Final Report: Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium: Biogeochemistry and Bioavailability Component

EPA Grant Number: R828676C003
Subproject: this is subproject number 003 , 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: Biogeochemistry and Bioavailability Component
Investigators: Higashi, Richard M. , Cao, Yiping , Collins, Joshua N , Córdova-Kreylos, Analucis , Fan, Teresa W-M. , Green, Peter , Green, Sarah , Hechinger, Ryan , Holden, Patricia , Hollibaugh, James T. , Huspeni, Todd , LaMontagne, Michael , Lafferty, Kevin , Lay, Mui , Li, Lin , Melack, John , Myers, Monique , Page, Henry M. , Rosso, Pablo , Scow, Kate , Ustin, Susan L. , VanDeWerfhorst, Laurie
Institution: University of California - Davis , San Francisco Estuary Institute , U.S. Geological Survey , University of California - Santa Barbara , University of Georgia
EPA Project Officer: Hiscock, Michael
Project Period: March 1, 2001 through February 28, 2005
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 was to develop field indicators and the knowledge base to help assess the consequences of changes in chemical form of pollutants in tidal marshes. This project’s particular emphasis was assessment of metals and organic pollutant bioavailability in relation to sedimentary lower trophic level biomarkers. The emphasis on rooted plants and sediment microbes was because they often are the entry point of pollutants into the food chain and are major drivers of the biogeochemistry of the tidal marsh. The specific objective of this research project was to uncover the chemical, biochemical, and biotic markers that herald the bioavailability, transport, and/or biotransformation of selected metal and organic pollutants. These markers, in appropriate concert with others generated by the Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium, can comprise indicators of pollutant stress on marsh ecosystems.

Summary/Accomplishments (Outputs/Outcomes):

Plant Salt Exudates as Landscape-Scale Measures of Metals Mobilization in Marshes

Issue. Coastal marshes are a known repository for metal pollutants and this presents a recurring question for managers: Are metal pollutants that are bound in sediment being remobilized? As salt marsh plants establish habitat and their roots seek nutrient metals, they inevitably mobilize heavy metals, often in the form of salt crystals extruded through the leaves. These are known as exudates. How does such a phenomenon on the detailed scale of meters affect landscape-sized habitats? For example, where are the “hot spots” of exposure? Connecting these questions is a problem in spatial scale integration, among the most confounding in ecotoxicology.

Approach and Rationale. The salt marsh cordgrass, Spartina sp., is a dominant plant that exudes salts from its leaves, forming exudates (Figure 1). This transport of metal salts from the sediment has been implicated in reproductive failures of fish in the Chesapeake estuary.

Figure 1. Salt Exudates (White Clumps) on Spartina (© Michael Rigsby)

Stege Marsh in California’s San Francisco Bay (Figure 2a) was selected for an unprecedented landscape-scale survey of salt-metal exudation. During low tide, salt exudations were rinsed off of leaves and directly analyzed by inductively-coupled plasma mass spectrometry (ICP-MS) at the sampling locations shown by yellow dots in Figure 2b. This study represents a high-throughput approach that can cover a large amount of sampling and analysis quickly, with minimum labor. This enables analysis on a landscape-scale to facilitate spatial scale integration.

Figure 2. Sampling Locations at Stege Marsh. Figure 2b enlarges the area indicated by the red arrow in 2a. Yellow dots are specific sampling sites.

Findings and Impact. The findings include the following:

  • Relative concentrations of mercury (Hg) in the salt exuded by Spartina leaves are shown in an overview photo of Stege Marsh in Figure 3a (green to red is lowest to highest concentrations, respectively).
  • To obtain a mass emission estimate of Hg via leaf exudation, we also must determine the plant density. Hyper-spectral remote sensing by airborne visible/infrared imaging spectrometer, combined with a remote-sensing light detection and ranging (LIDAR) elevation survey, identified Spartina marsh-wide, and was used to estimate its density (Figure 3b).
  • Multiplying the previous two images (Hg leaf exudate concentration in Figure 3a x plant density in Figure 3b) results in the final image, Figure 3c, which is an estimate of the relative emissions of Hg via the Spartina conduit.

