Lower Columbia River Ecosystem Monitoring Project
Statement of Work and Budget FY2010

BPA Project Number:  2003-007-00
Contract Request Number:  CR-132915
Performance/Budget Period: September 1, 2010– August 31, 2011

Technical Contact:  Jennifer Morace
Technical Projects Coordinator
USGS
2130 SW Fifth Ave.
Portland, OR 97201
Phone: 503-251-3229
jlmorace@usgs.gov

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

Date of Submission:  July 2010

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 United States Geological Survey (USGS) is working closely with the Lower Columbia River Estuary Partnership (Estuary Partnership) to implement elements of the Estuary Partnership’s Ecosystem Monitoring Project (EMP) in order to provide information on salmonids and their habitat in the LCRE.  This project builds on previous projects under the EMP and will continue to implement aspects of the comprehensive status and trends assessment of 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 work efforts that USGS will implement from September 1, 2010 to August 31, 2011 as part of the Estuary Partnership’s Ecosystem Monitoring Project.

Review of Prior Work
The USGS was a subcontractor under the Estuary Partnership’s BPA contract from September 1, 2003 to August 31, 2005. During this time, USGS collaborated with the University of Washington (UW) to create the LCRE Ecosystem Classification System (Ecosystem Classification) using LANDSAT TM imagery and bathymetry data. They, then, used the Ecosystem Classification to develop metrics for monitoring habitat in the LCRE. Additionally, USGS conducted monthly fixed station and high- and low-flow supplemental water quality monitoring and deployed semipermeable membrane devices (SPMDs) to characterize water quality conditions.

Starting September 1, 2005, USGS began contracting directly with BPA to conduct their work with the Estuary Partnership. From September 1, 2005 to August 31, 2006, USGS completed chemical analyses of the water samples and generated a data report detailing this information (http://pubs.water.usgs.gov/ds213).

During September 1, 2006 to August 31, 2007, 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 EMP. Additionally, USGS collaborated with the Estuary Partnership and NOAA’s National Marine Fisheries Service (NOAA Fisheries)to integrate 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, USGS deployed probes to monitor the water column for dissolved oxygen, temperature, water-surface elevation, and conductivity at 2 sites (1 in reach F and 1 in reach H) where Battelle/Pacific Northwest National Laboratories (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 outlined a strategy for future sampling efforts that relates number of sites with available financial resources.

During September 1, 2008 to August 31, 2009, USGS deployed probes to monitor the water column for dissolved oxygen, temperature, water-surface elevation, and conductivity at 2 sites (1 in reach F and 1 in reach C) where PNNL and NOAA Fisheries collected vegetation and salmon data, respectively. Additionally, USGS worked with UW to develop criteria based on river geomorphology and hydrology for delineating habitats at smaller spatial scales, which UW incorporated into the Ecosystem Classification. USGS also delineated floodplain Ecosystem Complexes and draft Geomorphic Catena for Reach F. USGS together with UW and the Estuary Partnership 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.

During September 1, 2009 through August 31, 2010, USGS continued to collaborate with the Estuary Partnership and UW to develop the Ecosystem Classification. USGS delineated floodplain Complexes and draft Catena for most Reaches in the LCRE and assisted UW in merging the floodplain and bathymetric Complexes into a finalized GIS data layer. Additionally, USGS along with the Estuary Partnership, NOAA Fisheries, and PNNL synthesized datasets for two repeated sample sites (Campbell Slough and Franz Lake) in order to identify the statistical methods and procedures for integrated analyses of vegetation, salmonid, prey, and water quality datasets and ultimately support more in-depth data roll-ups for the EMP. This data synthesis task is critical for reporting on past monitoring efforts, linking habitat conditions with biological communities like salmonids, and refining the existing monitoring effort. Finally, the USGS deployed water quality probes to monitor the water column for dissolved oxygen, temperature, water-surface elevation, and conductivity at one site (Campbell Slough in reach F) where PNNL and NOAA Fisheries collected vegetation and salmon data, respectively. For the first time since the inception of the EMP, USGS also collected food web, specifically primary productivity, data and tested methods, at this site.

Work Efforts for September 1, 2010 to August 31, 2011
USGS will provide analyses of water-quality and primary-productivity data for the development of a joint synthesis report with NOAA Fisheries, PNNL, and the Estuary Partnership. The report will include status assessments of all sites where fish and prey; vegetation; food-web and water-quality datasets have been collected by NOAA Fisheries, PNNL, and USGS from the inception of the EMP, as well as comprehensive analyses across sites and monitoring indicators. Additionally, USGS will continue to collaborate with the UW and Estuary Partnership to finish the Ecosystem Classification. Specifically, USGS will: (1) complete delineation of all floodplain Complexes and draft Catenae for Reaches A-H in the LCRE; (2) merge the floodplain and bathymetric Complexes into a finalized GIS data layer and develop associated metadata; and (3) develop a report describing the delineations of the CREEC Levels 1-5, general assumptions made in the delineations, data used by UW and the USGS, and how to use the Ecosystem Classification. In addition, USGS will deploy a monitoring sonde at four “fixed” sites (Campbell Slough, Franz Lake, White’s Island, and a TBD site in Reach A) to collect continuous water-quality data relevant to salmonids (water temperature, dissolved oxygen, pH, and water depth) from April through July. This information will be used to characterize abiotic water column conditions and factors limiting primary productivity. Finally, USGS will collect food web characteristics at the four “fixed” stations three times between April and July. For this assessment USGS will include measurements of biomass and net productivity of phytoplankton (free-floating algae) and periphyton (attached algae); stable-isotope analysis of plant, plankton, invertebrate, and fish tissue 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.

2010-2011 Objectives for USGS’s contribution to the Ecosystem Monitoring Project include:
1. Complete delineation of all floodplain Level 4 (Ecosystem Complexes) for the Ecosystem Classification.
2. Complete delineation of Level 5 (Geomorphic Catena) for the Ecosystem Classification.
3. Provide a report describing the delineations of the Ecosystem Classification Levels 1-5, general assumptions made in the delineations, data used by UW and the USGS, and an overview of how to use the Ecosystem Classification.
4. Provide analyses of water-quality and primary-productivity data for the development of a joint synthesis report with NOAA Fisheries, PNNL, and the Estuary Partnership.
5. Collect abiotic environmental conditions and elements of food web characteristics at four “fixed” sites that will be jointly assessed for fish and habitat condition by NOAA Fisheries and PNNL, respectively.