Ecosystem Monitoring Program
BPA Project Number:  2003-007-00
CR-280436
Performance/Budget Period: October 1, 2014 – September 30, 2015

Technical Contact/Project Lead:  Catherine Corbett
Lower Columbia Estuary Partnership
811 SW Naito Parkway, Suite 410
Portland, Oregon  97204
Phone: (503) 226-1565 Ext. 240
Fax:  (503) 226-1580
ccorbett@estuarypartnership.org

Contracting Contact: Tom Argent
Lower Columbia River Estuary Partnership
811 SW Naito Parkway, Suite 410
Portland, Oregon  97204
Phone: (503) 226-1565 Ext. 242
Fax:  (503) 226-1580
targent@estuarypartnership.org

BPA Project Manager:  Anne Creason
KEWL-4, Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  (503) 230-3859
amcreason@bpa.gov

SUMMARY

Ecosystem Monitoring Program
The Lower Columbia Estuary Partnership (Estuary Partnership) Ecosystem Monitoring Program is an integrated status and trends program for the lower Columbia River. The study area extends from the mouth of the estuary to the Bonneville Dam. The program is designed to provide an inventory of the different types of habitats within the lower river; track trends in the overall condition of these habitats and the ecosystem; provide a suite of reference sites for use as end points in the region’s habitat restoration actions, and place findings from management actions into context with the larger ecosystem. The Program is a collaborative effort with NOAA National Marine Fisheries Service (NOAA Fisheries), Pacific Northwest National Laboratory (PNNL), University of Washington (UW), US Geologic Survey (USGS), and Oregon Health & Science University (OHSU).

When the program was created in 2004, most previous research in the lower river had occurred in a small section of the lower, close to the river mouth in Reaches A and B. There was a considerable lack of research and monitoring within the tidal freshwater section of the lower river, resulting in little basic understanding of habitats, fish use and food web dynamics in this region.

The Estuary Partnership and its monitoring partners have focused on providing an inventory of salmon habitats (or “status”) across the lower river stratifying by hydrogeomorphic reach (A–H) and including a growing number of fixed sites for interannual variability (or “trends”). The focus of the EMP has been on minimally disturbed tidally influenced emergent wetland sites. Each year prior to 2013, three to four “status” sites, in a previously unsampled reach, were selected along with the continued sampling of a growing number of “trend sites.”

In 2012, the EMP scope was reduced to monitoring only the 6 trend sites: Campbell Slough in the Ridgefield National Wildlife Refuge (2005–2014), Whites Island (2009-2014), and Franz Lake (2008-2009, 2011-2014), Ilwaco (2010-2013), Secret River (2010-2013), Welch Island (2010-2014). Habitat structure and hydrology data began to be collected in 2005, fish data collection began in 2007, fish prey data collection began in 2008, and water quality data and food web data collection began in 2010.  Data collection includes:
• Salmonid occurrence, composition, growth, diet, condition and residency
• Habitat structure, including physical, biological and chemical properties of habitats
• Food web characteristics, including primary and secondary productivity of habitats and in the mainstem lower river and
• Biogeochemistry of tidal freshwater region of the lower river for comparison to the biogeochemistry of the estuary, key for assessing hypoxia, ocean acidification and climate change impacts.

Applications of Results to Management – funded under BPA’s Columbia River Estuary Ecosystem Restoration Program (CEERP), a primary goal of the EMP is to collect key information on ecological conditions for a range of habitats in the lower river characteristic of those used by out migrating juvenile salmon and provide information towards implementation of the 2008 FCRPS BiOp. Information collected describes synoptic conditions and changes over time in vegetated floodplain habitats and the opportunity, capacity and realized function (Simenstad and Cordell 2000) they afford juvenile salmonids. These habitats are the targets of regional restoration efforts, which make the program integral for understanding the success of the regional habitat restoration program. The results of the EMP provide information on ambient environmental conditions and insight into the cumulative effects of existing and new management actions and anthropogenic impacts as they occur.

