This FY2015 Statement of Work and Budget is part of the Lower Columbia Estuary Partnership  Ecosystem Monitoring Program


Date of Submission:  July 2014

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 Geological 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.  

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.

WORK ELEMENTS FOR OCTOBER 1, 2014 TO SEPTEMBER 30, 2015
This statement of work describes the work elements, deliverables, and costs for work efforts that USGS will implement from October 1, 2014 to September 30, 2015 as part of the Estuary Partnership’s Ecosystem Monitoring Program.

Under the Estuary Partnership Ecosystem Monitoring Project, there are six “trend” core stations (Ilwaco, river kilometer [rkm] 6; Secret River, rkm 37; Welch Island, rkm 53; Whites Island, rkm 72; Campbell Slough at Ridgefield National Wildlife Refuge, rkm 149; Franz Lake at Franz Lake National Wildlife Refuge, rkm 221) monitored for wetland habitat conditions, food-web resources and salmonid presence and abundance. In 2015, USGS shall monitor four of the six sites (Ilwaco, Whites Island, Campbell Slough at Ridgefield National Wildlife Refuge, and Franz Lake at Franz Lake National Wildlife Refuge). USGS shall deploy a monitoring sonde at each of these four sites to collect continuous water-quality data relevant to salmonids (water temperature, dissolved oxygen, pH, and specific conductance) from April through July, 2015. USGS shall use this information to characterize abiotic water-column conditions, factors limiting primary productivity, and food-web resources during times when juvenile salmonids are present.

USGS shall assess food-web resources supporting juvenile salmonids at the four “trend” stations. The assessment shall occur three times between April and July with sampling occurring before, during and after the freshet. The assessment shall include measurements of biomass and net productivity of phytoplankton (free-floating algae) and periphyton (attached algae), stable-isotope analysis of plants, insects, and fish tissues collected by USGS and NOAA Fisheries to identify the relative importance of different compartments within the overall food web, and measurements of habitat conditions and nutrient concentrations. Additionally, USGS shall collect phytoplankton, zooplankton, chlorophyll a, and nutrient samples for Oregon Health Sciences University (OHSU). USGS shall implement these data-collection activities in close coordination with other estuary Research, Monitoring and Evaluation projects.

Sampling and Processing Protocols for Food-Web Resources
USGS shall collect the following samples for each site:
• Obtain samples from each location for phytoplankton net primary productivity measurement and species identification.  
• Collect individual 1 liter samples at each location, composite water from each 1 liter sample into a plastic churn, obtain three samples from churn for phytoplankton net primary productivity measurement and add 13C solution to each phytoplankton net primary productivity sample and incubate in-situ for three hours. Obtain samples for particulate organic matter analysis, nutrient analysis, phytoplankton biomass analysis (chlorophyll a [chl a] and Ash Free Dry Mass [AFDM]) and inorganic carbon analysis. Retrieve phytoplankton net primary productivity samples and filter onto glass-fiber filters.
• Collect representative periphyton samples at each station.
• Preferably taken from submerged rocks or from other substrates (e.g., fines or wood). Protocol will be modified to account for site conditions.
• Composite and filter into one sample for periphyton biomass (chl a and AFDM).
• Deploy periphytometers and retrieve after two weeks.
• Obtain samples for net primary productivity analysis.
• Measure habitat and field parameters, including air temperature, ambient photosynthetically active radiation through water column, water depth and substrate type.
• Obtain fresh macrophyte, dead/dying macrophyte, invertebrate samples, composite as needed and preserve for stable-isotope analysis (five samples for each potential salmon food source). Obtain fish tissue samples from NOAA Fisheries, process, and submit samples for stable-isotope analysis.
• Collect three benthic cores from each site for the identification of species present. Preserve a portion for stable-isotope analysis from each core.
• Collect quality-control samples (blanks and replicates) as directed by the project quality-assurance plan.
• Deliver samples to appropriate laboratories for processing, including University of California in Davis, California, for stable-isotope and 13C analyses, Oregon Health Sciences University for phytoplankton-species identification, nutrient, chl a, and AFDM analyses, and University of Washington for benthic invertebrate identification.

USGS shall provide data files and a summary report (describing collection methods, data analyses, and results) in electronic file format to the Estuary Partnership. USGS’s summary report shall serve as their annual-report contribution to the Estuary Partnership. USGS will provide the results of food web sampling (listed in Sampling and Processing Protocols for Food-Web Resources section above) to OHSU for inclusion in the Annual Report contribution. OHSU will perform statistical analyses and write-up results for inclusion in the Annual Report. Novel analyses shall be discussed and agreed upon by the Estuary Partnership and USGS at a 2014 meeting with NOAA, OHSU and PNNL. The Estuary Partnership will compile Contractor’s portion of the Annual Report with sections by the other contractors (OHSU, PNNL, and NOAA). Contractor shall make the data available on the internet.

Specifically, the objectives for USGS’s contribution to the Ecosystem Monitoring Program in 2014-2015 include the following:
1. Collect abiotic environmental conditions and elements of food web characteristics at four “trend” sites that will be jointly assessed for fish and habitat condition by NOAA Fisheries and PNNL, respectively.
2. Provide data, analyses and report contributions to the Estuary Partnership on monitored indicators for the Estuary Partnership’s annual report to BPA.
3. Provide data, analyses and report contributions for an annual report of data collected between 2013 and 2014.
4. Participate in Science Work Group meetings and a food web meeting (with PNNL, NOAA,UW and OHSU) and other discussions on refining the EMP design.
5. Participate with Estuary Partnership and others in discussions on data management and exchange.