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Northwest Fisheries Science Center (NWFSC) Fish Ecology FE - Estuarine and Ocean Ecology - Lower Columbia River Salmon Ecology

Information

Project
Lower Columbia Ecosystem Program
Title
Lower Columbia Ecosystem Program
Description
The tidal fluvial Columbia River and estuary (hereafter referred to as the Columbia River estuary or CRE) is a key transition area for Pacific Salmon and other protected species. The CRE is a matrix of habitats that provide forage and rearing opportunities to salmon from throughout the basin. The CRE is the last place we can influence the trajectory of salmon (e.g., via restoration, hydro ops, hatchery ops) before they disperse into ocean waters. Understanding the estuary ecology and ecosystem processes that influence the growth and survival of salmon through the CRE supports NMFS missions of conserving and recovering managed/protected species, restoring critical habitat, and maintaining healthy ecosystems.

The focus of the LCEP is to understand how physical, chemical, and biological estuarine environments affect Pacific salmon, and to use our findings to promote species recovery. Products of this work support the efforts of the WCRO in enforcing regulations and creating policy pertinent to the ESA, Mitchell Act, and the MMPA.

Our work focuses on five intersecting research areas: 1) salmon ecology, 2) food web and trophic interactions, 3) restoration science, 4) hatchery and human impacts, and 5) climate change impacts. Our objective is to provide a robust conceptual ecosystem framework for the CRE that can be used to identify data gaps, support adaptive ecosystem management initiatives, and inform management and policy decisions.


Data Sets

no data found

Research Themes

Habitats to support sustainable fisheries and recovered populations
Healthy oceans, coastal waters, and riverine habitats provide the foundation for aquatic resources used by a diversity of species and society. Protecting marine, estuarine and freshwater ecosystems that support these species relies on science to link habitat condition/processes and the biological effects of restoration actions. The NWFSC provides the habitat science behind many management actions taken by NOAA Fisheries and other natural resource agencies to protect and recover aquatic ecosystems and living marine resources. The NWFSC also maintains a longstanding focus on toxic chemical contaminants, as a foundation for regional and national research on pollution threats to fisheries and protected resources.
Recovery and rebuilding of marine and coastal species
The Pacific Northwest is home to several iconic endangered species, including Pacific salmon and killer whales, and several rockfish species. Mandates such as the Endangered Species Act, MagnusonStevens Act, and the Marine Mammal Protection Act, grant NOAA Fisheries the authority to manage the recovery of depleted species and stocks. The NWFSC contributes to species recovery through research, monitoring and analysis, providing NOAA managers and regional stakeholders the tools and information they need to craft effective regulations and develop sustainable plans for recovery.

Research Foci

Characterize relationships between habitat and ecosystem processes, climate variation, and the viability of organisms
Developing effective conservation and restoration strategies for species or populations requires a clear understanding of how ecosystem processes and climate change will influence the viability of organisms in the future. Key research needs include (1) evaluating the vulnerability of organisms and ecosystems to climate change and human impacts (e.g., fishing, pollution, land use), and (2) devising adaptation strategies that will help achieve conservation goals despite climate change and increasing human pressures. Understanding how climate change or trends in human impacts might influence organisms is based on an understanding of linkages between ecosystem processes, habitat conditions, and abundance, survival or demographics of organisms. This necessitates modeling influences of ecosystem processes on habitats and species, or developing models to examine influences of human pressures on population or ecosystem dynamics. With this foundation, vulnerability assessments can focus on understanding how interactions between climate change and human impacts influence vulnerability of species or populations. Adaptation strategies require knowledge of current conservation needs, predictions of how those needs might change as a result of climate change or future human impacts, and assessments of the robustness of alternative conservation strategies or techniques to climate trends.
Characterize the interaction of human use and habitat distribution, quantity and quality
The ability to define the state of an ecosystem requires insight into the natural processes within habitats, and how anthropogenic interactions with these processes can alter ecosystems and marine organisms. A wide diversity of human activities -- land use and water withdrawals, industrialization and dredging, fishing practices and climate change (e.g., ocean acidification) -- directly and indirectly impact critical freshwater, estuarine, and marine habitats. To best manage west coast marine, estuarine and freshwater habitats in a sustainable fashion, it is necessary to map the spatial and temporal footprint of human impacts and review their potential biological impact on each species of interest. Measurement parameters will be developed to determine the full range of human impacts using spatial data and improved habitat classification.
Describe the relationships between human activities and species recovery, rebuilding and sustainability
Human activities play a major role in determining the status of species and stocks. Rebuilding and recovery therefore need to address how these activities affect their status. At the NWFSC, biophysical modeling is used to link specific human activities such as land use and pollution to habitat conditions, and then to link these conditions and other activities to particular life stages. These models can be used to quantitatively assess how human activities influence species abundance, productivity, distribution and diversity. Not surprisingly, altering human activities in some way is often necessary for species or stock recovery and rebuilding. It is therefore important to understand the socio-economic effects of alternative management structures. Gathering data on their economic costs and social impacts helps identify actions that are cost-effective. These actions will need to be resilient to potential changes in climate throughout the region. Research on how humans react to management strategies helps policy makers avoid those that lead to unintended consequences that can hinder rather than help recovery.
Develop effective and efficient habitat restoration and conservation techniques
Maintaining and re-establishing viability and sustainability of living marine resources requires conservation and rehabilitation or restoration of habitats upon which species depend. Common habitat restoration approaches and tech-niques often presume that habitats are static features of the environment, and that creation of stable habitats is a desirable restoration strategy. However, riverine, nearshore, and marine habitats are created and sustained by dynamic landscape, climatic, and oceanographic processes and biota are adapted to changing habitats that are within the range of natural variability. Hence, current restoration strategies often have limited success, in part because they fail to recognize larger scale processes that drive habitat change, and in part because they fail to recognize intrinsic habitat potential of individual restoration sites. The main goals of this research focus are to: improve understanding of how large-scale processes create diverse and dynamic habitats that support marine and anadromous species, better understand how human activities alter habitat-forming processes and habitats, develop new restoration techniques that are compatible with sustainable habitat-forming processes, and understand the variety of actions needed to adequately conserve intact critical habitats. In addition, NWFSC’s research will improve understanding of how new and existing habitat restoration and protection techniques affect fish and habitat at multiple scales (i.e., reach, watershed, Evolutionarily Significant Unit).

