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Columbia River Contaminants and Habitat Characterization: Tracking the Occurrence and Foodweb Effects of Polybrominated Flame Retardants and Endocrine Disrupting Compounds

Contact: Elena Nilsen or Jennifer Morace



Osprey nesting along the Columbia River eat fish that contain contaminants from urban areas, industries, and agricultural operations. These contaminants are then concentrated in the bodies and eggs of the birds.(Photograph by Anthony Long, Vancouver, Washington)


The Columbia River provides important hydroelectric power generation, valuable recreational and tribal fisheries, extensive recreational areas and scenic beauty, and habitat for wildlife and fish. The lower Columbia River below Bonneville is the largest remaining free-flowing reach not impounded by hydroelectric dams, and is critical to the viability of culturally significant fish populations (anadromous and resident) in the Columbia Basin, as well as a myriad of other aquatic and terrestrial organisms. Fish, wildlife, and human populations along the lower Columbia River are exposed to an ever-growing variety of contaminants as a result of increasing urbanization, industrialization, and agricultural development.  This study is a demonstration project designed to combine the expertise within the USGS disciplines to address how emerging contaminants, such as polybrominated diphenyl ether flame retardants (PBDEs) and endocrine disrupting compounds (EDCs) impact fish, osprey, and other wildlife in the basin. (See a video explaining the study [9:31])

The study will investigate transport pathways, chemical fate and effects of PBDEs and EDCs in aquatic media and through several levels of the foodweb in the lower Columbia River. This will require innovative, interdisciplinary technologies and strategies, such as passive sampling, novel analytical methods, endocrine and reproductive biomarkers, cDNA microarrays, and coupling geochemical data to habitat classification and hydrodynamic and sediment transport modeling. The work will be carried out in concert with ongoing efforts by multiple agencies and partnerships to understand impacts of these contaminants on the natural environment, associated species, and human health in the Columbia River Basin.

Filling knowledge gaps associated with the occurrence and bioaccumulation of PBDEs and EDCs will improve the ability of management agencies to evaluate the actions that are the most likely to result in improving lower river and estuarine conditions for salmonids and other organisms. The presence and effects of these emerging contaminants are important issues that have high scientific and public visibility and potentially important implications for people, fish, and wildlife in the Columbia River Basin. By framing the investigation as a conceptual example of an integrated sampling project, our results could be used as a foundation for future efforts to establish a monitoring program for emerging contaminants, indicators of biotic integrity, and/or other issues of concern in the basin.

Principal Investigators

Study Synopsis and Flow Chart

Video: Emerging Contaminants in the Columbia River
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A transcript is available at


Study Objectives

  1. Assess contaminant concentrations in multiple levels of the foodweb (invertebrates, salmonids, resident fish, osprey) and the environment (sediment and water) in the lower Columbia River Basin.
  2. Determine the biological effects on fish using biomarkers (vitellogenin induction, gonadal histopathology, cDNA microarrays) and relate these to contaminant concentrations measured in the foodweb and environment to the extent possible.
  3. Characterize sampling locations using the Columbia River Estuary Ecosystem Classification System and samples collected for sediment characterization to allow comparisons among sites and to provide context within the Columbia River Basin.
  4. Evaluate the transport of fine-grained sediments and associated contaminants in the system, as possible, by combining the hydrodynamics and sediment transport model (that will be expanded as part of this project), Ecosystem Classification System, and sampling results.
  5. Develop a conceptual example of an integrated sampling project with the future intent of expanding this example into an integrated monitoring strategy.
  6. Produce a synthesis report that provides insight and unique results achieved through an interdisciplinary approach capitalizing on the breadth of expertise of the team members.


Largescale Sucker Contaminants

  • Fish tissue contaminant concentrations increase moving downstream with increasing urbanization. Contaminant levels are of concern for subsistence fisher populations based on aquatic life ratios
  • Bioaccumulation and biomagnification were observed for PBDE flame retardant compounds in the food web

Biomarker and Sediment Transport

  • Biomarkers show fish more stressed downstream sites relative to upstream (some statistically correlated to measured contaminants)
  • Biomarker that differed among sites: abnormal morphology, viability, mitochondrial membrane potential, live apoptotic cells, total apoptotic cells, ATP content, DNA fragmentation, and percent haploid testicular cells
  • Statistical correlations showed relationship between contaminant concentrations and biomarker effects
  • A gene expression microarray developed for the project identified 69 genes with expression patterns that correlated with hepatic tissue contaminants
  • The sediment transport model developed for the project is a very useful tool to predict accumulation of fine-grained sediments and contaminants, and allows extrapolation of contaminant results from point samples to the larger modeled area

Take home

  • Contaminants are present at levels of concern in the food web of the lower Columbia River
  • A sediment transport and habitat model developed for the project may allow prediction of sediment and contaminant distributions under different flow scenarios and potential for management applications to track effluent, spills, etc.


Foodweb transfer, sediment transport, and biological impacts of emerging and legacy organic contaminants in the lower Columbia River, Oregon and Washington, USA: USGS Contaminants and Habitat (ConHab) Project, by Elena Nilsen and Jennifer Morace. Science of the Total Environment, 484 (2014), pp. 319–321

Spatial and temporal trends in occurrence of emerging and legacy contaminants in the Lower Columbia River 2008–2010, by D.A. Alvarez, S. Perkins, E. Nilsen, J. Morace. Science of the Total Environment, 484 (2014), pp. 322–330.

Correlation of gene expression and contaminant concentrations in wild largescale suckers: A field-based study, by H.E. Christiansen, A.C. Mehinto, F. Yu, R.W. Perry, N.D. Denslow, A.G. Maule et al. Science of the Total Environment, 484 (2014), pp. 379–389.

A survey of benthic sediment contaminants in reaches of the Columbia River Estuary based on channel sedimentation characteristics, by T. Counihan, I. Waite, E. Nilsen, J. Hardiman, E. Elias, G. Gelfenbaum, Science of the Total Environment, 484 (2014), pp. 331-343.

Wastewater Dilution Index Partially Explains Observed Polybrominated Diphenyl Ether Flame Retardant Concentrations in Osprey Eggs from Columbia River Basin, 2008–2009, by Charles J. Henny, Robert A. Grove, James L. Kaiser, Branden L. Johnson, Chad V. Furl, and Robert J. Letcher. Ecotoxicology, June, 2011, v. 20, no. 4.

Assessing reproductive and endocrine parameters in male largescale suckers (Catostomus macrocheilus) along a contaminants gradient in the lower Columbia River, USA, by J.A. Jenkins, H.M. Olivier, R.O. Draugelis-Dale, B.E. Eilts, L. Torres, R. Patiño et al. Science of the Total Environment, 484 (2014), pp. 365–378.

Contaminants of legacy and emerging concern in largescale scucker (Catostomus macrocheilus) and the foodweb in the lower Columbia River, Oregon and Washington, USA, by E. Nilsen, S. Zaugg, D. Alvarez, J. Morace, I. Waite, T. Counihan et al. Science of the Total Environment, 484 (2014), pp. 344–352.

Health status of Largescale Sucker (Catostomus macrocheilus) collected along an organic contaminant gradient in the lower Columbia River, Oregon and Washington, USA, by L. Torres, E. Nilsen, R. Grove, R. Patiño, Science of the Total Environment, 484 (2014), pp. 353–364.


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