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| A | 72601 | 119 | Manage and Administer Projects | Project management | Work Element 119: Project Management and Administration
Prepare a project management plan. We will write a project management plan for review by project participants and BPA staff. The project management plan will include a schedule of project activities, milestones, and deliverables; a list of personnel and their duties and contact information; a staff organization chart; and a description of the scope of work. The project management plan will include topics organized similarly to the following outline:
1.0 Introduction
1.1. Project Scope
1.2. Deliverables and Schedule
1.3. Budget
2.0 Roles, Responsibilities, Accountabilities, and Authorities
3.0 Project and Administrative Controls
3.1. Work and Expenditure Authorization
3.2. Project Performance Measurement
3.3. Change Management
3.4. Procurement and Subcontracts
3.5. Communications
4.0 Risk Management
5.0 Records Management
6.0 Project Closeout
Convene quarterly project meetings. To ensure excellent communication among project participants, the project manager will hold in-person meetings or conference calls at least quarterly. During these meetings we will discuss project status and accomplishments, planned activities, and issues and/or problems.
Prepare a scope of work and budget for FY10 (Year 4) and enter this information into Pisces. (This task depends on the process the NPCC establishes for “2010+.”) We will draft the FY10 scope of work and budget based on results and experience gained from FY07–09. The project scope will be communicated regionally using Pisces. | $16,086 | 2.19% | 08/14/2009 | 04/30/2010 |
| B | 72602 | 132 | Produce Progress (Annual) Report | Annual report | Work Element 132: Annual Report
Annually report results from the study. We will publish an annual report applying to standard technical reporting procedures. That is, the report will include sections on the goal and objectives, background and problem description, methods, results, discussion, recommendations, and literature cited. The report also will document the coordination between this study and other monitoring efforts, such as the Estuary Partnership’s Ecosystem Monitoring Project.
Disseminate the annual report and solicit peer-review comments. Technical reports invariably are improved when they are reviewed by peers. We will ask BPA to post the draft report on their Fish and Wildlife Division website and invite comments.
Finalize the annual report. The method is self-explanatory. After the report is finalized, the draft on the BPA website will be replaced with the final version. | $40,226 | 5.47% | 01/04/2010 | 12/31/2010 |
| C | 72603 | 157 | Collect/Generate/Validate Field and Lab Data | Data collection | Work Element 157: Collect and Validate Data
WE 157, Sub-Objective 1a. At regular monthly monitoring sites and seasonally at other sites in tidal freshwater, collect shallow (0–3 m) beach seine data to characterize the fish community and juvenile salmon migration, including species composition, length-frequency, density (#/m2), and temporal and spatial distributions.
Fixed Sampling Sites: Fish composition will be evaluated on a monthly basis at eight fixed sites in the vicinity of the Sandy River delta (see Figure 3). The sample sites were purposefully selected to sample fish in the shallow water of three particular habitats—river confluence floodplain, shallows, and mainstem island —that are the most common habitats found in the tidal freshwater area (LCREP 2004a).
Nine sites (Figure 3) were chosen as a trade-off between cost, spatial sampling intensity, and temporal sampling intensity. A minimum of one sampling episode per month is necessary to obtain adequate temporal sampling of migration characteristics. The sampling frequency therefore limits the number and spatial extent of regularly sampling sites. The sampling sites within the regularly sampled area of the Sandy River delta and the spatial blitz efforts will be geo-referenced and mapped on publicly available aerial photographs and bathymetric maps.
The eight regular sampling sites (Figure 3) for TFM Study Year 3 are as follows:
• Site A: North shore of Reed Island on the Washington State side of the Columbia River—side channel, mainstem island, fine substrate
• Site B: Beach side of Chatham Island, upstream of Sandy River Delta on the Oregon State side of the Columbia River—side channel, mainstem island, sandy substrate
• Site C: Near the mouth of the old channel at Sandy River Delta on the Oregon State side of the Columbia River—river delta, sandy substrate
• Site D: Near the mouth of the current channel at Sandy River Delta on the Oregon State side of the Columbia River—mainstem channel, sandy-to-mixed course substrate
• Site E: West shore of Gary Island on the Oregon State side of the Columbia River—side channel, mainstem island, fine substrate
• Site F: Oregon State side of the mainstem Columbia River upstream of the Sandy River delta—main channel, pike dikes and large woody debris upstream and downstream, sandy substrate
• Site H: McGuire Island downstream of the mouth of the Sandy River—side channel, mainstem island, sandy substrate
• Site I: Ackerman Island downstream of the mouth of the Sandy River—main channel island, sandy substrate
• Site N: Downstream (east) of the blockage in the old channel of the Sandy River.
