horizontal scale. Following this, we will use the LIDAR elevation data in the AVIRIS classifier after co-registering them with the AVIRIS pixels and creating two layers for the classifier (mean elevation and standard deviation) for each AVIRIS pixel.

Technical publications for director Anderson’s laboratory are listed in the annual report for subproject R828676C002. As stated above, a major accomplishment of this year was organization of three technical sessions at: the national meeting of the Society of Environmental Toxicology and Chemistry (SETAC), the Northern California Regional meeting of SETAC, and the semi-annual science conference of the California Bay Delta Authority. These talks are presented in the component reports.

Future Activities:

The top priority during Year 5 of the project is the completion of manuscripts. These include those discussed in previous annual reports that are now near completion, as well as those discussed above. Work still to be completed includes the mudsucker model and further analysis of statistical measures of organism condition.

References:

Epiphanio JCN, Huete AR. Dependence of NDVI and SAVI on sun/sensor geometry and its effect on fAPAR relationships in Alfalfa. Remote Sensing of Environment 1995;51(3):351-360.

Rosso PH, Ustin SL, Hastings A. Use of lidar to study changes associated with Spartina invasion in San Francisco Bay marshes. Remote Sensing of Environment 2006;100(3):295-306.

Sanderson EW, Zhang M, Ustin SL, Rejmankova E. Geostatistical scaling of canopy water content in a California salt marsh. Landscape Ecology 1998;13(2):79-92.

Zhang M, Ustin SL, Rejmankova E, Sanderson E. Monitoring Pacific coast salt marshes using remote sensing. Ecological Applications 1997;7(3):1039-1053.


