BPA Project Number:  2003-007-00
CR-209217
Performance/Budget Period: October 1, 2011 – September 30, 2012

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

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

BPA Project Manager:  Russell Scranton
Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  (503) 230-4412
Fax:  (503) 230-4564
rwscranton@bpa.gov

BACKGROUND

Understanding of the relationships between salmonids and their habitat in the lower Columbia River and estuary (LCRE) is hindered by substantial data gaps, including the following:
1. specific (especially shallow-water) habitats used by salmon during rearing and outmigration;
2. effects of physiochemical and biological conditions on estuarine residence times, growth, or survival of juvenile salmon;
3. food-chain relationships (feeding and predation) among juvenile salmon, invertebrate prey, and vertebrate predators; and
4. differences in estuarine habitat needs and ecological relationships among salmon species, life history types, and source populations (Bottom et al., 2005).

The Lower Columbia River Estuary Partnership (Estuary Partnership) will implement elements of its Ecosystem Monitoring Program to provide information on salmonids and their habitat in the LCRE and address data management needs. This project builds on our previous projects under Bonneville Power Administration funding that created and began an ecosystem based monitoring program focused on improving the survival of juvenile salmonids through the LCRE. This project will continue to comprehensively assess habitat, fish, food web and abiotic conditions in the lower river, focusing on shallow water and vegetated habitats used extensively by juvenile salmonids for rearing and refugia.

This statement of work describes the work elements, deliverables, and costs for Ecosystem Monitoring Project (EMP) efforts that will be implemented from October 1, 2011 to September 30, 2012.


REVIEW OF PRIOR WORK

During September 1, 2003 to August 31, 2004, this contract was placed on hold for the majority of the contract year due to the Northwest Power and Conservation Council's (NPCC) request for further review by their Independent Scientific Review Panel (ISRP). After the ISRP completed their review, three months remained in the contract year to complete the work. Thus, a number of tasks were delayed and completed during September 1, 2004 to August 31, 2005.

The original design of the EMP that was reviewed by the ISRP was designed to capture status and trends of habitat opportunity and capacity for ESA listed species using a rotational panel design. Rotational panel designs allow more sample sites than other designs given a limited budget and a greater ability to detect change over time. The EMP design called for eight fixed sites (one per Hydrogeomorphic Reach) and twelve additional sites randomly distributed within Reaches C-E. Monitoring analytes included primary and secondary production; water quality (including nutrients, carbon, suspended sediment, and field parameters such as pH, dissolved oxygen, conductivity, and temperature); vegetation structure, species composition, elevation and sediment characteristics along elevation gradients; juvenile salmon health and occurrence at a variety of habitats; and salmon prey information. However, due to limited financial resources, the EMP design was modified to generally include two fixed vegetation stations in Reach F (where fish and water quality were monitored at one of those fixed stations) and four-five additional sites within one river reach which in turn rotated annually between Reaches C-H. In addition, sampling for primary and secondary productivity, nutrients, and carbon was eliminated from the contract.

From September 1, 2004 to August 31, 2005, this contract facilitated the creation of a Columbia River Estuary Ecosystem Classification (Ecosystem Classification) by the University of Washington (UW) and the U.S. Geological Survey (USGS). The Ecosystem Classification was developed to support monitoring, research, and restoration efforts because no existing ecosystem classification was applicable to the lower Columbia River estuary due to its large tidal-freshwater portion. UW and USGS derived the Ecosystem Classification from LANDSAT TM imagery and bathymetry data. They then used the Ecosystem Classification to locate sampling sites for habitat monitoring in the LCRE. During July 2005, Battelle/Pacific Northwest National Laboratories (PNNL) collected biological and habitat data in Reaches D and F of the LCRE using these metrics. NOAA Fisheries developed three contaminant models to assess the sources, pathways, and potential effects of contaminants on salmonids in the LCRE. NOAA Fisheries also monitored fish from March 2005 to August 2005 and incorporated these results into the models. Additionally, USGS conducted fixed station and seasonal variation water quality monitoring, and deployed semipermeable membrane devices (SPMDs) to provide water chemistry data for NOAA Fisheries’ models.