Figure 3. Satellite (top) and Map (bottom) Views of the Nine Regular Monthly Sampling Sites for Year 3 of the TFM Study.
During Years 1 and 2, Site N near the current blockage in the old channel of the Sandy River Delta was sampled for baseline data for effectiveness monitoring of the rechannelization. Because this potential restoration action is currently in the developmental stage and the timeline for restoration is unclear, sampling at Site N will be suspended once we have achieved 2 years of baseline data collection (i.e., by June 2009). Also, note that Site G on the mainstem side of Lady Island was discontinued after one sampling event because of underwater debris and obstructions; it was replaced by Site I on Ackerman Island.
Spatial Blitz Sampling Sites: To expand the geographic extent and diversity of tidal freshwater habitats sampled, we will perform four seasonal sampling blitzes during Year 3. A minimum of 10 sites will be included in each blitz trip, which will occur concurrently with the regular monthly sampling at the fixed sites. The blitz sites will occur within Reaches D, E, F, and/or H. Based on field reconnaissance and satellite photographs, we will identify the sampling universe suitable for beach seining and then generate a list of stratified sites. Blitz sites will be randomly selected from the full suite of stratified sites. During the spatial blitzes, we will collect the usual ancillary data (see below) and perform a rapid assessment of vegetation and substrate. An example of blitz sample locations from Year 2 is shown in Figure 4.
Equipment and Deployment: A 46-m floating beach seine will be used to sample fish. The seine design was based on the results of a gear comparison study of the standard 37-m beach seine versus a longer, deeper beach seine in winter 2007-2008 (Sobocinski et al. 2008). The new seine was first used at the existing study sites during May 2008. Several studies have used different capture techniques for collecting fish in nearshore and offshore habitats and have found that larger fish (generally yearlings) are found in deeper water (Healey 1980, Levings 1982; Dawley et al. 1986). Offshore sampling has included tow nets (Fresh et al. 1981), purse seines (Levings 1982; Dawley et al. 1986) and other techniques; however, beach seining is generally accepted as the best method for nearshore sampling (Hayes et al. 1996).
Figure 4. Example of Blitz Sites in Three Segments of Reach E Sampled in Year 2. Sites were randomly selected from a sampling frame of all possible 500-m beach seine sampling locations within Reach E.
The custom net is constructed of 1.3-cm stretch mesh netting in the wings and 3.2-mm netting in the bag. The seine is 46-m long and 3-m high at the center. A boat will be used to facilitate setting the seine, which will be deployed parallel to the shore using 15-m-long tow ropes then pulled shoreward onto the beach. The beach seine will be hauled evenly and gradually pursed as it reaches the waterline. Fish will be removed from the net using wet brail techniques and placed in buckets with fresh river water aerated with battery powered air stones until they are processed. Fish will be identified and counted, and returned to their original environment. The hatchery and wild status of salmonids will be determined to the extent possible by recording clipped adipose-fins, and testing with coded-wire tag and PIT-tag readers. The fork lengths and weights of salmonids will be recorded to at least n = 20 for each 1) species, 2) hatchery or wild status, and 3) size class. Total or fork lengths of all other fish will be recorded for at least the first 20 individuals. The data resulting from the seine net sampling will produce estimated density (number of fish per area swept) for juvenile salmon and other fish. Data will be recorded on a field form and later entered into a spreadsheet for analysis.