Figure 3. Determining the Relative Mercury Emissions from Spartina at Stege Marsh

Such maps can provide critical linkages for understanding different biological effects across the marsh.

Applications. The combination of high-throughput technologies, ICP-MS and hyperspectral remote sensing, enabled marsh-wide coverage at analytical and spatial detail that would otherwise be too laborious and costly to obtain. More importantly, this was used to obtain detail on a toxic metal exposure route that currently is not considered in modeling nor even regularly monitored. The fact that this conduit is biologically-mediated (leaf exudation) makes it a pivotal new method for examining food chain effects of toxic metals. The salt exudate technique using ICP-MS coupled with remote sensing is ready to be used in partnership between coastal management agencies and University of California at Davis researchers.

Plant Metabolites as Indicators of Metal Bioavailability in Salt Marshes

Issue. Management of contaminated salt marshes often requires answers to questions such as: How do salt marsh plants tolerate toxic metals? Could such tolerance decrease or increase exposure risk of other organisms? How might we track this process?

Salt marshes are fast disappearing, yet are vital to the functioning of estuaries. Marsh plants often dominate salt marshes, serving as habitat for birds and invertebrates and providing feeding areas for fishes and other animals. They also are the primary producers of new biomass, anchoring the soils and supporting the base of the food web. Marshes are challenging to understand because they are neither submerged nor dry land (hence they are “wetlands”); so much of the past research on dry land and marine habitats just does not fit. An unusual characteristic of salt wetlands is that they often are dominated by a small number of plant species.

The salt marsh cordgrass, Spartina sp. (Figure 4), is a dominant salt marsh plant in the tidal marshes of North America. It readily acquires toxic metals such as cadmium (Cd) from sediments, exuding it through salt glands on its leaves. This transport of salts from the sediment can carry with it metal contaminants that would otherwise largely be locked in the mud.

Figure 4. Plants Can Mobilize Soil-Bound Metals into Bioavail­able Compartments

In addition to this exudation of metals, Spartina can synthesize cysteine-rich peptides known as phytochelatins (PCs) that tightly sequester toxic metals within the plant. Although this process is considered to be a protective mechanism for the plant, it also binds the metal into an organic matrix that constitutes food for other organisms. Therefore, this process can also introduce toxic metals into the food web.

Approach and Rationale. Despite the importance of PCs, research into and their application as indicators have been hampered by the lack of analytical methods. Under this U.S. Environmental Protection Agency support, a pair of methods was developed, one for rapid screening for PCs using gel electrophoresis, the other high-pressure liquid chromatography/mass spectrometry (HPLC-ES/tandem MS) providing most detailed chemical verification available for PCs as a confirmation step. Together, they comprise an approach that is more practical than existing techniques and provides greater confidence in the results.

The electrophoretic analysis for PCs is shown in Figure 5, illustrating four different molecular forms of PC in the four leftmost lanes, whereas the rest are analyses of Spartina roots. The analytical run time for these 10 samples is about 1 hour. Using this approach, laboratory studies were conducted using field-collected Spartina foliosa, a species native to the West Coast, to study the allocation of Cd between PCs and shoot exudation. The rapid-screening method then was used to survey relationships in field Spartina.

Figure 5. Electrophoretic Analysis for PCs

Findings and Impact. Root and shoot tissues were analyzed for Cd via ICP-MS along with the PC induction profile.

  • Laboratory results (Figure 6) showed that PCs are strongly induced in Spartina in response to Cd, and that most of the PCs as well as the Cd were accumulated in the roots, but neither accumulated in the shoots.

Figure 6. Spartina Responses to Cd Exposure

  • Leaf exudation of Cd increased in response to Cd exposure. Thus, both sequestration into the organic matrix and leaf exudation occur simultaneously in Spartina for this toxic metal.
  • Spartina at Stege Marsh then was surveyed for Cd and PCs in a preliminary field study. With one exception PCs appear to track the Cd root concentrations, as shown in the laboratory. Not surprisingly, the root Cd concentrations did not relate to either Cd in the soils, nor to shoots.