During September 1, 2005 to August 31, 2006, efforts included updates to the Ecosystem Classification. These updates, however, were delayed by the completion of the Light Detection and Ranging (LiDAR) datasets. During July 2006, PNNL conducted habitat monitoring in Reaches G and F and collected data on wetland vegetation species, elevation, and water quality. NOAA Fisheries developed new versions of the three contaminant models and incorporated results from salmon sampling and analyses, which included salmon genetics and exposure to estrogenic compounds. USGS also completed chemical analyses of the water samples from the fixed station and seasonal water quality monitoring and from the SPMDs.

During September 1, 2006 to August 31, 2007, UW refined the Ecosystem Classification with the completed Light Detection and Ranging (LiDAR) and updated bathymetric datasets. The updated Ecosystem Classification guided PNNL’s habitat monitoring efforts in Reaches E and F where they collected data on wetland vegetation species, elevation, and water quality. At this time, USGS was using the Ecosystem Classification to develop a rotational panel sampling design for monitoring efforts during the subsequent three years (September 1, 2008 to August 31, 2011) of the Ecosystem Monitoring Project. Additionally, NOAA Fisheries and USGS completed contaminant analyses of salmon and water samples from prior collection efforts. NOAA Fisheries analyzed salmon samples for contaminants, growth rates, and body condition and analyzed salmon stomach contents for prey taxonomy. They also analyzed sediment samples for contaminants. NOAA Fisheries produced a report detailing the salmon and prey results and used the information to update the three contaminant models. USGS produced a report detailing the water quality results. The Estuary Partnership, NOAA Fisheries, and USGS integrated the salmon, salmon prey, and water quality results into one report that is available on the Estuary Partnership’s website (http://www.lcrep.org/pdfs/WaterSalmonReport.pdf).

During September 1, 2007 to August 31, 2008, UW finalized several GIS layers (diked areas, floodplain boundary, and dredge material/fill) relevant to the Ecosystem Classification. UW and the Estuary Partnership also began preplanning for bathymetry data acquisition. PNNL monitored vegetation and elevation at six sites (two in Reach F and four in Reach H). NOAA Fisheries sampled salmon and salmon prey at five sites (one in Reach F and four in Reach H). USGS deployed probes to monitor the water column for dissolved oxygen, temperature, water-surface elevation, and conductivity at two sites (one in Reach F and one in Reach H) where PNNL and NOAA Fisheries collected vegetation and salmon data, respectively. In lieu of the probabilistic sampling design, USGS collected sediment samples at vegetation and salmon sampling sites, and provided a limited strategy for future sampling efforts that relates number of sites with available financial resources. UW began sampling vegetation, birds, insects, and benthic macroinvertebrates at three sites to characterize the community profile of tidal freshwater riparian and floodplain forested/scrub-shrub wetlands in the LCRE.

During September 1, 2008 to August 31, 2009, the Estuary Partnership coordinated bathymetry data collection in the LCRE and regional monitoring data sharing efforts. UW and USGS further developed the Ecosystem Classification to include criteria based on river geomorphology and hydrology for delineating habitats at smaller spatial scales and developed a draft (intended for a peer-reviewed scientific publication) that describes the Ecosystem Classification’s conceptual basis, methods used to develop datasets, preliminary results, and management applications. PNNL monitored vegetation and elevation at six sites (three in Reach C, two in Reach F, and one in Reach H). NOAA Fisheries sampled salmon and salmon prey at five sites (three in Reach C, one in Reach F, and one in Reach H). USGS deployed probes to monitor the water column for dissolved oxygen, temperature, water-surface elevation, and conductivity at two sites (one in Reach C and one in Reach F) where PNNL and NOAA Fisheries collected vegetation and salmon data, respectively. UW sampled vegetation, birds, insects, and benthic macroinvertebrates at three additional sites to characterize biological communities of tidal freshwater riparian and floodplain forested/scrub-shrub wetlands.