Journal Articles: 40 Displayed | Download in RIS Format

Other center views: All 139 publications 42 publications in selected types All 40 journal articles
Type Citation Sub Project Document Sources
Journal Article Anderson SL, Cherr GN, Morgan SG, Vines CA, Higashi RM, Bennett WA, Rose WL, Brooks AJ, Nisbet RM. Integrating contaminant responses in indicator saltmarsh species. Marine Environmental Research 2006;62(Suppl 1):S317-S321. R828676 (Final)
R828676C002 (Final)
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  • Journal Article Cordova-Kreylos AL, Scow KM. Effects of ciprofloxacin on salt marsh sediment microbial communities. The ISME Journal 2007;1(7):585-595. R828676 (Final)
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  • Journal Article Cordova-Kreylos AL, Cao Y, Green PG, Hwang H-M, Kuivila KM, LaMontagne MG, Van De Werfhorst LC, Holden PA, Scow KM. Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments. Applied and Environmental Microbiology 2006;72(5):3357-3366. R828676 (Final)
    R828676C003 (Final)
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  • Journal Article Fan TW-M, Lane AN, Chekmenev E, Wittebort RJ, Higashi RM. Synthesis and physico-chemical properties of peptides in soil humic substances. Journal of Peptide Research 2004;63(3):253-264. R828676 (Final)
    R828676C003 (2003)
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  • Journal Article Fan TW-M, Lane AN, Higashi RM. An electrophoretic profiling method for thiol-rich phytochelatins and metallothioneins. Phytochemical Analysis 2004;15(3):175-183. R828676 (Final)
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  • Journal Article Field KG, Chern EC, Dick LK, Fuhrman J, Griffith J, Holden PA, LaMontagne MG, Le J, Olson B, Simonich MT. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. Journal of Water and Health 2003;1(4):181-194. R828676 (Final)
    R828676C003 (Final)
    R827639 (Final)
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  • Journal Article Fleming EJ, Mack EE, Green PG, Nelson DC. Mercury methylation from unexpected sources: molybdate-inhibited freshwater sediments and an iron-reducing bacterium. Applied and Environmental Microbiology 2006;72(1):457-464. R828676C003 (2004)
    R829388 (Final)
    R829388C001 (2005)
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  • Journal Article Fujiwara M, Kendall BE, Nisbet RM. Growth autocorrelation and animal size variation. Ecology Letters 2004;7(2):106-113. R828676 (2003)
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  • Journal Article Fujiwara M, Kendall BE, Nisbet RM, Bennett WA. Analysis of size trajectory data using an energetic-based growth model. Ecology 2005;86(6):1441-1451. R828676 (Final)
    R828676C001 (2004)
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  • Journal Article Gurney WSC, Nisbet RM. Resource allocation, hyperphagia and compensatory growth. Bulletin of Mathematical Biology 2004;66(6):1731-1753. R828676 (2004)
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  • Journal Article Gurney WSC, Jones W, Veitch AR, Nisbet RM. Resource allocation, hyperphagia, and compensatory growth in juveniles. Ecology 2003;84(10):2777-2787. R828676 (Final)
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  • Journal Article Hechinger RF, Lafferty KD. Host diversity begets parasite diversity: bird final hosts and trematodes in snail intermediate hosts. Proceedings of the Royal Society B–Biological Sciences 2005;272(1567):1059-1066. R828676 (Final)
    R828676C001 (2004)
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  • Journal Article Huspeni TC, Lafferty KD. Using larval trematodes that parasitize snails to evaluate a saltmarsh restoration project. Ecological Applications 2004;14(3):795-804. R828676 (Final)
    R828676C001 (2002)
    R828676C003 (Final)
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  • Journal Article Hwang H-M, Green PG, Young TM. Tidal salt marsh sediment in California, USA. Part 1: Occurrence and sources of organic contaminants. Chemosphere 2006;64(8):1383-1392. R828676 (Final)
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  • Journal Article Hwang H-M, Green PG, Higashi RM, Young TM. Tidal salt marsh sediment in California, USA. Part 2:occurrence and anthropogenic input of trace metals. Chemosphere 2006;64(11):1899-1909. R828676 (Final)
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  • Journal Article Hwang H-M, Green PG, Young TM. Historical trends of trace metals in a sediment core from a contaminated tidal salt marsh in San Francisco Bay. Environmental Geochemistry and Health 2009;31(4):421-430. R828676 (Final)
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  • Journal Article Hwang H-M, Green PG, Young TM. Tidal salt marsh sediment in California, USA: Part 3. Current and historic toxicity potential of contaminants and their bioaccumulation. Chemosphere 2008;71(11):2139-2149. R828676 (Final)
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  • Journal Article Lafferty KD. Is disease increasing or decreasing, and does it impact or maintain biodiversity? Journal of Parasitology 2003;89(Suppl):S101-S105. R828676 (Final)
    R828676C001 (2002)
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  • Journal Article Lafferty KD, Holt RD. How should environmental stress affect the population dynamics of disease? Ecology Letters 2003;6(7):654-664. R828676 (Final)
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  • Journal Article Lafferty KD, Porter JW, Ford SE. Are diseases increasing in the ocean? Annual Review of Ecology, Evolution, and Systematics 2004;35:31-54. R828676C001 (Final)
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  • Journal Article Lafferty KD, Hechinger RF, Lorda J, Soler L. Trematodes associated with mangrove habitat in Puerto Rican salt marshes. Journal of Parasitology 2005;91(3):697-699. R828676C001 (2004)
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  • Journal Article Lafferty KD, Dunham EJ. Trematodes in snails near raccoon latrines suggest a final host role for this mammal in California Salt Marshes. Journal of Parasitology 2005;91(2):474-476. R828676C001 (2004)
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    Journal Article LaMontagne MG, Astorga V, Giblin AE, Valiela I. Denitrification and the stoichiometry of nutrient regeneration in Waquoit Bay, Massachusetts. Estuaries and Coasts 2002;25(2):272-281. R828676 (Final)
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  • Journal Article LaMontagne MG, Holden PA. Comparison of free-living and particle-associated bacterial communities in a coastal lagoon. Microbial Ecology 2003;46(2):228-237. R828676 (Final)
    R828676C003 (2003)
    R828676C003 (Final)
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  • Journal Article LaMontagne MG, Leifer I, Bergmann S, Van De Werfhorst LC, Holden PA. Bacterial diversity in marine hydrocarbon seep sediments. Environmental Microbiology 2004;6(8):799-808. R828676 (Final)
    R828676C003 (2003)
    R828676C003 (Final)
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  • Journal Article Li L, Ustin SL, Lay M. Application of multiple endmember spectral mixture analysis (MESMA) to AVIRIS imagery for coastal salt marsh mapping: a case study in China Camp, CA, USA. International Journal of Remote Sensing 2005;26(23):5193-5207. R828676 (Final)
    R828676C003 (Final)
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  • Journal Article Magalhaes C, Bano N, Wiebe WJ, Hollibaugh JT, et al. Comparison of ammonium oxidizing bacterial phylotypes and function between biofilms and sediments of the Douro River Estuary, Portugal. Environmental Microbiology (in review, 2005). R828676C001 (2004)
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    Journal Article Magalhaes C, Bano N, Wiebe WJ, Bordalo AA, Hollibaugh JT. Dynamics of nitrous oxide reductase genes (nosZ) in intertidal rocky biofilms and sediments of the Douro River Estuary (Portugal), and their relation to N-biogeochemistry. Microbial Ecology 2008;55(2):259-269. R828676 (Final)
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  • Journal Article McGourty CR, Hobbs JA, Bennett WA, Green PG, Hwang H-M, Ikemiyagi N, Lewis L, Cope JM. Likely population-level effects of contaminants on a resident estuarine fish species: comparing Gillichthys mirabilis population static measurements and vital rates in San Francisco and Tomales Bays. Estuaries and Coasts 2009;32(6):1111-1120. R828676 (Final)
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  • Journal Article Morgan SG, Spilseth SA, Page HM, Brooks AJ, Grosholz ED. Spatial and temporal movement of the lined shore crab Pachygrapsus crassipes in salt marshes and its utility as an indicator of habitat condition. Marine Ecology Progress Series 2006;314:271-281. R828676 (Final)
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  • Abstract: Marine Ecology Progress Series
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  • Journal Article Nisbet RM, McCauley E, Gurney WSC, Murdoch WW, Wood SN. Formulating and testing a partially specified dynamic energy budget model. Ecology 2004;85(11):3132-3139. R828676 (Final)
  • Abstract: ESA
    Exit
  • Other: Ecology
    Exit
  • Journal Article Pillai MC, Vines CA, Wikramanayake AH, Cherr GN. Polycyclic aromatic hydrocarbons disrupt axial development in sea urchin embryos through a β-catenin dependent pathway. Toxicology 2003;186(1-2):93-108. R828676C002 (2003)
  • Abstract from PubMed
  • Full-text: Science Direct Full Text
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  • Other: Science Direct PDF
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  • Journal Article Rose WL, Hobbs JA, Nisbet RM, Green PG, Cherr GN, Anderson SL. Validation of otolith growth rate analysis using cadmium-exposed larval topsmelt (Atherinops affinis). Environmental Toxicology & Chemistry 2005;24(10):2612-2620. R828676 (Final)
    R828676C002 (2004)
  • Abstract from PubMed
  • Abstract: Environmental Toxicology & Chemistry
    Exit
  • Journal Article Rosso PH, Ustin SL, Hastings A. Mapping marshland vegetation of San Francisco Bay, California, using hyperspectral data. International Journal of Remote Sensing 2005;26(23):5169-5191. R828676 (Final)
    R828676C003 (Final)
  • Abstract: Taylor&Francis-Abstract
    Exit
  • Journal Article Rosso PH, Pushnick JC, Lay M, Ustin SL. Reflectance properties and physiological responses of Salicornia virginica to heavy metal and petroleum contamination. Environmental Pollution 2005;137(2):241-252. R828676 (Final)
  • Abstract from PubMed
  • Full-text: Science Direct Full Text
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  • Other: Science Direct PDF
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  • Journal Article Rosso PH, Ustin SL, Hastings A. Use of lidar to study changes associated with Spartina invasion in San Francisco Bay marshes. Remote Sensing of Environment 2006;100(3):295-306. R828676 (Final)
    R828676C003 (Final)
  • Full-text: ScienceDirect-Full Text HTML
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  • Abstract: ScienceDirect-Abstract
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  • Other: ScienceDirect-Full Text PDF
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  • Journal Article Shaw JC, Aguirre-Macedo L, Lafferty KD. An efficient strategy to estimate intensity and prevalence: sampling metacercariae in fishes. Journal of Parasitology 2005;91(3):515-521. R828676C001 (2004)
  • Abstract from PubMed
  • Other: UCSB PDF
    Exit
  • Journal Article Spilseth SA, Morgan SG. Evaluation of internal elastomer tags for small, mature crabs. Crustaceana 2005;78(11):1383-1388. R828676 (Final)
    R828676C001 (2004)
    R828676C001 (Final)
    R825689C028 (Final)
  • Abstract: JSTOR-Preview
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  • Journal Article Steets BM, Holden PA. A mechanistic model of runoff-associated fecal coliform fate and transport through a coastal lagoon. Water Research 2003;37(3):589-608. R828676 (Final)
    R828676C003 (2002)
    R828676C003 (Final)
  • Abstract from PubMed
  • Full-text: ScienceDirect-Full Text HTML
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  • Abstract: ScienceDirect-Abstract
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  • Other: ScienceDirect-Full Text PDF
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  • Journal Article Ward JR, Lafferty KD. The elusive baseline of marine disease: are diseases in ocean ecosystems increasing? PLoS Biology 2004;2(4):542-547. R828676C001 (2003)
    not available