None of these relationships were previously known for any Spartina spp., and this research developed the tools needed to assess toxic metal bioavailability and sequestration into the foodweb at the primary producer level.

Applications. The rapid analysis for PCs enables the practical assessment of potential sequestration of toxic metals into foodwebs, a major step beyond “bioavailability”. The electrophoretic method is inexpensive and successfully learned by hundreds of thousands every year in colleges, high schools, and industry. Used in conjunction with the Spartina leaf exudation conduit, the relative allocation of metal exposure pathways via plants might be determined.

Landscape-Scale Mapping of Salt Marsh Species Distributions

Issue. The spatial structure of salt marshes is a significant aspect of the functioning of estuaries. Few plant species flourish in the tidal salt marshes of the Pacific Coast, and salinity and flooding gradients control salt marsh species distributions. Traditional field surveys are too labor intensive to map the distribution of the dominant plant species across the landscape.

Approach and Rationale. We investigated the potential for high spatial and spectral remote sensing data to map salt marsh species distributions using an airborne imaging spectrometer at two sites in San Pablo Bay, California. Imaging spectroscopy is a remote sensing technology that measures a detailed spectrum in hundreds of bands across the visible and reflected infrared for each pixel. This information allows identification of species and conditions by their biochemical and structural characteristics (Li, et al., 2005; Rosso, et al., 2005).

Findings and Impact. Data about marsh size, conditions within the marsh, adjacent land use, and whether the tidal creek structure was intact were measured directly. The findings include:

  • The highly disturbed Stege Marsh (Figure 7a) covered an area one-fifth of the size of China Camp, had lost its tidal creek structure, and was surrounded by urban and industrial development.
  • China Camp (Figure 7b), a less-disturbed site, had relatively uniform plant cover and an extensive network of tidal channels and was surrounded by native vegetation.
  • Dominant species were mapped and showed significantly different patterns of plant growth between the two marshes. Vegetation distribution at China Camp was typical of healthy marshes. Cordgrass (Spartina) covered the tidal edge of the marsh and the larger channels, pickleweed (Salicornia) covered most of the interior marsh, except for an area near the mouth of the Petaluma Creek where bullrush (Scirpus) dominated, and the berms along the creek margins, where gumweed (Grindelia) occurred.
  • The distribution of species in Stege Marsh was unusual because cordgrass is widespread and patchy over much of the interior of the marsh, whereas pickleweed is located predominantly along the marsh edges.
  • In this case, elevation differences are likely the primary cause of the species distribution differences we observed.

Figure 7. Maps of Dominant Species in Stege Marsh (a) and China Camp (b) Based on Classification Derived from Remotely Sensed Elevation and Spectral Features

Applications. This methodology can be used to: (1) identify indicators of the health and condition of wetlands caused by fragmentation, hydrologic structure, and presence of threats as a result of external conditions in surrounding area; (2) detect changes in marsh species abundances and distribution that can provide an early warning indicator about threats to the integrity of the marsh; and (3) monitor wetland recovery following mitigation or restoration.

This promising methodology requires a level of technologic infrastructure and expertise that is not yet available in most agencies. University and agency partnerships are recommended for implementation in the near future.

Topographic Indicators of Salt Marsh Disturbance

Issue. Marshes superficially seem to have no topographic features and occur only slightly above mean high tide elevation. However, small elevation differences, just centimeters, control many marsh functions from flooding and nutrient cycling to draining of the marsh interior. This microtopography is critical for development and maintenance of foraging habitat for invertebrates, fish, and birds. Yet, traditional methods for quantifying marsh plane elevation are labor intensive, and new methods are needed to cover an entire marsh.

Approach and Rationale. Airborne LIDAR data can be used to make a detailed topographic map of the wetland. LIDAR instruments can be flown to acquire high spatial resolution measurements of small changes in surface height (~5 cm). These data were used to develop an elevation map for two tidal salt marshes in San Pablo Bay, California (China Camp and Stege Marsh).