During September 1, 2009 to August 31, 2010, the Estuary Partnership contracted the completion of bathymetry data collection for all high and medium priority data gaps following the strategic plan for bathymetric data collection developed by the Estuary Partnership and UW.  The Estuary Partnership also contracted for the creation of an up-to-date landcover dataset, needed to support the completion of the Ecosystem Classification. UW provided technical assistance in the development of a sampling design to support the on-the-ground data collection of training/ground-truth data so that the final landcover product can best inform the Ecosystem Classification. In support of the Ecosystem Classification, USGS drafted floodplain Complexes (Level 4) and Catenae (Level 5) for most hydrogeomorphic reaches of the LCRE. UW merged these floodplain Complexes with bathymetric Complexes developed by UW. PNNL monitored vegetation and elevation at six sites (four in Reach C, two in Reach F). NOAA Fisheries sampled salmon and salmon prey at five sites (four in Reach C, one in Reach F). USGS deployed probes to monitor the water column for dissolved oxygen, temperature, water-surface elevation, and conductivity at one site (one in Reach F) where PNNL and NOAA Fisheries collected vegetation and salmon data, respectively. USGS also collected primary productivity data at this site for the first time since the inception of the Ecosystem Monitoring Program. UW completed the tidal freshwater forest characterization project by sampling vegetation, birds, insects, and benthic macroinvertebrates at three additional sites and producing a final report that characterizes biological communities of tidal freshwater riparian and floodplain forested/scrub-shrub wetlands.

During September 1, 2010 to December 31, 2011, Sanborn completed a high-resolution land cover mapping effort to support the Classification and regional mapping needs. The Estuary Partnership, UW and USGS completed the Ecosystem Classification including delineations of draft Catena (Level 5) for all reaches rolled up into floodplain Complexes and merged with UW’s bathymetric Complexes (to complete Level 4).  The Estuary Partnership, UW and USGS produced a peer-reviewed report to describe the creation of the Ecosystem Classification (Simenstad et al. In Press). PNNL, NOAA Fisheries, USGS, Oregon Health and Science University (OHSU), and Columbia River Estuary Study Taskforce (CREST) monitored habitat, abiotic environmental conditions, foodweb resources, and salmonids at four “fixed” sites in the lower Columbia River (Campbell Slough in Reach F, Franz Lake in Reach H, Whites Island in Reach C and the new fixed site in Reach A, Baker Bay). In addition, PNNL monitored vegetation (vegetation species, elevation, peak macrophyte biomass and water stage) and NOAA monitored fish (salmon, salmon prey and foodweb resources) at 3 “status” located at Deer Island, Burke Island and Goat Island in Reach F. For the first time, NOAA also began fall fish sampling at all the fixed and status sites. PNNL, NOAA Fisheries, USGS, Environment International (EI) and the Estuary Partnership completed a comprehensive status and trends data analysis for the coordinated vegetation, fish, prey, and water quality monitoring data from all sites between 2005 and 2011. Results were provided in an interpretive report and presented to the Science Work Group in August 2011 for review and comment.

WORK ELEMENTS FOR OCTOBER 1, 2011 TO SEPTEMBER 30, 2012

During the upcoming contract period, PNNL, NOAA Fisheries, USGS, Oregon Health and Science University (OHSU), and Columbia River Estuary Study Taskforce (CREST) will implement the FY2012 monitoring work. In FY 2012 PNNL, NOAA Fisheries, and USGS will collect co-located data at six “fixed” stations:
1. Campbell Slough, which has been monitored yearly since 2007 to assess inter-annual variation in wetland habitat conditions and salmonid presence and abundance;
2. Franz Lake (monitored in 2008, 2009 and 2011)
3. Whites Island (monitored since 2009)
4. Baker Bay (monitored in 2011)
5. and two TBD sites in Reach B
and 3 “status” sites. The “status” sites are located in TBD reaches of the LCRE with data gaps and are determined based on several factors: 1) using the CREEC, landcover maps, and Google Earth, identification of  all potential sites within reaches, 2) elimination of sites being monitored through other estuary RME projects through discussions with managers of other estuary RME projects, 3) incorporation of comments and considerations of the Estuary Partnership Science Work Group, 4) site visits to assess access and feasibility and 5) permission from landowner.