Keywords

Chinook salmon
species of interest
Chinook salmon growth rates
salmon growth rates as estimated from otoliths
chemical contaminants
bioaccumulative contaminants in salmon bodies and prey
chum salmon
species of interest
coho salmon
Oncorhynchus kisutch
fish community composition
species of interest
fish diet
diet of fish
salmon lipid content
lipid content and classes in bodies of Chinook salmon
salmon prey availability
invertebrate macroinvertebrates in habitat, based on emergent vegetation and open water tows

Products

Residency and movement of juvenile Chinook salmon at multiple spatial scales in a tidal marsh of the Columbia River estuary.
McNatt, R. A., D. L. Bottom, S. A. Hinton. 2016. Residency and movement of juvenile Chinook salmon at multiple spatial scales in a tidal marsh of the Columbia River estuary. Transactions of the American Fisheries Society, 145(4):774-785.
Benthic video landers reveal impacts of dredged sediment deposition events on mobile epifauna are acute but transitory.
Roegner, G. C., S. A. Fields, S. Henkel. 2021. Benthic video landers reveal impacts of dredged sediment deposition events on mobile epifauna are acute but transitory. Journal of Experimental Marine Biology and Ecology, 538(151526). doi:10.1016/j.jembe.2021.151526
Characterizing juvenile salmon predation risk during early marine residence
Phillips, E. M., J. K. Horne, J. E. Zamon. In press. Characterizing juvenile salmon predation risk during early marine residence. PLoS ONE. doi:10.1371/journal.pone.0247241
Columbia Estuary Ecosystem Restoration Program 2012 sythesis memorandum
Thom, R. M., N. K. Sather, G. C. Roegner, D. L. Bottom. 2013. Columbia Estuary Ecosystem Restoration Program 2012 sythesis memorandum. Report of the Pacific Northwest National Laboratory and National Marine Fisheries Service to the U.S. Army Corps of Engineers. Portland, Oregon.
Comparative use by Pacific salmon of shallow and deep water habitats in the Columbia River estuary prior to ocean entry.
Roegner, G. C., L. A. Weitkamp, D. J. Teel. 2016. Comparative use by Pacific salmon of shallow and deep water habitats in the Columbia River estuary prior to ocean entry. Marine and Coastal Fisheries, 8(1):536-552.
Comparison of experimental and computational methods for discharge measurements from tidal wetlands.
Harding, S. F., A. M. Coleman, G. C. Roegner. 2020. Comparison of experimental and computational methods for discharge measurements from tidal wetlands. River Research and Applications, 36(9):1954-1961. doi:https://doi.org/10.1002/rra.3709
Density and condition of subyearling Chinook salmon in the lower Columbia River and estuary in relation to water temperature and genetic stock of origin
Roegner, G. C., D. J. Teel. 2014. Density and condition of subyearling Chinook salmon in the lower Columbia River and estuary in relation to water temperature and genetic stock of origin. Transactions of the American Fisheries Society, 143(5):1161-1176.
Distribution, size, and origin of juvenile Chinook salmon in shallow water habitats of the lower Columbia River and estuary, 2002-2007.
Roegner, G. C., R. A. McNatt, D. J. Teel, D. L. Bottom. 2012. Distribution, size, and origin of juvenile Chinook salmon in shallow water habitats of the lower Columbia River and estuary, 2002-2007. Marine and Coastal Fisheries, 4(1):450-472.
EMP Database
Access database of EMP data from 2017-present
Ecosystem Monitoring Program Annual Report
Technical report
Ecosystem Monitoring Program Annual Report
Technical report
Ecosystem Monitoring Program Annual Report
Technical Report
Ecosystem Monitoring Program Annual Report
Technical Report
Ecosystem Monitoring Program Annual Report
Technical Report
Estuarine habitat and demographic factors affect juvenile Chinook (Oncorhynchus tshawytscha) growth variability in a large freshwater tidal estuary.
Goertler, P. A., C. A. Simenstad, D. L. Bottom, L. Stamatiou, S. A. Hinton. 2015. Estuarine habitat and demographic factors affect juvenile Chinook (Oncorhynchus tshawytscha) growth variability in a large freshwater tidal estuary. Estuaries and Coasts , 39 (2) : 542-559. (http://dx.doi.org/10.1007/s12237-015-0002-z)