Findings and Impact. The findings include the following:

  • Marsh vegetation hid microtopographic gradients in standard aerial imagery.
  • China Camp (less disturbed site) had an extensive network of tidal creeks and a pattern of increased elevation from the tidal edge of the marsh to the interior, where dryland vegetation dominated (Figure 8a).
  • Elevation contours showed that marsh elevation increased about 2 m from the mudflats to the back of the marsh at China Camp.
  • Most of Stege Marsh (more disturbed site) was at lower elevation than China Camp. Levees and dredged berms created unnatural elevation patterns, including a road that bisects the wetland, creating a drainage barrier (Figure 8b).

Applications. Elevation patterns control many functions in wetlands. The applications of the research include:

  • Knowledge of the microtopography provides an indicator of how nutrients, water, and contaminants are transported in the wetland.
  • Elevation patterns determine the duration of tidal flooding within the marsh.
  • Elevation patterns determine habitat suitability for many animal and invertebrate species.
  • Flooding patterns may govern the distribution of invasive species (Rosso, et al., 2006).
  • Knowledge of microtopography provides a rapid method to characterize many types of habitat disturbances and is important for evaluating the multiple stressor that affect a marsh.

Figure 8. Microtopographic Gradients in Tidal Marshes Influence Water Transport and Drainage. In the upper image, elevation contours are color coded, with dark green having the lowest elevation to lighter green, yellow, orange, and red at the highest points in the tidal marsh. Areas outside the marsh have been removed or are shown in gray scale. China Camp (a) has a typical marsh structure with lowest elevations along the shoreline and meandering tidal channels. In contrast, Stege Marsh (b) has had dredged spoils deposited along the shoreline, reversing the usual elevational gradients. Additionally, with the road across the interior marsh, the dredged cove in the center, and the loss of most of its channel structure, the hydrology and functioning of the wetland has significantly changed. Note: The images are not to scale; China Camp (a) is about five times larger than Stege (b).

To implement this technology in the near future, university/agency partnerships may be required to obtain and interpret the LIDAR data.

Parasites as Indicators of Wetland Biodiversity

Issue. Scientists, resource managers, and the public all appreciate the meaning and significance of biodiversity. Therefore, monitoring and evaluating the status of biodiversity in coastal wetlands is a key goal and can influence management decisions with respect to restoration, mitigation, and conservation.

It is difficult and costly, however, to assess the biodiversity of wetlands. There currently are several problems with standard biodiversity monitoring techniques—they are expensive, frequently unreliable, and sometimes environmentally destructive. Thus, a new integrative and cost-effective method to characterize wetland biodiversity and ecosystem function is needed.

Approach and Rationale. Our approach is to use the diversity of trematode parasites of snails to indicate diversity of other organisms in salt marsh ecosystems, including benthic invertebrates and birds. Because the parasites we use have multiple-host life cycles that require several important components of wetland animal communities (Figure 9), we have been able to demonstrate that larval trematodes can serve as indicators of other community components:

  • Trematode species richness and abundance increased after a wetland restoration.
  • Positive correlations exist between the diversity and abundance of birds and trematodes infecting snails across several sites in a wetland.

Figure 9. The Complex Life Cycle of Trematode Parasites. The various trematode species are intimately connected to several types of animals throughout their life cycles. Trematodes should serve as good indicators because their existence is fully connected too much of the surrounding biodiversity.

In this study, we investigated whether trematode communities in snails also are positively associated with local fish and benthic invertebrate communities.

Findings and Impact. We found evidence suggesting the existence of associations between free-living benthic communities and the communities of trematode parasites in snails (Figure 10). This is important because it demonstrates that trematode parasites in snails may not only serve as indicators of bird populations but also benthic fauna, such as crabs, clams, and polychaete worms. These parasites use several types of hosts, as well as predator-prey interactions, to complete their life cycles; so they are intimately and necessarily connected to the abundance, diversity, and the food web interactions of the ecosystem.

Figure 10. Relationships Between Trematodes in Snails and the Benthos (the Animals that Live in and on the Mud) in Three Tidal Wetlands. Large benthos are primarily animals such as crabs and clams. Small benthos are animals like segmented worms and amphipods. All the benthos are important components of wetland biodiversity, partly because of the fact that they are the main food source for most birds and fishes. Data are represented as circles for Carpinteria Salt Marsh, squares for Mugu Lagoon, and triangles for Morro Bay.