Sampling Design: Monthly sampling will occur throughout the year (Table 3). Once each month, the fixed monitoring sites (e.g., within the vicinity of the Sandy River delta) will be sampled in random order over a 2-day consecutive period. Seasonal blitzes (e.g., intensive sampling within reaches excluding Reach G; the location of our fixed monitoring sites) are scheduled for May, August, and November 2009 and February 2010 (Table 3). At each site, two replicate seine samples will be collected from the designated sampling station. All fish collected will be identified by species (or genus if species identification not possible) and their lengths will be recorded. The second seine set will be performed at least 0.5 h after the first to allow the fish population to reestablish itself so that independent index data on fish densities can be collected.
Prior to handling, all Pacific salmon Oncorhynchus spp. and steelhead O. mykiss will be anaesthetized in a 10% tricaine methanesulphonate (MS-222) solution to minimize stress. After processing, all salmonids will be held in a container filled with river water at ambient temperature and dissolved oxygen until they have recovered fully. All salmonids will then be released at the site of capture.
WE 157, Sub-Objective 1b. Determine the stock of origin for the yearling and subyearling Chinook salmon captured at the sampling sites.
We will determine the stock of origin using genetic analysis. We will use the genetic data to determine the presence of Snake River fall Chinook salmon in the area, which has implications for management decisions about habitat restoration in the area. Stock-of-origin data will also be critical because juvenile salmon produced in the Sandy River sub-basin may be prevalent in the study area and knowing the abundance of these fish in relation to other populations using the area will provide further understanding of these shallow water systems and how they are used by fish. Fin clips on sub-samples of collected salmon (~20 per sample site per trip) will be preserved for genetic mixture analysis by NMFS.
WE 157, Sub-Objective 1c. Characterize vegetation composition and percent cover, conventional water quality, water surface elevation, substrate composition, bathymetry, and beach slope at the status and trends monitoring sites. Habitat characterizations were performed at five of the sampling sites (A, B, C, D, N) in Year 1 and four more sites (E, F, G, H) in Year 2. During Year 3, we will sample the remaining Site I and collect bathymetry data at Site C. Habitat characterizations are intensive efforts conducted once per year during summer. We will follow the protocols offered by Roegner et al. (2006). The following habitat characteristics are assessed:
• Bathymetry: We will conduct bathymetry surveys to determine beach slope topography at the sample sites.
• Vegetation and Percent Cover: Ground surveys will be performed using the standard protocols (Roegner et al. 2008).
• Hydrology: Data loggers will be deployed to continuously monitor water surface elevation and temperature at all sampling sites.
• Beach Material: Sediment characteristics at each site will be observed and recorded during each visit. Samples will be taken for analysis of grain size from each sample site. Grain size will be characterized using sieves sized 2 mm (very coarse), 1 mm (coarse), 0.5 mm (medium), and 0.25 (fine).
• Slope: Beach slope at each site will be measured using a Real-Time Kinematic global positioning system (RTK GPS).
WE 157, Sub-Objective 1d. Collect the data necessary to assess statistical relationships between salmonid abundance and habitat characteristics, including ancillary variables such as temperature and river stage.
We will acquire relevant environmental data (e.g., water temperature, tide stage, daylight, river stage, river flow) and enter the data into our database so that they are available for analysis. Ancillary data relevant to the study will include the following:
• Photographs: Digital photographs from a standard location at each sample site will be taken during each trip to visually record site conditions.
• Depth: Water depth at each sample site during each visit will be measured from a known benchmark. Depth will be continuously recorded using data loggers.
• Dissolved oxygen: A water quality instrument will be used to measure dissolved oxygen levels on site during fish sampling.
• Hatchery release data: The DART (Data Accessed in Real Time) website (http://www.cbr.washington.edu/dart/hatch.html) will be accessed to obtain real-time information on hatchery releases of fish that could be present at the study sites.
• Positions: All measurement sample sites, instrument placement positions, survey area boundaries, and other important locations will be documented using a differential GPS.
• Water temperature: Water temperature will be recorded with a submersible thermometer and/or water quality instrument.
• Weather conditions: General weather conditions will be recorded every 4 hours during field operations. Sunrise and sunset information can be found online (http://aa.usno.navy.mil/data/docs/RS_OneYear.html).