The EMP has provided key information on a suite of 51 reference sites across the lower river. These sites will be used as end points for restoration projects and used in combination with the Action Effectiveness Monitoring and Research (AEMR) Program data described below. Data collected through the EMP on vegetation, elevation and hydrologic patterns from these sites have been used to create regionally specific restoration design considerations for use by restoration practitioners in designing more successful restoration actions. Patterns include 5 vegetation zones and 3-4 hydrologic zones and elevation tolerance of the invasive species, reed canarygrass. Data collected through the EMP have also documented preferential use of regions of the lower river by different salmonid ESUs.    

Importance of this Program and its Future
• Status and trends monitoring of estuary ecosystem condition–important to “keep pulse on the river” – doesn’t matter what kind of doctor you visit, they always take your blood pressure, pulse and weigh you; cannot roll-up AEMR data and assess benefits of restoration actions without an understanding of what’s also going on across the estuary (can only understand conditions at individual restoration sites)
• Provides basic information on how estuary functions  – lack of research and monitoring in tidal freshwater section of river still limits basic understanding
• Provides the only inventory of habitats across the estuary-river continuum – still gaps in degraded habitats, tidal tributaries
• Provides the only “long-term” dataset of fish use across tidal freshwater sections – ranging 2-6 years; previous studies were temporally or spatially limited
• Provides only information on inter-annual variability of habitat, instream conditions, food web resources and fish use
• Leverages other key programs for more comprehensive analyses:
1. Only consistent toxic contaminant data collection in lower Columbia. Analysis of juvenile Chinook salmon, Chinook stomach contents and macroinvertebrates at sampling sites are completed by NOAA researchers under this program. If the program changes sufficiently, NOAA will no longer be able to leverage the program or have samples to perform and report out analyses. These provide the only consistent information we have in the lower river on concentrations in juvenile salmon and how salmon are being exposed to contaminants.
2. Only mainstem water quality monitoring station above Beaver Army Terminal Center.  Coastal Margin Observation and Prediction (CMOP) by OHSU. CMOP station installed and maintained through this program provides not only the data collection but our ability to tie into research by OHSU and NANOOS under CMOP. The CMOP station will be important for modeling and predicting mainstem conditions for the Columbia River Treaty. It is the only monitoring station above Beaver Army Terminal and below Bonneville that tracks mainstem water quality conditions.
• Results are used for identifying, designing and monitoring restoration projects – for example:
• Findings on the elevation and inundation period where reed canarygrass thrives (invasive, nuisance species) are used in designing restoration projects by CREST, CLT, WDFW, Estuary Partnership, others to reduce its occurrence at restoration sites
• Fish use data are used for ERTG templates by CREST, CLT, WDFW, Estuary Partnership, others and scoring of SBUs by ERTG
• Hydrologic characteristics of estuary regions are used to provide context for inundation anticipated at restoration sites by CLT, WDFW, Estuary Partnership, others
• Sites are used as reference sites for restoration projects by CREST, CLT, WDFW, Estuary Partnership, others. We have done comparisons of reference site conditions with restoration sites action effectiveness data (completed in 2012)
• In stream mainstem conditions used in determining if “greening of river” (macrodetritus versus plankton base of salmon foodweb) is correct and whether system is nutrient limited or nutrient enriched

Past Results - From fiscal years 2004 through 2012, with funding from NPCC/BPA, EMP partners have accomplished the following major tasks: 1) developed a statistically valid, ecosystem-based monitoring plan for the estuary (focusing on juvenile salmon habitats); 2) developed and published a hierarchical estuarine ecosystem classification system (CREEC) in which to base sampling designs and habitat restoration strategies; 3) mapped over 19,000 acres of high and medium priority shallow water bathymetry gaps; 4) mapped land cover of the lower river floodplain in 2000 and 2010; 5) collected water chemistry data and juvenile salmonids to support the creation of three models related to salmonid uptake, transport, and ecological risk of toxic contaminants; 6) collected habitat structure data at 28 sites and comprehensively monitored 22 sites throughout the lower river for habitat structure; salmon occurrence, diet, condition, stock, and growth; prey availability and preference, providing in some areas the only contemporary juvenile salmon use data available; 7) initiated the characterization of the salmon food web at six “trend” sites representing the estuarine-tidal freshwater gradient; 8) collected abiotic environmental/water column condition data at trend sites annually; 9) installed and maintained a CMOP Land Ocean Biogeochemical Observatory (LOBO) platform above the Willamette River confluence with the Columbia to better understand influence of Willamette biogeochemistry on mainstem conditions and 10) provided technical assistance to the USACE in creation of a terrain model of the lower river, resulting in a seamless bathymetry/topography map which will be invaluable in mapping salmon habitat opportunity in combination with river flow data.  