These findings further support the idea that larval trematodes in snails may provide resource managers with comprehensive, temporally integrative, environmentally safe, and cost-effective information about community structure and trophic linkages operating in coastal wetlands.

Applications. Larval trematodes in snails may be used to monitor changes in biodiversity over time, as well as to compare the current state of biodiversity across several sites. We have articulated the steps required to use trematodes as indicators in a book chapter (Huspeni, et al., 2005) and have demonstrated the utility of this technique in a wetland restoration. This technique is ready for implementation by management agencies in Southern California but has not yet been verified for Northern California marsh sites. In their regional monitoring framework, the Southern California Wetlands Recovery Project has recommended that trematodes be considered for use in wetland assessment and monitoring.

Utility of Nitrogen Isotope Measurements as an Indicator of Nutrient Enrichment in Coastal Marshes

Issue. Inputs of anthropogenic nitrogen (N) and perennial freshwater runoff are high priority management concerns for many of the small salt marsh systems in central and southern California. Nutrients typically are monitored through point sampling in the water column; however, in tidal marshes, nutrient concentrations are variable in time and space, and there is a need for a time-integrated “indicator” of anthropogenic nutrient inputs. Recent work suggests that stable isotope analysis may be useful in identifying anthropogenic nitrogen subsidies and freshwater inputs to estuarine and marine ecosystems. The overall objective of this study was to develop stable isotope analysis as one tool to indicate anthropogenic inputs into the small Mediterranean coastal wetlands of central and southern California.

Approach and Rationale. Our approach was to examine relationships between N and carbon (C) isotope values in representatives of three trophic groups along presumed gradients of anthropogenic N and freshwater inputs in two salt marshes that differed in land use in the adjoining watershed. We also measured the turnover times of N and C in algal and animal tissues to provide information on the timeframe over which the isotopic signal integrates.

Findings and Impact. The findings include the following:

  • The snail, Cerithidea californica, and crab, Pachygrapsus crassipes (Figure 11) were more useful as indicator taxa than the macroalga, Enteromorpha, because they were less ephemeral in occurrence and more widely distributed across a range of exposure to anthropogenic N and freshwater inputs.
  • Stable N isotope values of snails and crabs in tidal creeks decreased with increasing distance from sources of anthropogenic N inputs (Figure 12).
  • Stable C isotope values of snails increased with increasing distance from sources of freshwater inputs (Figure 12).

Figure 11. The (a) Snail, Cerithidea californica, and (b) Crab, Pachygrapsus crassipes, Are Potentially Useful Bioindicators of Nutrient and Freshwater Inputs. © Kevin Lafferty.

  • N and C isotope values of these taxa did not vary predictably along tidal creeks in the absence of a gradient in N and freshwater inputs.
  • Variation in the isotope values of snails and crabs appear useful for identifying influences of land derived N and C over small spatial scales (10 to 100s of meters).
  • Complete turnover of N and C occurs in approximately 3.5 months for Cerithidea in the summer and is closely tied to the growth of the snail. Turnover time in the winter is much slower. Thus, isotope measures may not reveal short-term pulses (on the order of days to weeks) or changes in ambient conditions when N and C turnover rates are slow (e.g., when the animals are not growing). The values reflect longer-term chronic inputs.

Figure 12. Example of relationship between stable N and C isotope values of C. californica and P. crassipes and low tide nitrate-N concentration and salinity taken within a tidal creek in Carpinteria Salt Marsh (red) and Mugu Lagoon (blue). Samples taken in summer (solid) and winter (open) 2003. Winter samples are composites of five individuals. Regression lines are computed through summer data.

Applications. The applications of the research include the following:

  • Our results support the concept of using variation in the stable isotope values of widely distributed indicator organisms as one tool to identify and track chronic anthropogenic N inputs into the small salt marsh systems of southern California.
  • Stable C isotope values may also be useful to track freshwater inputs.
  • Our data suggest that samples spaced along suspected gradients of anthropogenic influence will be most useful in identifying the spatial extent of these inputs.
  • This approach is ready to be implemented in university and agency partnerships provided that isotope turnover time, the choice of appropriate indicator species, and other issues regarding the use and interpretation of isotope analysis are taken into consideration.

