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Northwest Fisheries Science Center (NWFSC) Fish Ecology FE - Estuarine and Ocean Ecology

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Project
Lower Columbia Ecosystem Monitoring Project (LCEP)

Title
Lower Columbia River Ecosystem Monitoring Project

Description
The Ecosystem Monitoring Program (EMP) is managed by the Lower Columbia Estuary Partnership (funded through BPA) and is an integrated status and trends program for the lower Columbia River and estuary. The project is a collaborative effort among many entities including, UW, OHSU, and PNNL. The NWFSC portion of the study centers around collection, processing, and analysis of fish community data (FE), salmon genetics (CB), otoliths (EFS), and lipids (EFS). The EMP aims to collect key information on ecological conditions for a range of habitats throughout the lower river characteristic of those used by migrating juvenile salmon and provide information toward the recovery of threatened and endangered salmonids. The program inventories different types of habitats within the lower river (mouth to Bonneville Dam), tracks trends in the overall condition of these habitats over time, provides a suite of reference sites for use as end points in regional habitat restoration actions, and places findings from management actions into context with the larger ecosystem. This study also includes components of the Estuary Partnership’s Action Effectiveness Monitoring and Research (AEMR) program(different from the USACE-funded AEMR study in the lower Columbia), whereby the NWFSC maintains and analyzes data from two in-stream PIT detection arrays located in the lower Columbia River, and conducts “5-year check-ins” of restoration sites to determine salmonid use.

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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.

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).

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

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

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

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.

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

Daniel Lomax
Internal Collaborator

David Kuligowski
Internal Collaborator

Keri Baugh
Internal Collaborator

Paul Chittaro
Internal Collaborator

Regan McNatt
Principal Investigator

Susan Hinton
Internal Collaborator

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