In addition, NPCC/BPA funding  provides leverage that allowed the Estuary Partnership to accomplish these additional estuary RME-related activities: 1) convened five technical workshops for researchers and managers on topics of interest such as land cover, bathymetry, toxic contaminants, and restoration; 2) provided monitoring coordination for entities involved in monitoring the lower river, exemplified by the estuary RME coordination meeting in spring 2010, 2011 and 2012 involving NMFS, PNNL, CREST, USACE, BPA, LCRFB and others; 3) compiled information and presented overviews of on-going monitoring activities at various events, including the Estuary and Ocean Subgroup, EPA Toxics Reduction Working Group; and regional and national conferences; 4) played a key role in efforts supporting regional monitoring coordination, including Pacific Northwest Aquatic Monitoring Partnership’s Integrated Status and Trends Monitoring group, an inventory of on-going effectiveness monitoring at restoration sites, and refinements to standardized protocols for restoration effectiveness monitoring; 5) acted as a central clearinghouse for GIS data while developing mapping website to house monitoring data collected in estuary; 6) supported on-going regional toxic contaminants reduction efforts, such as preparing the State of the River Report, presenting monitoring information at the workshops, developing a basin-wide contaminant monitoring strategy with EPA's Toxics Reduction Workgroup, and supporting the institution of an Oregon Drug Take Back Program; 7) presented monitoring efforts at several regional and national conferences, including the Coastal and Estuarine Research Federation and National Conference on Ecosystem Restoration, 2012 National Water Quality Monitoring Conference and the 2012 Columbia River Estuary Conference; 8) chaired an all-day session on monitoring and restoration efforts in Pacific Northwest estuaries at the 2009 Coastal and Estuarine Research Federation conference with co-chairs, PNNL and South Slough National Estuarine Research Reserve and 9) participated in regional forums, such as Pacific Estuarine Research Federation (PERS), NANOOS, American Fisheries Society, and Pacific Joint Venture, to share information and coordinate RME and restoration efforts. Information exchanged and gained and networking with other researchers doing related work during these events provides invaluable insight and guidance for future RME and restoration efforts in the lower river.

Current Work -
In 2015 PNNL will collect data on wetland vegetation species, elevation, peak macrophyte biomass, and water stage at the six trend sites. NOAA Fisheries will monitor salmon, salmon prey and foodweb resources (i.e., phytoplankton and zooplankton), at these sites to provide information on juvenile salmon use of the vegetated and shallow water habitats of the lower Columbia River. NOAA Fisheries will process salmon samples for stock, growth rates, stomach contents, and fish condition and send zooplankton samples to OHSU for processing and identification. USGS will collect data at four of the six “trend” sites to characterize the foodweb resources supporting juvenile salmonids, specifically primary productivity and stable isotope analysis, and deploy probes to monitor the water column for parameters relevant to salmonids (e.g., temperature and dissolved oxygen). USGS will send phytoplankton samples to OHSU and macroinvertebrate benthic cores to UW for processing and taxonomic identification. NOAA will continue to operate and maintain a PIT tag array at Campbell Slough to assess salmon residency in floodplain habitats. Additionally, OHSU will continue to maintain the CMOP LOBO Platform in the tidal freshwater section of the lower river for another year. Through this project, researchers will track and report on 1) seasonal primary production biomass and taxonomy for lower river from Bonneville to plume; 2) sources of dissolved organic carbon, turbidity and nutrients in tidal freshwater and estuarine sections of lower river; and 3) water temperatures, pH, dissolved oxygen levels in tidal freshwater and estuarine (except pH) sections of lower river. The Estuary Partnership Science Work Group will review the data on a periodic basis and recommend possible research studies to address key questions as they arise.