Controls on Microbial Nitrogen Cycling in Coastal Estuaries

Issue. Nutrients, especially N, strongly influence the productivity and environmental quality of coastal estuaries. Upland development and human activity have increased N loading into coastal zones by as much as 50 percent during the past century, and eutrophication has become an increasingly serious problem worldwide. It is thus critical to understand the environmental and biological controls on the cycling of nitrogen, which is predominately mediated by microbial processes such as N fixation, nitrification, and denitrification (Figure 13). Ammonium (NH4+), resulting from soil microbial N fixation and organic decomposition, is oxidized during nitrification to NO2- and then to NO3-. Denitrification, on the other hand, reduces oxidized N to nitrogen gases and is the only means to permanently remove fixed N from a system.

Figure 13. Conceptual Diagram of Nitrogen Cycling in Coastal Regions

Given the extreme importance of N cycling in coastal estuaries, there have been many studies regarding N budgets in estuaries, its import from the uplands, and storage and export into the open ocean. However, nutrient budget models often rely on estimating the microbial contribution using “black boxes,” whereas effective management relies on understanding and working with the controlling processes. This work investigated the underlying controls on microbial N processing including biophysical controls, microbial community compositional influences, environmental effects, and pollutant-microbial interactions. The goal was to provide estuarine ecosystem managers useful information towards managing N loading and eutrophication of estuaries and coastal waters.

Approach and Rationale. Our approach was to characterize both the physicochemical and the biological aspects of N cycling and also the interactions between them. Linking the environmental traits and the biological entities in the environment thus provides a more accurate and complete understanding of N cycling in coastal estuaries.

The estuaries were characterized physically and chemically by quantifying nitrogen species, organic matter, and rates of nitrification and denitrification. Microbial communities responsible for the processes were characterized via molecular tools: DNA extraction, PCR, terminal restriction fragment length polymorphism (TRFLP), and clone library analysis.

Findings and Impact. The findings include the following:

  • Rocky biofilms exhibited both higher nitrification and denitrification rates as compared to intertidal sediments.
  • Denitrification preferentially occurred in particle-attached microbial communities, and the attached communities possessed a higher denitrification capacity on a per cell basis as compared to free-living denitrifiers.
  • Differences in environmental factors (physicochemical characteristics including pollutants) led to the selection of particular ammonia oxidizing bacteria, different functional communities, and different N-cycling rates.
  • Denitirification potential was positively related to organic carbon content and the abundance of denitrifiers.

Applications. Given that N-cycling processes exhibit spatial heterogeneity or even “hot spots” in the estuarine systems, coastal managers can use the tools herein to identify local regions of concern and to focus human and financial efforts. For example, if managers intend to use a wetland to ameliorate excessive nitrate loading from uplands, they can increase the residence time of the nitrate input into the local “hot spot” to increase overall nitrate removal. Similarly, information on the environmental factors can be used for a more accurate estimation of N-cycling conditions in a salt marsh so that managers can more effectively evaluate the marsh’s buffering capacity during storm events.

Microbial Assemblages as Indicators of Chemical Pollution in Estuaries

Issue. Multiple chemical stressors commonly coexist in contaminated marsh sediments. Individual chemical assays are ineffective at fully revealing all contaminants. Suites of assays may be more useful, but no suite is comprehensive and few would reveal toxic metabolites of parent pollutants. Analytical endpoints are not necessarily biologically relevant and thus monitoring chemicals will not achieve the needs of restoration and environmental quality managers. Individual bioindicators typically are based on acute dose-response relationships. Yet pollution is often chronic, at low levels, and affecting multiple organisms at once.