WE 157, Sub-Objective 1e. Determine species composition, release locations, and distributions of JSATS-tagged fish from other studies and estimate run timing, residence times, and migration pathways for these fish in the study area.
Equipment and Deployment: We propose to use the JSATS at the Sandy River delta study area, where we will deploy acoustic telemetry receiving equipment at four sites to monitor the presence of tagged fish (from other studies) migrating through the study area. The Sandy River delta study area lies between JSATS arrays deployed for the Corps at Reed and Lady islands. The micro-acoustic tags used in this study transmit 417 kHz sound once every 5 seconds for about 60 days. This task depends on sharing equipment from the USACE.
Fish Tagging and Release: As part of other projects (e.g., Corps SPE-P-08-3), over 20,000 juvenile salmon and steelhead will be tagged and released in the hydrosystem above Bonneville Dam (the exact sample sizes for these studies will be finalized at a later date). These will be migrating through the TFM study area.
Sampling Sites: Four autonomous hydrophones (nodes) would be deployed at the study area (Figure 5). We will also use data from hydrophones deployed upstream and downstream (Figure 5) for other studies to calculate detection probabilities. Placing hydrophones upstream of the delta, in the main channel along the outer side of the delta, and in two sites within the delta will be important to demonstrate whether the area is used by upriver juvenile salmonids. The assumption is that hydrophones at the river confluence sample site will detect migrants passing by, while hydrophones at the mainstem island sample site will detect any use of shallow water habitats. Along these same lines, estimates of detection range for the hydrophones will be useful in deciding on placement of the hydrophones. The maximum range of detection based upon the receiving sensitivity of JSATS autonomous nodes and the source levels of acoustic micro-tags ranges from about 600 to 800 ft depending upon ambient acoustic conditions in the river. We will move tags through known positions to provide information on detection range at specific sample sites in the study area.
Data Downloading: Acoustic data will be downloaded from the mini-nodes each week during the May through August telemetry field season. Node “servicing” will consist of recovering each node, replacing the batteries, and replacing the data media (CompactFlash card). Data will be immediately backed up on the project laptop computer and CD media.
Figure 5. Locations of the Four Acoustic Telemetry Receiver Nodes. The red dots depict the location of hydrophone arrays for other studies.
WE 157, Sub-Objective 2a. Determine the diet of juvenile salmon captured for Objective 1. We will use gastric lavage to remove stomach contents from juvenile Pacific salmon greater that are at least 50-mm fork long. Fish will be lavaged with filtered river water via an appropriately sized syringe fitting (Bowen 1983). Gastric lavage has been reported to be 99% effective at removing prey organisms, with no impacts on survival, from the stomachs of coho salmon O. kisutch (Meehan and Miller 1978). At each site, contents from the anterior alimentary canal (esophagus and stomach) of up to 20 fish from each Pacific salmon species encountered will be flushed into individual polyethylene sample bottles using filtered river water at ambient temperature. Samples will then be preserved in a 10% ethanol solution to slow degradation. Samples will be labeled with fish and site data. Within 24 hours all samples will be preserved in a 70% ethanol solution for later analysis. All fish diet samples will be processed in the lab; with identification of prey items to the lowest taxon possible and with some consideration of functional groups. The stomach content samples will also be weighed in order to calculate the index of relative importance (see details in WE 162, Data Analysis). We will exchange information on juvenile fish diets with U.S. Geological Survey staff who are performing a separate study of shad ecology in the lower Columbia River.
WE 157, Sub-Objective 2b. Ascertain the species composition and abundance of available prey from terrestrial, planktonic, and benthic sources.
Field activities to assess prey availability for salmon in specific tidal freshwater habitats of the Columbia River will be conducted quarterly beginning in January 2010. Samples will be collected from eight established sites (Figure 3) in the vicinity of the Sandy River Delta over a period of 1 week.