    Supplemental Keywords:

    watersheds, estuaries, ecological effects, bioavailability, ecosystem indicators, aquatic, integrated assessment, EPA Region IX, watersheds, ecological effects, ecosystem indicators, integrated assessment, estuarine research, aquatic ecology, environmental indicators, ecosystem assessment,, RFA, Scientific Discipline, Air, Geographic Area, Waste, Ecosystem Protection/Environmental Exposure & Risk, Bioavailability, Aquatic Ecosystems & Estuarine Research, exploratory research environmental biology, Ecosystem/Assessment/Indicators, Ecosystem Protection, climate change, State, Air Pollution Effects, Aquatic Ecosystem, Ecological Effects - Environmental Exposure & Risk, Ecological Risk Assessment, Atmosphere, Ecological Indicators, environmental monitoring, wetlands, plant indicator, ecological exposure, biomarkers, estuaries, Western Center for Estuarine Research, ecosystem integrity, environmental stressor, ecosystem condition, environmental consequences, ecological assessment, estuarine ecosystems, ecosystem indicators, aquatic ecosystems, ecosystem health, environmental indicators, environmental stress, environmental stressors, GIS, water quality, biological indicators, biological markers, fish , California (CA), statistical evaluation

    Relevant Websites:

    http://www.bml.ucdavis.edu/peeir Exit

    Progress and Final Reports:

    Original Abstract
  • 2001 Progress Report
  • 2002
  • 2003 Progress Report
  • Final Report
  • 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