Approach and Rationale. Our approach was to assay whole microbial community biochemicals extracted from marsh sediments sampled along pollution and elevation gradients. DNA and fatty acids were extracted from split samples, and TRFLPs and phospholipid fatty acids (PLFAs) were profiled. The two resulting multivariate datasets were statistically evaluated for their relationships to pollutants analyzed (Figure 14). The rationale was that microbial assemblages, which are species-rich, highly responsive to environmental pressures, and rapidly growing, would be quantifiably related to pollutant levels. If this were true, then sentinel groups might be discernable from such profiles; the approach could also suggest microbial communities as comprehensive bioindicators for long term monitoring.

Figure 14. Ordination Diagram from Partial Canonical Correspondence Analysis (pCCA) of TRFLP Community Data Where Selected Metals Were Environmental Variables and Spatial Locations Were Covariables. Metal stressors, from a panel of over 20 candidates, are associated with long arrows in the diagram. See Cao, et al. (2006) for the study details and approaches.

Findings and Impact. The findings include the following:

  • Microbial assemblages differ between marshes.
  • Within marshes, microbial assemblages appear correlated to heavy metal (e.g., Zn) concentrations along chemical gradients but not to organic pollutant concentrations.
  • PLFA and TRFLP revealed similar relationships between pollutants and assemblages.
  • As might be expected by knowing their biological basis, TRFLP and PLFA provide slightly different insights; that is, PLFA appears more sensitive to low pollutant concentrations and acute environmental changes, whereas shifts in TRFLP profiles occur with higher pollutant concentrations over longer time scales.
  • Using the appropriate statistical approaches (e.g., partial canonical correspondence analysis), it is fully possible to separately assess the effects on microbial assemblages of pollutants and other environmental factors (e.g., salinity, oxygenation, dissolved organic carbon).
  • This work suggests that microbial communities are indeed sentinels of environmental pollution and could be employed as bioindicators.

Applications. Microbial assemblages can be assayed for any environment and their composition over time and along gradients could be monitored to track the recovery of marshes from pollution. Because they are so sensitive and represent comprehensive environmental signals, microbial assemblages also may be used to reveal chronic low level pollution. In addition, if shifts in assemblages along gradients are known to be specifically related to pollutants, the absence of those shifts may indicate recovery.

Tracing Bacterial Pollution in Coastal Environments

Issue. Fecal indicator bacteria (total coliform [TC], fecal coliform [FC], and enterococci [ENT]) are monitored in coastal waters to infer the presence of human waste and thus pathogens. These tests do not reliably indicate either the presence or origins of fecal material, however, because:

  • Fecal indicator bacteria can survive, which leads to “false positive” test results. They also survive differently from pathogens, and thus their absence doesn’t mean that water is pathogen-free.
  • Fecal indicator bacteria are in all warm-blooded animals, but the tests do not discern between human, pet, livestock, or wildlife sources.
  • Bacteria released into the environment can become nonculturable; this results in false negative testing results.

Coastal jurisdictions, although required to regularly monitor for TC, FC, and ENT in the surf zone, can improve their efforts to diagnose water quality and find contamination sources by employing diagnostic tools including state-of-the-art DNA-based methods. Here, we describe the development of one potential tool in the manager’s kit: whole bacterial community profiling for differentiating fecal material from various sources.

Approach and Rationale. To test the concept, our approach used fecal sources (cow, human, sewage, gull, and dog) and environmental waters into which those fecal sources were spiked. Culturable TC, FC, and ENT were measured using traditional methods. DNA was extracted and whole bacterial communities were profiled using TRFLP analysis of PCR-amplified genes encoding 16S rRNA. Extracted DNA also can be analyzed for published DNA-based markers of fecal sources (i.e. human, cow, and horse) by PCR amplification using source-specific primers. However, such markers have only been identified for a few waste sources. Further, our rationale is that rich datasets from multiple markers are potentially embedded in whole community profiles, thus making them powerfully comprehensive in their capacity to distinguish wastes.

Findings and Impact. The findings include the following:

  • Raw TRFLP profiles appear different for different wastes.
  • Thus, “signature groups” of terminal restriction fragments (TRFs) could be identified for detecting and tracing bacterial assemblages associated with source wastes.
  • In multivariate analysis of TRFLP profiles, wastes appear to be different (Figure 15).
  • Thus, TRFLP data lends itself to source discrimination and source detection, potentially against a complex background of environmental waters.

