Ecosystem Monitoring Program
BPA Project Number:  2003-007-00
CR-265807
Performance/Budget Period: October 1, 2013 – September 30, 2014

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:  Julie Doumbia
KEWR-4, Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  (503) 230-7641
jadoumbia@bpa.gov

SUMMARY

Ecosystem Monitoring Program
The Ecosystem Monitoring Program (EMP) is an integrated status and trends program. The overall objectives of the EMP are to track trends in the overall condition of the lower river, provide a suite of reference sites for use as end points in the region’s restoration actions, and place results of findings into the context with the larger ecosystem. The EMP specifically collects status and trends data on the following:
• Salmonid occurrence, diet, condition and residency at shallow water and vegetated sites in the mainstem and tributary confluences;
• Habitat structure, including physical, biological and chemical properties of these habitats;
• Food web characteristics, including primary and secondary productivity at these habitats and in the mainstem lower river and
• provides information allowing other researchers to assess the biogeochemistry of tidal freshwater region of the lower river to the biogeochemistry of the estuary, which is key in tracking ocean acidification and climate change impacts on estuary habitat capacity.

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 makes 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.    

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 3 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 6 “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 5 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 provide invaluable insight and guidance for future RME and restoration efforts in the lower river.

Current Work -
In 2014 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 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 CREST 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. 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.

Action Effectiveness Monitoring and Research Program
The AEMR program 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 4 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 will occur in summer 2013.

Applications of Results to Management –
The AEMR Program provides information about the efficacy of restoration actions in the tidally influence 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 the Estuary Partnership initiated implementing the pilot phase of the new programmatic AEMR plan. Work included post restoration action effectiveness monitoring of sites with core (Level 2) pre-restoration monitoring in 2013. Coordination with project sponsors will continue to collect standard (Level 3) post monitoring metrics and work to establish data transfer protocols to improve the movement of data from the field to applicable databases. In addition, the AEMR programmatic plan will be evaluated to apply lessons learned and improve aspects of site prioritization and AEMR level assignment.

BACKGROUND FOR EMP AND AEMR PROGRAMS
Since 1991, 13 different evolutionarily significant units (ESUs) of anadromous salmonids that reproduce in the Columbia River basin have been listed as threatened or endangered under the Endangered Species Act (ESA) of the United States. These include steelhead (Oncorhynchus mykiss), chum salmon (O. keta), Chinook salmon (O. tshawytscha), lower Columbia River coho salmon (O. kisutch), and sockeye salmon (O. nerka) populations that spawn from the upper Snake River basin to tributaries of the lower river below Bonneville Dam. NMFS uses 4 viable salmonid population (VSP) performance criteria to define the viability status of salmonids: abundance, productivity, spatial structure, and diversity; all 4 of these VSP criteria are critical to salmon recovery and are interrelated (Fresh et al., 2005). NMFS recommends that the lower Columbia River and estuary contributes to the viability and persistence of all anadromous salmonid populations within the Columbia River Basin in the following ways: 1) the amount of estuarine habitat that is accessible affects the abundance and productivity of a population; 2) the distribution, connectivity, number, sizes, and shapes of estuarine habitats affect both the life history diversity and the spatial structure of a population; and 3) attributes of estuarine habitats (e.g., temperature and salinity regimes, food web interactions) affect diversity and productivity of populations (Fresh et al., 2005). Diverse habitats and the expression of life history strategies based on use of these habitats are directly linked to salmon population viability (i.e., persistence) over long time scales (McElhany et al., 2000). The Independent Scientific Review Panel (ISRP) for the Northwest Power Conservation Council (NPCC) concluded that estuary and ocean dynamics help control salmon productivity (Beamish and Bouillon, 1993; Beamish et al., 1999) and salmon biodiversity (including the diversity of life history strategies) helps reduce impacts from changing ocean and other conditions (ISG, 2000). Hence, changes to the estuarine ecosystem such as degradation and loss of estuarine habitat, can directly alter salmonid population viability.