The Estuary Partnership is currently developing an estuarine condition index to provide a framework for illustrating and reporting ecosystem conditions, how they are changing over time, and management implications to the public, scientists and managers. This indicator system will use the US Environmental Protection Agency’s Biological Condition Gradient (BCG) framework (Davies and Jackson 2006). As this indicator system and numeric management targets are developed, they will be integrated into the Greater Ecosystem Restoration Program, including the monitoring design of the EMP.

Critical Uncertainties Research - In September 2013, BPA asked the Estuary Partnership to develop and carry-out a scientific study aimed at addressing an ERTG uncertainty (see ERTG Uncertainties #2012-02, version 6/19/12). This request reduced the EMP budget for status and trends work for one year, and redirected it to this study. The study investigates the question “What are the effects of aquatic invasive species on food webs supporting juvenile salmon?” from the “Riparian Habitats” topic (p.4 of the ERTG Uncertainties document).  The study addressed the questions:  1) Are there significant differences between the macroinvertebrate community structure or availability and biomass of important juvenile salmon prey taxa in vegetation patches dominated by the invasive plant species Phalaris arundinacea and the native plant species Carex lyngbyei, and 2) does the supply, quality or retention of macrodetritus differ significantly between patches of these two vegetation types?

Based on funding, this was designed as a one-year study with University of Washington and PNNL. The sampling strategy involves a paired site approach to assess differences in macroinvertebrates and macrodetritus between these two vegetation types. In order to answer the above questions, we compared the following variables in emergent wetland vegetation patches dominated by either P. arundinacea or C. lyngbyei in the lower river:
o macroinvertebrates (community, biomass, and the abundance of Diptera and other important salmon prey);
o plant structure (composition, cover, and substrate);
o food resources (macrodetritus quantity and quality); and,
o macrodetritus production and export (biomass)

Using the following methods:
UW
• Sample the macroinvertebrate community during three time periods (April, May and June) in each ‘patch’ with three different macroinvertebrate sampling methods: fall-out traps to sample the terrestrial insect community, emergent traps to sample the emerging aquatic insects and benthic cores to sample the larval stage of invertebrates, in the benthic community.
• Identify insects collected by each sampling method, to Order and potentially family. Enumerate densities of top salmon prey taxa (Diptera, Amphipoda).
• Weigh macroinvertebrates from each sample to assess biomass of salmon prey
• Identify the macroinvertebrates (to order, potentially family) that colonize each leaf litter bag for two time periods (bags collected in June and August) and weigh for biomass
• Statistical analyses and reporting

PNNL
• Measure composition, percent cover of vegetation, and sediment structure within each ‘patch’
• Assess the quantity (dry weight) of detritus at the time of invertebrate sampling to understand macrodetritus available to macroinvertebrates, particularly salmon prey.
• Assess the quality of detritus (C: N ratio) at the time of invertebrate sampling to understand the quality of detrital food resources that are available to macroinvertebrates, particularly salmon prey.
• For leaf litter bags collected on two occasions, assess the change in detrital biomass over time for both vegetation types (P. arundinacea and C. lyngbyei), change in biomass of each vegetation type that is due to macroinvertebrate consumption, and the change in quality of each vegetation type over time
• Assess the quantity of plant biomass in summer and winter to quantify the contribution of organic matter from these habitats to the wetland and to the mainstem ecosystem.
• Statistical analyses and reporting

Action Effectiveness Monitoring and Research Program
The Action Effectiveness Monitoring and Research program (AEMR) was transferred from the Habitat Restoration Program contract (2003-11-00) to this contract in fiscal year 2013. Since summer 2008 the Estuary Partnership and partners have implemented action effectiveness monitoring based on recommendations from the plan for “Research, Monitoring, and Evaluation for the Federal Columbia River Estuary Program” (Johnson et. al 2008). The Estuary Partnership, with input from the Estuary and Oceanic Subgroup (EOS) and Science Work Group, identified four pilot sites (Mirror Lake, Sandy River Delta, Scappoose Bottomlands, and Fort Clatsop). Sites were chosen to represent different restoration activities (culvert enhancement to improve fish passage; large wood installation; re-vegetation and cattle exclusion; and culvert removal for tidal reconnection), different habitats (bottomland forest, riparian forest, emergent wetland, and brackish wetland), and different geographic reaches of the river (reaches H, G, F, and A, ranging from tidal freshwater in reach H, the Columbia River Gorge, to saltwater intrusion in reach A, Astoria area). Action effectiveness monitoring partners are implementing the Roegner et al. (2009) protocols, which were designed for estuary-wide action effectiveness research, and are collecting data on parameters such as water quality, sediment accretion, channel cross-sections, vegetation cover, vegetation planting success, salmon, and salmon prey. Action effectiveness monitoring occurred at these sites from 2007-2013, except for the Scappoose Bottomlands site, which was not repeated in 2013 as a result of access issues with the private landowner. Also, NOAA Fisheries installed a pit tag array at the Horsetail Creek restoration site for baseline data collection in 2013; construction at this site occurred in summer 2013. The pit tag array will continue collecting post construction AEM data through 2015.