Figure 15. Principal Components (PC) Analysis of TRFLPs Generated from Two Sewage Samples (S) and Cattle (C), Dog (D), Human (H) and Seagull (G) Feces. PCA was estimated from the number of peaks shared between Hha I generated TRFLPs (see Field et al. 2003). Variation explained by PCs is indicated. The TRFLP technique clearly discriminated among waste sources.

Applications. The applications of the research include the following:

  • This approach can be used by consultants or large water agencies to trace bacterial pollution through statistically comparing profiles from environmental samples to profiles from wastes.
  • Whole community approaches are a first step towards developing more comprehensive suites of indicators that can more fully diagnose water and protect public health.
  • Waste signatures, comprised of single or multiple peaks in concert, could be embedded in whole profiles and their identification could lead to more deterministic diagnosis approaches if those peaks are waste-specific.
  • The use of DNA-based methods, including whole assemblage profiling, coupled with fecal indicator bacterial enumeration and with fate and transport modeling, will enable managers to know when water is contaminated and contamination origins.

Journal Articles on this Report : 10 Displayed | Download in RIS Format

Other subproject views: All 45 publications 14 publications in selected types All 13 journal articles
Other center views: All 139 publications 42 publications in selected types All 40 journal articles
Type Citation Sub Project Document Sources
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)
  • Full-text from PubMed
  • Abstract from PubMed
  • Associated PubMed link
  • Full-text: AEM-Full Text HTML
  • Abstract: AEM-Abstract
  • Other: AEM-Full Text PDF
  • 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)
  • Abstract from PubMed
  • Full-text: IWA - Full Text PDF
  • Abstract: IWA - Abstract
  • Other: So. California Coastal Water Research Project - Full Text PDF
  • 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)
    R828676C003 (Final)
  • Full-text from PubMed
  • Abstract from PubMed
  • Associated PubMed link
  • Full-text: Royal Society Publishing-Full Text HTML
  • Abstract: Royal Society Publishing-Abstract
  • Other: Royal Society Publishing-Full Text PDF
  • 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)
  • Full-text: University of California-San Diego-Full Text PDF
  • Abstract: ESA-Abstract
  • 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)
  • Abstract from PubMed
  • Abstract: Springer-Abstract
  • 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)
  • Abstract from PubMed
  • Abstract: Wiley-Abstract
  • 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)
  • Abstract: Taylor&Francis-Abstract
  • 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
  • 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
  • Abstract: ScienceDirect-Abstract
  • Other: ScienceDirect-Full Text PDF
  • 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
  • Abstract: ScienceDirect-Abstract
  • Other: ScienceDirect-Full Text PDF
  • Supplemental Keywords:

    watersheds, estuaries, ecological effects, bioavailability, ecosystem indicators, aquatic, integrated assessment, ecological effects, ecosystem indicators, , estuarine research, aquatic ecology, environmental indicators, ecosystem assessment, biological markers, biomarker, biomarkers, ecological assessment, ecological exposure, ecosystem condition, ecosystem health, ecosystem indicators, ecosystem integrity, environmental consequences, environmental indicators, environmental stress, environmental stressor, environmental stressors, estuaries, estuarine ecosystems, fish, plant indicator, statistical evaluation,, RFA, ENVIRONMENTAL MANAGEMENT, Water, ECOSYSTEMS, Ecosystem Protection/Environmental Exposure & Risk, estuarine research, exploratory research environmental biology, Ecosystem/Assessment/Indicators, Ecosystem Protection, Ecological Effects - Environmental Exposure & Risk, Aquatic Ecosystems, Terrestrial Ecosystems, Ecological Monitoring, Ecological Indicators, Risk Assessment, anthropogenic stresses, ecological risk assessment, wetlands, aquatic ecosystem, bioindicator, anthropogenic stress, biomarkers, ecosystem assessment, estuaries, wetland ecosystem, bioavailability, nutrients, trophic effects, ecosystem indicators, environmental indicators, water quality, coastal ecosystems, ecosystem restoration, aquatic ecology, biogeochemistry

    Relevant Websites: Exit

    Progress and Final Reports:

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

  • 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