BPA Project Number:  2003-007-00
CR-116983
Performance/Budget Period: September 1, 2009 – August 31, 2010

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:  Tracey Yerxa
Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  (503) 230-4738
Fax:  (503) 230-4564
tyerxa@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 and poor access to existing data. The Lower Columbia River Estuary Partnership (Estuary Partnership) will implement elements of its Ecosystem Monitoring Project to provide information on salmonids and their habitat in the LCRE and address data management needs.  

This statement of work describes the work elements, deliverables, and costs for Ecosystem Monitoring Project (EMP) efforts that will be implemented from September 1, 2009 to August 31, 2010.

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 LCRE Ecosystem Classification System (Ecosystem Classification) by the University of Washington (UW) and the U.S. Geological Survey (USGS). The 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.

WORK ELEMENTS FOR SEPTEMBER 1, 2009 TO AUGUST 31, 2010

During this contract year, the Estuary Partnership will continue coordinating efforts to map the bathymetry of the LCRE following the strategic plan for bathymetric data collection developed by the Estuary Partnership and UW. Additionally, the Estuary Partnership will coordinate efforts to compile landcover data for the LCRE as needed to support the completion of the Ecosystem Classification. UW will provide planning assistance and technical guidance for development of a sampling design to support the on-the-ground data collection, collection of training/ground-truth data collection, and interpretation of landcover imagery so that the final landcover product can best inform the Ecosystem Classification.

The Estuary Partnership will complete bathymetry data collection for all high and medium priority gaps and data processing. They will deliver these data to UW and USGS for incorporation into the Ecosystem Classification. USGS will further develop the Ecosystem Classification by finalizing floodplain Complexes (Level 4). UW will merge these floodplain Complexes with bathymetric Complexes finalized by UW for the entire LCRE. USGS will also provide draft Catena (Level 5) for all or most reaches with UW providing technical guidance. As landcover data become available, USGS, UW, and the Estuary Partnership will complete delineation of Level 5 Catena and Level 6 Primary Cover Class (expected to occur in next year’s contract). UW will incorporate tidal-freshwater wetland monitoring data and GIS layers (diked areas, floodplain boundary, and dredge material/fill), resulting from work in the prior year, into the Ecosystem Classification.

As of November 24, 2009, the anticipated timeline for completing Classification Level 4 (Ecosystem Complexes) is as follows; timeline is formatted as “Approx. Due Date. Task (Lead Entities).”       
Jun 2010. Complete collection of high and medium bathymetric gaps (EP, DEA)
Aug 2010. Process /QA/QC bathymetry layers; deliver to UW on reach-by-reach basis (EP, DEA)
Aug 2010. Produce floodplain Complexes and initial Catena for most LCRE reaches (USGS)
Aug 2010. Produce GIS layers of bathymetric Complexes for most LCRE reaches (UW)
Sept 2010. Review two sets of Complexes; merge Complexes into one dataset (UW, USGS)
Sept 2010. Deliver finalized Complex GIS layer and metadata to EP (UW, USGS)

As of November 24, 2009, the anticipated timeline for completing Classification Levels 5 and 6 is as follows; timeline is formatted as “Approx. Due Date. Task (Lead Entities)”

Sept 2009. Release RFP to select contractor to develop sampling design, coordinate training/ground-truth data collection, and process LandSat images (EP)
April 2010. Collect training data for leaf-off images (train/coordinate volunteers; TBD Contractor)
Aug 2010. Collect training data for leaf-on images (train/coordinate volunteers; TBD Contractor)
Jan 2011. Deliver processed cover classes to EP and UW (TBD Contractor)
Mar 2011. Complete development of initial Catena for LCRE (USGS, if needed)
Apr 2011. Develop draft Level 6 data for use in refining Catena (UW)
Jul 2011. Complete Catena using USGS delineations and acquired cover data (UW, USGS)
Sept 2011. Deliver finalized Catena GIS layer and metadata to EP (UW, USGS)
Mar 2012. Deliver final Classification documentation and data layers