Estuarine habitat and juvenile salmon: current and historical linkages in the Lower Columbia River and estuary. Final report, 2002-2008.
Bottom, D. L., A. M. Baptista, J. Burke, L. A. Campbell, E. Casillas, S. A. Hinton, D. A. Jay, M. Lott, G. T. McCabe Jr., R. A. McNatt, M. Ramirez, G. C. Roegner, C. A. Simenstad, S. Spilseth, L. Stamatiou, D. J. Teel, J. E. Zamon. 2011. Estuarine habitat and juvenile salmon: current and historical linkages in the Lower Columbia River and estuary. Final report, 2002-2008. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Portland, Oregon.
Genetic identification of Chinook salmon in the Columbia River estuary: Stock-specific distributions of juveniles in shallow freshwater habitats.
Teel, D. J., D. L. Bottom, S. A. Hinton, D. R. Kuligowski, G. T. McCabe Jr., R. A. McNatt, G. C. Roegner, L. A. Stamatiou, C. A. Simenstad. 2014. Genetic identification of Chinook salmon in the Columbia River estuary: Stock-specific distributions of juveniles in shallow freshwater habitats. North American Journal of Fisheries Management, 34(3):621-641.
Indexing habitat opportunity for juvenile anadromous fishes in tidal fluvial wetland systems.
Roegner, G. C., G. E. Johnson, A. M. Coleman. 2021. Indexing habitat opportunity for juvenile anadromous fishes in tidal fluvial wetland systems. Ecological Indicators, 124(107422). doi:https://doi.org/10.1016/j.ecolind.2021.107422
Juvenile salmon assemblages at the Mirror Lake Complex in the lower Columbia River before and after a culvert modification
This study examined salmonid assemblages upstream of a culvert connecting the Mirror Lake Complex (MLC) with the lower Columbia River before and after the culvert was modified to improve habitat connectivity and fish passage. Initially the culvert limited water flow between the Columbia River and the MLC. The outlet and interior of the culvert was reconfigured to create a more ¿natural¿ and suitable passageway for salmonids, through the removal of rip rap, and strategic placement of boulders, cobbles, gravels, baffles, and weirs. Prior to the culvert modification, three sites were sampled monthly between April and August of 2008, 5.0 km and 0.5 km upstream of the culvert, and immediately downstream of the culvert. After the culvert modification, the same sites were sampled from 2009¿2012 with two additional sites added in 2010. Sites near the culvert supported Chinook Salmon Oncorhynchustshawytscha,Coho Salmon O. kisutch, and Chum Salmon O. keta; while sites further from the culvert supported unmarked Coho Salmon and Rainbow/Steelhead Trout O. mykiss, and Cutthroat Trout O. clarkii. Clear trends in salmonid occurrence were not observed, although densities of Chinook Salmon tended to be higher in years post-modification than before modification. Culvert modifications should focus on alleviating site specific fish passage conditions to result in substantial changes to habitat connectivity.
Legacy EMP database
Access database of EMP data from 2005-2016
Migration rates of hatchery Chum Salmon (Oncorhynchus keta) fry in the Columbia River estuary
Homel, K., G. C. Roegner. 2020. Migration rates of hatchery Chum Salmon (Oncorhynchus keta) fry in the Columbia River estuary. Report to Oregon Department of Fish and Wildlife 2020-03, 25 p.
Multnomah Channel wetland restoration monitoring project (2014-2016).
McNatt, R. A., B. Cannon, S. A. Hinton, L. D. Whitman, R. Klopfenstein, T. A. Friesen, D. L. Bottom. 2017. Multnomah Channel wetland restoration monitoring project (2014-2016). Report of the National Marine Fisheries Service, Oregon Department of Fish and Wildlife, and Oregon State University t the Oregon Metro Natural Areas Program.
Predator-prey interactions influenced by a dynamic river plume.
Phillips, E. M., J. K. Horne, J. E. Zamon. 2017. Predator-prey interactions influenced by a dynamic river plume. Canadian Journal of Fisheries and Aquatic Sciences, 74(9):1375-1390. doi:10.1139/cjfas-2016-0302
