BPA Project Number:  2003-007-00
CR-128590
Performance/Budget Period: September 1, 2010 – August 31, 2011

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, 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 September 1, 2010 to August 31, 2011.

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.

WORK ELEMENTS FOR SEPTEMBER 1, 2010 TO AUGUST 31, 2011

During the upcoming contract year, the Estuary Partnership, UW and USGS will complete all delineations and an introductory report describing the use of the Ecosystem Classification. Delineations of draft Catena (Level 5) for most reaches will be complete by September 2010 and for all reaches by March 2011. These Catena will be rolled up into floodplain Complexes and merged with UW’s bathymetric Complexes to complete Level 4. As this process has changed somewhat since 2009, the timeline for finishing specific steps in the Ecosystem Classification has been revised slightly. However, all delineations of Levels 4 and 5 for the Ecosystem Classification are expected to be complete on time by August 31, 2011. As landcover data become available, USGS, UW, and the Estuary Partnership will complete delineation of Level 5 Catena and Level 6 Primary Cover Class. 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 July 1, 2010, the anticipated timeline for completing the Ecosystem Classification is as follows; timeline is formatted as “Approx. Due Date. Task (Lead Entities)”:       
Jul 2010. Produce floodplain Complexes and draft Catena for most LCRE reaches (USGS)
November 2010. Produce GIS layers of bathymetric Complexes for all LCRE reaches (UW)
Jan 2011. Deliver processed landcover classes to EP and UW (Sanborn)
Feb 2011. Merge bathymetric Complexes with floodplain Complexes for all reaches (UW)
Mar 2011. Complete development of initial Catenae for all reaches in LCRE (USGS)
Apr 2011. Develop draft Level 6 data for use in refining Catena (UW)
Jul 2011. Complete Catenae using USGS delineations and acquired landcover data (UW, USGS)
Sept 2011. Deliver finalized Complex and Catenae GIS layers and metadata to EP (UW, USGS)
Mar 2012. Final integration of all 6 levels. Deliver final Classification documentation and data layers.

Since the Ecosystem Monitoring budget has not increased substantially, funds programmed toward completion of the Ecosystem Classification will continue to limit funding available for on-the-ground monitoring. Like the Ecosystem 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. Additionally, on-the-ground monitoring yields reference site data for implementation and evaluation of restoration actions. Due to the estimated costs (~$200,000) of processing imagery to produce an up-to-date landcover dataset and costs for the completion of the Ecosystem Classification, on-the-ground monitoring actions will be reduced by the funding level needed to complete the Ecosystem Classification.

PNNL, NOAA Fisheries, USGS, Oregon Health and Science University (OHSU), and Columbia River Estuary Study Taskforce (CREST) will implement the FY2010 monitoring work. PNNL, NOAA Fisheries, and USGS will collect co-located data at four “fixed” stations:
1. Campbell Slough, which has been monitored yearly since 2007 to assess interannual variation in wetland habitat conditions and salmonid presence and abundance;
2. Franz Lake (monitored in 2008 and 2009)
3. Whites Island (monitored in 2009 and 2010)
4. and a TBD site in Reach A
and 3 “status” sites. The “status” sites are located in TBD reaches of the LCRE with data gaps and are determined based on discussions with managers of other estuary RME projects and the Estuary Partnership Science Work Group. PNNL will collect data on wetland vegetation species, elevation, peak macrophyte biomass, and water stage at 8 sites. NOAA Fisheries will monitor salmon, salmon prey and food web resources (i.e., zooplankton), at 7 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 to characterize the food web 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 identification. PNNL, NOAA Fisheries, USGS, and the Estuary Partnership will analyze data and provide results for the coordinated vegetation, fish, prey, and water quality monitoring implemented by the PNNL, NOAA Fisheries, and USGS at all sites between 2007 and 2011. The Estuary Partnership will contract for the compilation and synthesis of analyses and produce an interpretive report on the findings and management implications. 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.

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 Northwest Environmental Data Network (NED) so that our data can be accessible and usable to interested parties.

2010-2011 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. Complete development of landcover dataset to support completion of the Ecosystem Classification
3. Complete delineations of Levels 4 and 5 of Ecosystem Classification and an introductory report describing datasets and how to use the Ecosystem Classification
4. Monitor habitat, abiotic environmental conditions, food web resources, and salmonids at 4 “fixed” sites and 3 “status” sites within tidally influenced wetlands within TBD reach(es) of the LCRE
5. Analyze data collected through the Ecosystem Monitoring Program from 2007 through 2011 and produce an interpretative report
6. Develop Annual Report detailing the results of Objectives 1-5