Applications of Results to Management –
The AEMR Program provides information about the efficacy of restoration actions in the tidally influenced areas of the lower Columbia River and estuary.  AEMR data shows a quantifiable change in ecosystem condition related to specific restoration actions and helps determine if restoration actions are meeting project sponsors objectives and goals.  The standardization of monitoring metrics allows the efficacy of restoration actions to be compared across the landscape to help determine the cumulative effects of restoration efforts.  

Past Results-
AEMR conducted from 2007-2013 demonstrated the need for standardized monitoring metrics, a site prioritization strategy, and an increase in the amount of sites monitored.  The development of “Protocols for Monitoring Habitat Restoration Projects in the Lower Columbia River and Estuary” (Roegner et al. 2009) in 2007 and revised in 2009 provided a framework for the when, where, why, and how of action effectiveness monitoring.  In addition, the Estuary Partnership has added the Roegner et al. protocols to monitoringmethods.org to promote access and sharing.  In 2009, researchers from PNNL, Estuary Partnership, NOAA, USACE and CREST, compiled AEMR data from multiple restoration sites in a pilot meta-analysis for the USACE Cumulative Effects of Restoration project.  Also, the standardization of AEMR methods allowed data collected at restoration and EMP sites to be compared (Borde et al. 2012).  Based on lessons learned, the Estuary Partnership with BPA, USACE, and PNNL developed “A Programmatic Plan for Restoration Action Effectiveness Monitoring and Research in the Lower Columbia River and Estuary” (Johnson et al. 2013) to improve and standardize AEMR site selection, create different levels of monitoring effort (Standard, Core, and Intensive) for AEMR, and designate how AEMR levels will be determined.  
  
Current work-
In 2013 and 2014 the Estuary Partnership began implementing  the new programmatic AEMR plan. The Estuary Partnership, BPA and US Army Corps of Engineers (USACE), used the programmatic AEMR prioritization process in Johnson et al. (2013) to identify four sites (Kandoll Farm Phase 2, Steamboat Slough, Sauvie Island North Unit, and Dibblee Point) for Level 2 monitoring in 2013. In 2014, we collected Level 2 AEMR data at 5 sites (Kandoll Farm Phase 2; Sauvie Island North Unit Phases 1 and 2; Wallacut Slough; Sandy River Delta). Along with these restoration sites, nearby reference sites were identified and monitored to create a pair of sites to ensure the requirements for a Before After Control Impact (BACI) statistical design were met. AEMR monitoring at restoration and reference sites included characterizing vegetation, sampling macroinvertebrate communities, and collecting channel cross sections and was preformed prior to restoration actions to capture pre-restoration ecological conditions. AEMR project partners CREST and PNNL conducted monitoring using the Roegner et al. (2009) protocols, which are designed for estuary wide action effectiveness monitoring and research. Standardized data collection also ensures data collected for the AEMR program is compatible with data collected under the Ecosystem Monitoring Program.

In addition to Level 2 monitoring, the Estuary Partnership coordinated with project sponsors collecting Level 3 AEMR to ensure standardized protocols in sampling design and metrics are being used (water elevation, water temperature, sediment accretion, and photo points) at all restoration sites receiving BPA funding. This coordination role included hosting a 2-day workshop with project sponsors and working with them to develop site sampling plans for each site.