Estuaries in general are presumed to offer 3 advantages to juvenile salmon in their transition from freshwater to saltwater environments: 1) a productive feeding area capable of sustaining increased growth rates; 2) a temporary refuge from marine predators; and 3) a physiological transition zone where fish can gradually acclimate to saltwater (Simenstad et al., 1982; Thorpe, 1994). All anadromous salmon and steelhead populations within the Columbia River Basin utilize the estuary as a critical migration corridor. In addition, research has well documented that Chinook salmon, especially subyearlings, and other salmon such as chum and coho to a lesser degree, can rear extensively in shallow water and vegetated habitats within the estuary, including tidal channels, tributary confluence and nearshore areas (e.g., Bottom et al., 2005; Fresh et al., 2005; Good et al., 2005; Fresh et al., 2006; Bottom et al., 2007; Roegner et al., 2008; Casillas, 2009). Subyearling migrants that enter the estuary as fry or fingerlings, or “ocean-type” salmon, exhibit a wide range of residence periods depending on the species, from days to weeks (chum) to several months (Chinook) (Thorpe, 1994). Juvenile salmon may occur in the estuary all year, as different species, size classes, and life history types continually move downstream and enter tidal waters from multiple upstream sources (Bottom et al., 2005). Peak estuarine migration periods vary among and within species, suggesting that different life history strategies may provide a mechanism for partitioning limited estuarine habitats (Myers and Horton 1982). In the Columbia River estuary, subyearling Chinook salmon are most abundant from March through September but are present all year (Rich, 1920; McCabe et al., 1986).

Because of the increasing awareness of the importance of the Columbia River estuary within salmonid life cycles, protection and restoration of important salmonid habitats within the estuary has been identified as a priority for salmon recovery. In addition, in life stage risk and sensitivity modeling, Kareiva et al. (2000) and McClure et al. (2003) found that to recover salmonid populations in the Columbia River Basin additional actions above and beyond passage improvements at the Federal Hydropower System dams were needed and that the life stages for rearing in the river, estuary and ocean were sensitive to disturbances (cited in Fresh et al., 2005). Kareiva et al. (2000) concluded that the maximum potential to contribute to anadromous salmonid recovery was associated with these life stages (Fresh et al., 2005). The questions of how much restoration will be necessary or which types of restoration are most beneficial for recovery within the estuary still exist.

The challenges of identifying, designing, implementing, and evaluating recovery actions in the estuary are significant, in part because managers know relatively little about the region and salmon habitat use patterns within it (Fresh et al., 2005). Recent past and ongoing RME efforts such as this project and the NMFS and PNNL projects funded by the USACE through the Anadromous Fish Evaluation Program: 1) “Estuarine Habitat and Juvenile Salmon: Current and Historical Linkages in the Lower Columbia River and Estuary 2002-2008”, 2) “Multi-Scale Action Effectiveness Research in the Lower Columbia River and Estuary” and 3) “Evaluation of Life History Diversity, Habitat Connectivity, and Survival Benefits Associated with Habitat Restoration Actions in the Lower Columbia River and Estuary” continue to expand our knowledge base. But many of our decisions are still based on conceptual ideas or assumptions (Fresh et al., 2005). In addition, the lower river is among the most heavily modified portions of the Columbia Basin (Thomas, 1983) due to the long history of coastal development and the cumulative effects of flow regulation, channel maintenance, habitat modification, and other changes upriver which have altered sediment transport, floodplain inundation patterns, and salinity regimes in the system (Simenstad et al., 1992; Weitkamp, 1994). Since the mid-1800s, these and other changes have decreased the amount of some types of wetland habitats in this region by as much as 70% from historical levels (Estuary Partnership 2012).

The Estuary Partnership implements the EMP and AEMR to provide information on salmonids, the benefits they derive from estuarine habitats, and effectiveness of restoration actions at restoring natural processes and reference conditions, as well as address regional data management needs. This statement of work describes the work elements, deliverables, and costs for EMP and AEMR efforts that will be implemented from October 1, 2013 to September 30, 2014.

REVIEW OF PRIOR WORK

For previous contracts (2004-2012), please see past annual reports.