Benthos. Benthic samples will be collected using a standard ponar dredge (525 m2). Because substrates at the sites are generally composed of soft material or fine-to-small stone, the ponar dredge should be an effective means of sampling the benthic community. Duplicate samples will be collected by boat at each site, 25 m from the existing water line, and at two points parallel to shore, selected randomly from the total linear length of the site. Upon retrieval, the contents of the dredge will be emptied into a sieve bucket (~500 µm mesh) then rinsed with filtered river water to remove fine particles. The contents of the sieve will be transferred into a 1-L sample bottle, preserved with 70% ethanol, and labeled appropriately. All samples will be stored in a cooler for transport to the laboratory.
Insect Drift. To describe the community composition of drifting aquatic invertebrates and terrestrial insects, drift nets (363 µm mesh) will be deployed at each site. General Oceanics mechanical flowmeters (model 2030; General Oceanics, Miami, FL) will be attached to each net to quantify the volume of water sampled (m2). Gear will be oriented with openings facing upstream; approximately 3 m and 6 m from the existing waterline, aligned with the pre-established benchmark. Nets will be set so that the bottom of the frame is positioned vertically at half the height of the water column. Because drift tends to vary throughout the day, with maximum drift occurring commonly at sunrise and sunset (Rabeni 1996), all nets will be set for 24 hours. After the effective sampling period has concluded, gear will be retrieved and the mesh will be rinsed with filtered river water to collect material in the cod end. Contents will then be rinsed into a 1-L sample bottle, preserved with 70% ethanol and labeled accordingly. As with benthic samples, all samples will be stored in a cooler for transport to the laboratory.
Settling Organisms. Settling organisms will be sampled using arrays of Hester-Dendy multiple-plate samplers (Hester and Dendy 1962). This type of multiple-plate sampler consists of a series of eight round (7.6-cm diameter; 0.068 m2 total surface area) masonite plates attached to an eyebolt. Spacers separate the plates at varying distances providing differently sized spaces for colonization. The sampling array will consist of six multiple-plate samplers attached to a length of polyvinyl chloride (PVC) pipe. Four floats will be attached to the PVC pipe; two to hold the array in position in the water column, and two to aid in retrieval. Two pyramid anchors will be attached at either end of the pipe by lengths of rope to secure the entire unit to the substrate (Friesen et al. 2005). Two units will be deployed at each site perpendicular to the current. Gear will be positioned 6 m and 9 m from the existing waterline, and at two points parallel to shore, selected randomly from the measured linear length of the site. Units will be set so that the bottom of the array is at approximately one-third the height of the water column. After an effective sampling period of 1 week, the multiple-plate sampler arrays will be retrieved. Upon recovery, individual multiple-plate samplers will be disassembled and all resting material will be scraped into a 500-µm sieve. The contents of the sieve will then be rinsed into a 1-L sample bottle, preserved with 70% ethanol, and labeled accordingly.
WE 157, Sub-Objective 2c. Model the bioenergetics of juvenile salmon in shallow tidal freshwater and compare results among species, seasons, and habitat types. This is a modeling effort that will be described in detail under WE 162, Analyze and Interpret Data. It will use data obtained from the diet samples.
WE 157, Sub-Objective 2d. Estimate residence time by mark-recapture of juvenile salmon during winter 2009/2010.
This pilot investigation into the residence times of overwintering juvenile Chinook salmon in tidal freshwater will involve a mark-recapture effort using acoustic telemetry to be conducted in conjunction with a regular sampling event at the fixed sites. Chinook salmon will be obtained from the regular beach seine samples and implanted with JSATS transmitters in the field. The approach may be summarized as listed below.
Time of year: Two months in late 2009 and early 2010 (tentatively December 2009 and January 2010)
Species: unmarked, uninjured Chinook salmon
Number: 20 to 25 fish
Length: Greater than 95 mm
Source of Fish: TFM beach seine samples
Measurements: All tagged fish will be measured, weighed, and a fin clip taken for genetic stock identification.
Tags: Micro-transmitters 0.43 g in air, 417 kHz, 10-sec transmit interval, manufactured by Advanced Telemetry Systems (version 2008; to be provided by the USACE)
Tagging: After being anesthetized, a tag will be surgically implanted in the fish. After a 1- to-2-h holding period, the fish will be returned to the river (see Ploskey et al. 2008 for details on the tagging procedure);
Release Strategy: Fish will be released in the vicinity of Sites B, C, and E near where they were originally captured.