WORK ELEMENTS FOR OCTOBER 1, 2014 TO SEPTEMBER 30, 2015
During the upcoming contract period, for the EMP PNNL, NOAA Fisheries, USGS, OHSU, and CREST will implement the FY2015 EMP monitoring work. In FY 2015 PNNL, NOAA Fisheries, OHSU and USGS will collect co-located data at six “trend” stations:
1. Campbell Slough (monitored since 2007)
2. Franz Lake (monitored in 2008- 2009 and 2011- 2013)
3. Whites Island (monitored since 2009)
4. Baker Bay (monitored since 2011)
5. Secret River (monitored since 2012) and
6. Welch Island (monitored since 2012).

In 2015 PNNL will collect data on wetland vegetation species, elevation, peak macrophyte biomass, and water stage at the 6 trend sites. NOAA Fisheries will monitor salmon, salmon prey and foodweb resources (i.e., phytoplankton and zooplankton), at these sites to provide information on juvenile salmon use of the vegetated and shallow water habitats of the lower Columbia River. NOAA Fisheries will process salmon samples for stock, growth rates, stomach contents, and fish condition and send zooplankton samples to OHSU for processing and identification. USGS will collect data at four of the six “trend” sites (1-4 above) to characterize the foodweb resources supporting juvenile salmonids, specifically primary productivity and stable isotope analysis, and deploy probes to monitor the water column for parameters relevant to salmonids (e.g., temperature and dissolved oxygen). USGS will send phytoplankton samples to OHSU and macroinvertebrate benthic cores to UW for processing and taxonomic identification. NOAA will continue to operate and maintain a pit tag array at Campbell Slough to assess salmon residency in LCRE floodplain habitats. Additionally, OHSU will continue to maintain the CMOP LOBO Platform in the tidal freshwater section of the LCRE for another year to better understand influence of Willamette biogeochemistry on mainstem conditions. Through this LOBO platform, researchers will track and report on 1) seasonal primary production biomass and taxonomy for lower river from Bonneville to plume; 2) sources of dissolved organic carbon, turbidity and nutrients in tidal freshwater and estuarine sections of lower river; and 3) water temperatures, pH, dissolved oxygen levels in tidal freshwater and estuarine (except pH) sections of lower river. The Estuary Partnership Science Work Group will review the data on a periodic basis and recommend possible research studies to address key questions as they arise.

The Estuary Partnership will also build upon previous AEMR efforts by continuing the collection of Level 2 AEMR data  at four to six sites to be identified by the AEMR Steering Committee (Estuary Partnership, BPA and USACE). The Estuary Partnership will also continue coordinating Level 3 data collection efforts of restoration project sponsors, including undertaking field quality assurance audits. The Estuary Partnership will also compile and quality check all Level 3 data prior to uploading it to the USACE Oncor database, when the database becomes available.

In addition to coordinating activities and on the ground work relevant to the EMP and AEMR, we will coordinate with the Pacific Northwest Aquatic Monitoring Program (PNAMP), Estuary Ocean Subgroup (EOS), researchers for the USACE Anadromous Fish Enhancement Program (AFEP), and the states’ recovery programs to ensure coordination, build monitoring efficiencies, and to increase the consistency of monitoring and sampling protocols used in the LCRE. We will also participate in the AFEP work to build a central RME database for the LCRE so that our data is accessible and usable to interested parties.

2014-2015 OBJECTIVES FOR THE ECOSYSTEM MONITORING and ACTION EFFECTIVENESS MONITORING AND RESEARCH PROGRAMS INCLUDE:
1. Monitor habitat, abiotic environmental conditions, food web resources, and salmonids at 6 “trend” sites within tidally influenced wetlands of the LCRE.
2. Continue maintenance and data collection at the CMOP LOBO Platform in the tidal freshwater section of the LCRE as well as annual reporting of food web conditions within the entire mainstem LCRE.
3. Collect pre and post construction Level 2 AEMR data at priority restoration sites, identified in summer 2014 by the AEMR Steering Committee, and, as funding allows, expand collection (pre-construction) to new priority restoration sites.
4. Coordinate Level 3 AEMR data collection and management with project sponsors (CREST, CLT, Cowlitz Indian Tribe, WDFW), including field quality assurance audits.
5. Analyze and report results of reed canarygrass and macroinvertebrate critical uncertainties study.
6. Develop an Annual Report detailing the results.