Since the Ecosystem Monitoring budget is not expected to increase substantially over time, funds programmed toward completion of the Classification will limit funding available for on-the-ground monitoring. Like the Classification, on-the-ground monitoring supports the 2008 Biological Opinion and feeds into the development of regional restoration strategies. In particular, on-the-ground monitoring provides critical data on juvenile salmonid stocks and habitat conditions in understudied reaches of the estuary and fills spatial and temporal data gaps. Additionally, on-the-ground monitoring yields reference site data for implementation and evaluation of restoration actions. Due to the estimated costs (~$200,000) of training/ground-truth data collection and processing landcover data as well as costs for the development of the Ecosystem Classification, on-the-ground monitoring actions may be reduced depending on level of funding needed to complete the Ecosystem Classification.

UW, PNNL, NOAA Fisheries, and USGS will implement 2009-2010 monitoring work. UW will conclude field sampling, analyze datasets, and report on the vegetation, avifauna, terrestrial insect, and benthic macroinvertebrate community profiles for freshwater-tidal forested/scrub-shrub wetlands in the LCRE. This data collection by UW will document biological conditions in relatively undisturbed forested wetlands and provide important reference site data for this type of wetland.

The Estuary Partnership will coordinate monitoring partners, PNNL, NOAA Fisheries, and USGS to ensure they collect data at the same set of sites, including one “fixed” station (Campbell Slough which has been monitored yearly to assess interannual variation in wetland habitat conditions and salmonid presence and abundance) and 4 “status” sites (sites located in areas of the LCRE with data gaps). PNNL will collect data on wetland vegetation species, elevation, and water quality at 5-6 sites in TBD reach(es) of the LCRE. NOAA Fisheries will monitor salmon and salmon prey at 5 sites to provide information on juvenile salmon use of the tidal freshwater portion of the Columbia River estuary. NOAA Fisheries will process salmon samples for stock, growth rates, stomach contents, and fish condition. USGS will collect data to characterize the foodweb resources supporting juvenile salmonids in understudied reaches of the LCRE, and deploy probes to monitor the water column for parameters relevant to salmonids (e.g., temperature and dissolved oxygen). PNNL, NOAA Fisheries, USGS, and the Estuary Partnership will synthesize results for coordinated vegetation, fish, prey, and water quality monitoring implemented by the PNNL, NOAA Fisheries, and USGS, respectively, at Campbell Slough (2005-2009) and Franz Lake (2009-2010), and produce an interpretive report on the findings. This will be a "pilot" or first step in a larger, joint USACE/ Estuary Partnership meta-analysis of monitoring data collected through this contract, the USACE's cumulative effects of restoration project and the Estuary Partnership's habitat contract. The Estuary Partnership Science Work Group will review the data and analyses on a periodic basis, provide input and recommend possible research studies to address key questions as they arise.

In addition to coordinating activities and on the ground work relevant to Estuary Partnership’s EMP, The Estuary Partnership and BPA will coordinate with the Pacific Northwest Aquatic Monitoring Program (PNAMP) to inform other agencies of our monitoring work efforts and to increase the consistency of monitoring and sampling protocols used in the LCRE. We will also participate in the Northwest Environmental Data Network (NED) so that our data can be accessible and usable to interested parties.

2009-2010 OBJECTIVES FOR THE ECOSYSTEM MONITORING PROJECT INCLUDE:
1. Coordinate on-going monitoring efforts in the LCRE with partners and groups such as the Science Work Group and PNAMP
2. Coordinate efforts to map the bathymetry of the LCRE and implement data collection
3. Coordinate efforts to compile and/or collect landcover data to support completion of Ecosystem Classification
4. Monitor habitat, water column, foodweb resources, and salmonids at tidally influenced wetlands within TBD reach(es) of the LCRE
5. Analyze biological community, vegetation, water column, and salmon data for the forested wetland sites
6. Synthesize and produce a summary report on results for multi-year vegetation, fish, prey, and water quality monitoring efforts at two sites
7. Develop Annual Report detailing the results of Objectives 1-5