In 2012 PNNL will collect data on wetland vegetation species, elevation, peak macrophyte biomass, and water stage at 10 sites. NOAA Fisheries will monitor salmon, salmon prey and foodweb resources (i.e., zooplankton), at 9 of 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 “fixed” sites to characterize the foodweb resources supporting juvenile salmonids, specifically primary productivity, 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. 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.

Additionally, OHSU will install and operate a Center for Coastal Margin Observation and Prediction (CMOP) LOBO (Land Ocean Biogeochemical Observatory) Platform in the tidal freshwater section of the LCRE for the first time. This new station will provide a high resolution, long term record of key water quality parameters for the assessment of primary production and the factors affecting the productivity of the  entire mainstem lower Columbia River from Bonneville Dam to the coastal ocean. By filling an important spatial data gap (there are no similar stations above Beaver Army Terminal), it will allow the Estuary Partnership to place the findings at the habitat monitoring sites into context with water quality of the mainstem Columbia River. It will also allow the Estuary Partnership to more fully integrate our research of on-going and projected worsening of ocean acidification, warming water temperatures and decreasing dissolved oxygen concentrations associated with climate change into the annual analyses and reporting completed under the EMP. Through this project, researchers will track and routinely report results of the following:
1. Seasonal primary production,  biomass and taxonomic classification for the lower river from Bonneville to the coast
2. Sources and variability of dissolved organic carbon, turbidity and nutrients in tidal freshwater and estuarine sections of lower river
3. Water temperatures,, conductivity, and dissolved oxygen levels in tidal freshwater and estuarine sections of lower river
This information will be key to understanding primary production throughout the lower river and instream processes controlling production and their influences on the dissolved oxygen levels found in the estuary, plume and outer continental shelf of Oregon and Washington.  

Following the completion of the Ecosystem Classification, the Estuary Partnership will contract to develop a refined monitoring design for the EMP. The contracted statistician will combine the ISTM tool developed through PNAMP, and overlay it with the population of interest from the Columbia River Ecosystem Classification (i.e., Ecosystem Complex or Catena). The intent is to develop a spatially balanced design (GRTS design), including a stratified, random selection of core and distributed (panel) sampling locations. In FY2013 and subsequent years, the Estuary Partnership will implement results from the refined monitoring design with a TBD number and location of sampling sites. Along with a refined monitoring design, the monitoring period will be extended to include year-round sampling of fish at selected sites.

In addition to coordinating activities and on the ground work relevant to Estuary Partnership’s EMP, 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.

Finally, the action effectiveness monitoring program was transferred from the Habitat Restoration Program contract (2003-11-00) to the EMP contract during this contract year. The 2008 Draft Biological Opinion includes a Reasonable and Prudent Alternative (RPA) to “evaluate the effects of selected individual habitat restoration actions at project sites relative to reference sites and evaluate post-restoration trajectories based on project-specific goals and objectives” (RPA 60, Appendix A, NMFS, 2008). Since summer 2008 the Estuary Partnership and partners have implemented action effectiveness monitoring that addresses this RPA 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; revegetation 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. During this contract period, action effectiveness monitoring will continue at three of these sites. The Scappoose Bottomlands site will not be repeated this year but the Estuary Partnership will work with the Science Work Group to identify an appropriate replacement site. Also, NOAA Fisheries installed a pit tag array at the Horsetail Creek restoration site for baseline data collection; monitoring of readers will continue through this contract period.

2011-2012 OBJECTIVES FOR THE ECOSYSTEM MONITORING PROJECT INCLUDE:
1. Coordinate on-going monitoring efforts in the LCRE with partners through facilitating annual estuary RME coordination meetings and the Science Work Group and participating in PNAMP
2. Monitor habitat, abiotic environmental conditions, foodweb resources, and salmonids at 6 “fixed” sites and 3 “status” sites within tidally influenced wetlands within TBD reach(es) of the LCRE
3. Install and operate a CMOP LOBO Platform in the tidal freshwater section of the LCRE
4. Develop and implement revised sampling design using the ISTM master sample tool from PNAMP and the Columbia River Estuary Ecosystem Classification
5. Evaluate the effects of selected individual habitat restoration actions at project sites relative to reference sites and evaluate post-restoration trajectories based on project-specific goals and objectives.
6. Develop Annual Report detailing the results of Objectives 1-5