Quantifying Restoration of Juvenile Salmon Habitat with Hyperspectral Imaging from an Unmanned Aircraft System
Roegner, G. C., A. M. Coleman, A. B. Borde, J. D. Tagestad, R. Erdt, J. Aga, S. A. Zimmerman, C. Cole. 2019. Quantifying Restoration of Juvenile Salmon Habitat with Hyperspectral Imaging from an Unmanned Aircraft System.
Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary
Weitkamp, L. A., P. J. Bentley, M. N. Litz. 2012. Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary. Fishery Bulletin , 110 (4) : 426-450. (http://fishbull.noaa.gov/1104/weitkamp.pdf)
Stock-specific size and timing at ocean entry of Columbia River juvenile Chinook salmon and steelhead: implications for early ocean growth
Weitkamp, L. A., D. J. Teel, M. Liermann, S. A. Hinton, D. M. Van Doornik, P. J. Bentley. 2015. Stock-specific size and timing at ocean entry of Columbia River juvenile Chinook salmon and steelhead: implications for early ocean growth. Marine and Coastal Fisheries , 7 (1) : 370-392. (http://dx.doi.org/10.1080/19425120.2015.1047476)
Storm-Driven Particulate Organic Matter Flux Connects a Tidal Tributary Floodplain Wetland, Main Stem River, and Estuary.
Thom, R. M., S. A. Breithaupt, H. L. Diefenderfer, A. Borde, G. C. Roegner, G. Johnson, D. L. Woodruff. 2018. Storm-Driven Particulate Organic Matter Flux Connects a Tidal Tributary Floodplain Wetland, Main Stem River, and Estuary. Ecological Applications. doi:DOI:10.1002/eap.1759
Synthetic EMP database
Single database that merges the legacy and contemporay data into a single format. To be used for estuary indicator analysis.
The contribution of tidal fluvial habitats in the Columbia River Estuary to the recovery of diverse salmon ESUs.
Roegner, G. C., D. L. Bottom, A. M. Baptista, L. A. Campbell, A. M. Claiborne, K. L. Fresh, S. A. Hinton, R. A. McNatt, C. A. Simenstad, D. J. Teel, R. W. Zabel. 2013. The contribution of tidal fluvial habitats in the Columbia River Estuary to the recovery of diverse salmon ESUs. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Portland, Oregon.
Variability in the performance of juvenile Chinook salmon is explained primarily by when and where they resided in estuarine habitats
We used otolith-derived estimates of somatic growth rate as an index of recent performance and together with a generalized linear modeling (GLM) approach investigated how variability in juvenile performance was explained by several abiotic and biotic factors. Our GLM approach indicated that variability in relative somatic growth rate (mm/mm/day) was best explained by when (i.e., Julian day and year) individuals were collected and to a lessor degree by where they were collected (i.e., river kilometer), fish and invertebrate density, stock of origin, and whether a fish was hatchery produced or unmarked. Using this information we argue there is potential for improving juvenile performance within estuarine and tidal freshwater habitats.
Video sleds effectively survey epibenthic communities at dredged material disposal sites
Fields, S., S. Henkel, G. C. Roegner. 2019. Video sleds effectively survey epibenthic communities at dredged material disposal sites. Environmental Monitoring and Assessment, 191(404):1-25.

Taxa

Species Oncorhynchus keta
chum salmon, dog salmon, Keta salmon
Species Oncorhynchus kisutch
Coho salmon, silver salmon
Species Oncorhynchus tshawytscha
Chinook salmon, king salmon, spring salmon

People

Brian Beckman
Internal Collaborator
Brian Burke
Internal Collaborator
Curtis Roegner
Internal Collaborator
Daniel Lomax
Internal Collaborator
David Huff
Program Manager
David Kuligowski
Internal Collaborator
Gabriel Brooks
Internal Collaborator
Jeannette Zamon
Internal Collaborator
Joe Smith
Internal Collaborator
Keri Baugh
Internal Collaborator
Laurie Weitkamp
Internal Collaborator
Michelle Rub
Internal Collaborator
Paul Chittaro
Internal Collaborator
Regan McNatt
Principal Investigator
Regan McNatt
Principal Investigator
Susan Hinton
Internal Collaborator