During October 1, 2012 through September 30, 2013, for the EMP, PNNL, NOAA Fisheries, USGS, OHSU, and CREST monitored habitat, abiotic environmental conditions, food web resources, and salmonids at six “trend” sites in the lower Columbia River (Campbell Slough in Reach F, Franz Lake in Reach H, Whites Island in Reach C, Baker Bay in Reach A and Secret River and Welch Island in Reach B). USGS collected food web and abiotic conditions at the first four sites only due to cost considerations. OHSU continued 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. The Estuary Partnership and monitoring partners completed the program synthesis for years 2005-2010 (Sagar, J.P., A. B. Borde, L.L. Johnson, C. A. Corbett, J. L. Morace, K. H. Macneale, W.B. Temple, J. Mason, R.M Kaufmann, V.I. Cullinan, S. A. Zimmerman, R. M. Thom, C.L. Wright, P.M. Chittaro, O. P. Olson, S. Y. Sol, D. J. Teel, G. M. Ylitalo, N.D. Jahns. 2013. “Juvenile Salmon Ecology in Tidal Freshwater Wetlands of the Lower Columbia River and Estuary: Synthesis of the Ecosystem Monitoring Program, 2005–2010”, Prepared by the Lower Columbia Estuary Partnership for the Bonneville Power Administration, April, 2013, Available from the Lower Columbia Estuary Partnership, Portland, OR.)

During October 1, 2012 through September 30, 2013, AEMR was transferred from the Habitat Contract (#2003-11-00) to the Monitoring Contract (#2003-007-00). The Estuary Partnership installed and maintained a Pit Tag array at the Horsetail Creek restoration site to collect baseline fish use and residency data. The Pit Tag data will continue to be collected post construction (construction is expected in summer 2013) for a comparison with baseline to test efficacy of fish passage improvements. Additionally, 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 Sandy River Delta) for Level 2 monitoring in 2013. 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 vegetation and macroinvertebrate communities 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 this monitoring, the Estuary Partnership coordinated with project sponsors collecting Level 3 AEMR to ensure standardized protocols in sampling design and metrics (water elevation, water temperature, sediment accretion, and photo points) at all restoration sites receiving BPA funding. In addition, the AEMR programmatic plan (Johnson et al. 2013) was evaluated to identify areas for improvement.

WORK ELEMENTS FOR OCTOBER 1, 2013 TO SEPTEMBER 30, 2014
During the upcoming contract period, for the EMP PNNL, NOAA Fisheries, USGS, OHSU, and CREST will implement the FY2014 EMP monitoring work. In FY 2014 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 2014 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 CREST 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 2013 AEMR data collection to collect post construction Level 2 AEMR data for the four sites (Kandoll Farm Phase 2, Steamboat Slough, Sauvie Island North Unit, and Sandy River Delta) and expand baseline Level 2 data collection at additional restoration 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 all Level 3 data and 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.

2013-2014 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 post construction Level 2 AEMR data at priority restoration sites, identified in summer 2013 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. Conduct a second major EMP synthesis, adding years 2011-2013, to incorporate additional data and food web analyses.
6. Develop an Annual Report detailing the results.

AMENDMENT March 2014
In 2012, the EMP scope was reduced further to monitoring only the 6 trend sites in order to accommodate Action Effectiveness Monitoring in the contract. The six trend sites are: Campbell Slough in the Ridgefield National Wildlife Refuge (2005–2013), Whites Island (2009-2013), and Franz Lake (2008-2009, 2011-2013), Ilwaco (2010-2013), Secret River (2010-2013),  and Welch Island (2010-2013; Figure 1). 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. In September 2013, the 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). The request required a reduction in the EMP budget for status and trends work and redirects it to the 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 changes requested by BPA resulted in the following reductions in the Status and Trends Program in 2014
1. Reduction of Trend sites from 6 to 4, elimination of Reach A site (Ilwaco) and one Reach B site (Secret River).
2. Fish sampling only February-July, November and December
3. Elimination of salmon diet data and analysis of prey availability data at all sites
4. Elimination of habitat and hydrology data collection at all sites
5. Center for Coastal Margin Observation and Prediction (CMOP) biogeochemical will not operate until April
6. Reduction in funding for primary research scientist in lieu of graduate student
7. Reduction in food web data collection--Elimination of primary production growth rates, periphyton sample and growth experiments
The added critical uncertainty study addresses 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 over FY14 and FY15. The sampling strategy involves a paired site approach to assess differences in macroinvertebrates and macrodetritus between these two vegetation types, and adds work by University of Washington and replaces work done by PNNL.