Recapture: Autonomous JSATS receiving nodes on loan from the USACE will be placed in the basin behind Gary Island (Figure 5). Data will be downloaded monthly during regular beach seine sampling trips.
WE 157, Sub-Objective 2f. Determine fish condition using specimens captured in the beach seine.
Because this effort is analytical and uses length and weight data obtained from WE 157 Sub-Objective 1a, it will be described in detail under WE 162, Analyze and Interpret Data. | $542,743 | 73.74% | 05/01/2009 | 04/30/2010 |
| D | 72604 | 162 | Analyze/Interpret Data | Data analysis | Work Element 162: Analyze and Interpret Data
WE 162, Sub-Objective 1a: Analyze and interpret the seine data to determine density (number per unit surface area) and temporal and spatial distributions and make sample size calculations for a large-scale sampling effort. Information about species composition and abundance will be assembled and presented in tabular and graphical form. Fish relative abundance will be summarized by species and grouped by family (e.g., salmonids) and functional groups (e.g., cold-water versus warm-water species, predators, etc.). For salmonids, hatchery versus unmarked salmonids (i.e., assumed wild due to lack of adipose fin clipped and/or coded wire tag counts over the seasons will be examined. Species composition and abundance trends will be compared and contrasted across sites and habitats (e.g., main channel versus backwater).
Fish data collected for the TFM Study can also be used to calculate sample sizes for a full-scale status and trends monitoring program for juvenile salmonids in shallow, tidal freshwater of the LCRE. Considering the replicate beach seines within a site as repeated measures of the same local response (i.e., measurement or sampling error), the data within a survey period can be used to estimate spatial variability and average measurement error by habitat type. For example, consider k replicate sites within a habitat and n replicate samples per site, then a one-way analysis of variance (ANOVA) can be used to estimate the variance components. From the one-way ANOVA table, average measurement error is estimated by mean square error (MSE) and spatial variance.
Repeated sampling across the seasons and habitats will be used to determine the best characterization for subsequent sample size calculations. Similar mean-variance relationships often hold for measurement error as well. Based on the most appropriate variance-to-mean relationship, data will be pooled across sampling events to obtain more precise estimates of the variance components for subsequent sample size calculations. The degree of temporal correlation between sites over time will be important in any monitoring program that uses a paired design. This correlation within a habitat category can be estimated using the intra-class correlation coefficient (Zar 1999:404-407) estimated from, again, a one-way ANOVA. Considering the case of k sites sampled over 4 years, the one-way ANOVA can then be constructed. Then the intra-class correlation is estimated by the variance components. Following the previous analysis, the estimate can be partitioned into natural variation and average measurement error, leading to a more accurate estimate of the actual temporal correlation.
Results of the variance component and correlation analyses will be used as input to designing a full-scale tidal freshwater monitoring program. The monitoring will be based on a rotational design, also called a panel design. Panel designs are the basis of long-term monitoring programs at all major US national parks (National Park Service, Vital Signs Monitoring http://science.nature.nps.gov/ im/monitor/SamplingDesign.cfm). The magnitude of the sampling error and spatial variance will help determine the size of the panels (i.e., the number of sites sampled at one time). The magnitude of the interannual correlation will be used to help determine the carry-over fraction of sites from one year to the next. The higher the interannual correlations, the fewer sites needed. Monthly sampling and blitz sampling will be used to help determine habitat stratification and key months to sample. In outyears, a formal monitoring program will be formulated that includes the construction of the lower Columbia River (LCR) sampling frame of inference, statistical design, and analysis plan for implementation.
