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Project: Emerging Contaminant Effects on Wetland Fish

Background and Objectives

Anthropogenic pressures in southern California have resulted in wetland loss, modification, and contamination. Wetland ecosystems often contain a diverse group of historically discharged (legacy) contaminants (e.g., PCBs, DDTs), as well as currently discharged contaminants of emerging concern (e.g., pharmaceuticals, personal care products, current use pesticides, and industrial chemicals) from multiple sources. California is developing policies and programs to mitigate the impacts of anthropogenic disturbance. To assess the net effect of wetland management efforts, a three-tiered monitoring program has been created utilizing the standardized California Rapid Assessment Method (CRAM), which measures the general condition of habitat but does not elicit contaminant impacts. Thus, very little information on the extent of exposure and effects of emerging contaminants on the organisms living in wetlands is available.

Rapid advances in biotechnology have resulted in the development of new methods to investigate environmental stressors. For example, microarray technology allows measurement of changes in gene expression, and therefore has the potential to provide a rapid and comprehensive evaluation of an organism's response to contaminants. However, microarrays have not been applied within southern California coastal wetlands and so their effectiveness, especially relative to more traditional assessment methods, is unknown.

The goal of this project was to apply a fish gene microarray as a tool for investigating contaminant impacts on wetland condition. The objectives were to:

1) Assess differences in fish status among sites having different contaminant exposure;
2) Compare microarray results to more intensive measures of chemical exposure and biological response; and
3) Determine how well the results correlate with other rapid assessment methods developed for wetlands.


This study was initiated in 2005 and completed in 2011.


The target species for this study was the longjawed mudsucker (Gillichthys mirabilis), a relatively common wetland fish. Fish were sampled from three wetlands known to be impacted by different types of contaminant sources (agricultural, urban and wastewater effluent). These included the Carpinteria Salt Marsh Reserve in Santa Barbara County, the Upper Newport Bay Ecological Reserve in Orange County, and the Tijuana River Estuary in San Diego County. In Carpinteria, contaminant exposure is likely dominated by agricultural runoff, while the Upper Newport Bay site receives urban runoff. The Tijuana Estuary, in contrast, receives periodic raw sewage inputs from treatment plant overflows.

The longjawed mudsucker is a year-round wetland resident with high site fidelity. Thus, the mudsucker's condition is likely to reflect local environmental conditions.
Location of wetland study sites.

Fish blood plasma, liver, and gonad samples were collected from each of the three sites. Liver tissues from individual fish were analyzed to determine changes in gene expression using microarray and quantitative polymerase chain reaction (qPCR) techniques. Additional indicators of biological effects (e.g., endocrine disruption) were measured via vitellogenin, choriogenins, steroid hormones, and gonad histopathology. Samples of sediment, water, and liver tissue were also collected for chemical analysis. These samples were analyzed for a suite of both legacy and emerging contaminants of concern. A CRAM assessment was also conducted at each sampling station.

The results from the microarray were compared to data from other intensive measurements of chemical contamination and biological effects. These comparisons evaluated the ability of the microarray to detect habitat condition differences among the sites. The chemical and biological indicators were finally compared to CRAM wetland condition results, in order to assess the magnitude and nature of impacts at each site.


Metals, legacy organochlorine pesticides, polychlorinated biphenyls, and contaminants of emerging concern were detected in sediments and whole fish. Overall gene expression patterns were characteristic to each of four sites investigated in this study. Differentially expressed genes belonged to several functional categories including xenobiotic metabolism, detoxification, disease and stress responses. In general, plasma estradiol concentrations were similar among fish from all areas. Some fish gonads had pathologic changes (e.g., infection, inflammation) that could indicate weakened immune systems and chronic stress. The differential expression of some genes involved in stress responses correlated with the prevalence of histologic gonad lesions. This study indicates that gene expression is a promising tool for assessing the biological condition of fish exposed to environmental contaminants.


University of California, San Diego
University of California, Riverside
University of California, Davis
California State University, Long Beach


Gene expression analysis as an indicator of fish health - January 2011 presentation to SCCWRP member agencies describing application of gene microarrays to examine contaminant exposure effects in fish.
For more information on Emerging Contaminant Effects on Wetland Fish, contact Steve Bay at (714) 755-3204.
This page was last updated on: 7/1/2014