This FY2013 Statement of Work and Budget is part of the Lower Columbia Estuary Partnership’s Ecosystem Monitoring Program.

BPA Project Number:  2003-007-00
Contract Request Number:  CR- 225871
Performance/Budget Period: October 1, 2012– September 30, 2013

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:  Russell Scranton
Bonneville Power Administration
905 NE 11th Avenue
Portland, Oregon  97208
Phone:  503-230-4412
rwscranton@bpa.gov


Date of Submission:  June 2012

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 Estuary Partnership (Estuary Partnership) to implement elements of the Estuary Partnership’s Ecosystem Monitoring Program (EMP) 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 October 1, 2012 to September 30, 2013 as part of the Estuary Partnership’s Ecosystem Monitoring Program.

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 (Classification) using LANDSAT TM imagery and bathymetry data. They, then, used the 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 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 Classification. USGS also delineated floodplain Ecosystem Complexes and draft Geomorphic Catena for Reach F. USGS together with UW and the Estuary Partnership developed a peer-reviewed scientific publication (USGS open file report) that describes the 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 Classification. USGS delineated floodplain Complexes and draft Catenae 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.

During September 1, 2010 through August 31, 2011 USGS provided an analyses of water quality data for the development of a joint, comprehensive status and trends analysis report with NOAA Fisheries, PNNL and the Estuary Partnership. The report included status and trends 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 monitored indicators. Additionally, USGS continued to collaborate with the UW and Estuary Partnership to finish the Classification. USGS completed the delineation of all floodplain Complexes and Catenae for Reaches A-H in the LCRE, merged the floodplain and bathymetric Complexes into a finalized GIS data layer and developed associated metadata, and developed 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 Classification. In addition, USGS deployed monitoring sondes at four “fixed” sites (Campbell Slough, Franz Lake, White’s Island, and Ilwaco) to collect continuous water quality data relevant to salmonids (water temperature, dissolved oxygen, pH, and water depth) from April through July. This information was used to characterize abiotic water column conditions and factors limiting primary productivity. Finally, USGS collected food web characteristics at the four “fixed” stations three times between April and July. For this assessment USGS included 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. This on the ground data collection was continued through September 30, 2012, and the Classification was also completed and distributed in summer 2012.

During October 1, 2012 through September 30, 2013, the USGS will continue to collaboratively work with the Estuary Partnership, NOAA Fisheries, and PNNL to collect the monitored indicators (food web and abiotic water conditions) of the EMP at the four “fixed” sites (Campbell Slough, Franz Lake, White’s Island, and Ilwaco) from April through July. When funding allows, USGS will expand the monitoring to two other “fixed” sites (Secret River and Welch Island) in Reach B that NOAA Fisheries and PNNL began sampling in 2012. In addition, the USGS will participate in Science Work Group meetings and other discussions pertaining to the EMP and refining the overall design of the EMP (see Estuary Partnership’s contract, project #2003-007-00, for more information).

Specifically, the objectives for USGS’s contribution to the Ecosystem Monitoring Program in 2012-2013 include the following:
1. 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.
2. Provide data, analyses and report contributions to the Estuary Partnership on monitored indicators for the Estuary Partnership’s annual report to BPA.
3. Participate in Science Work Group meetings and other discussions on refining the EMP design.
4. Participate with Estuary Partnership and others in discussions on data management and exchange.