WE 162, Sub-Objective 1b. Determine the stock of origin for the yearling and subyearling Chinook salmon captured at the sampling sites. Mixture analysis and estimation of stock-of-origin has two components, the construction of the baseline and the analysis of the unknown mixtures. The “baseline” is the whole set of reference samples representing spawning aggregates in known geographic locations. The “mixture” is a group of fish derived from different populations in different proportions. In this study the mixtures are groups of Chinook salmon individuals taken at different times and places. Standard mixed fishery methods will be used to compare the multi-locus genotypes in the mixture samples with the gene frequencies of the reference populations to estimate the likely proportional contribution from each of the baseline populations (Kalinowski 2007). Population data from a multi-laboratory standardized Chinook salmon genetic database (Seeb et al. 2007) will be used for the baseline. Mixture analyses will be carried out using the program ONCOR (Kalinowski 2007) which implements the methods of Rannala and Mountain (1997) for calculating genotype probabilities in the mixture sample. Mixture proportions and assignment probabilities for individual baseline populations will be summed to regional stock groups (Seeb et al. 2007). ONCOR will also be used to re-sample mixture and baseline data to estimate confidence intervals of the mixture proportions.
WE 162, Sub-Objective 1c. Characterize vegetation composition and percent cover, conventional water quality, water surface elevation, substrate composition, bathymetry, and beach slope at the status and trends monitoring sites.
Substrate. To characterize substrate, Columbia Analytical Services will perform grain-size analysis according to the Puget Sound Estuary Program protocol (Simenstad et al. 1991). Quality assurance measures will be followed by the laboratory. Reported values will include the average of the three samples per site, with percent contributions for each of eight size classes.
Slope and/or Bathymetry. All surveying will be referenced to the North America Vertical Datum 88 (NAVD 88); horizontal position will be referenced to North America Datum 83 (NAD 83). Data collected from the base receiver will be processed using the automated Online Positioning User Service (OPUS) provided by the National Geodetic Survey. To ensure proper spatial reference, OPUS provides a root-mean-square value—an estimate of error—for each set of static data collected by the base receiver. We will use a Trimble Geomatics Office (software version 2005) to process the data, importing, reviewing, and annotating each survey. Benchmark information that was entered and rover antenna heights will be corrected for disc sink measured at each survey point to the nearest half inch; this step is critical in soft-muddy sediments to assure an accurate measurement of elevation. The survey will then be recomputed within Trimble Geomatics Office and exported in a geographical information system (GIS) shapefile format. Surveys will be visually checked by Trimble Geomatics Office and ArcGIS (ESRI 2004) software for validity.
Vegetation. In the field, we will enter all data on data sheets and later transferred the data into Microsoft Excel at the lab. Quality assurance checks will be performed on a subset of the data entered. Additionally, a field notebook with written observations will be maintained. Using a Trimble GeoXT handheld GPS unit (Trimble Navigation Limited, Sunnyvale, CA), we will map the extent of each site (using reasonable natural boundaries) and delineate major vegetation bands and patches. Additionally, features of importance to the field survey (including benchmarks, transect start and end points, and photo points, see ancillary data below) will be also identified and cataloged. All data will be input to ArcGIS and maps of each site showing major communities and features will be created. The elevation data collected using the RTK GPS will be processed and used to analyze the occurrence of species at different elevations and to compare with other sites in the tidal freshwater area of the LCR. To compare the species occurrence at the suite of sites in our study we will use a simple similarity index (Czekanowski Index, Thom at al. 2002), whereby the percent similarity equals (2a/(2a + b + c))*100, where, a is the number of species in common between two sites, b is the number of species exclusive to the first record, and c is the number of species exclusive to the second record. By using the number of species common to two sites, as well as species unique to each site, this index allows for a coarse comparison of sites.
WE 162, Sub-Objective 1d. Assess statistical relationships between salmonid abundance and habitat characteristics, including ancillary variables such as temperature and river stage.
An important objective of this study is to understand the temporal and spatial use of shallow tidal freshwater habitats. Both univariate and multivariate analyses of the fish sampling data will be performed to better understand the associations between fish and habitat. This information will be valuable in both understanding the ecology of the system and how best to direct restoration efforts for salmonid recovery.
Univariate Juvenile Salmon and Habitat Associations. Multiple regression analysis will be used to assess relationships between observed salmonid densities and environmental and/or habitat variables measured at both the fixed and blitz sites. The purpose of the analysis is to identify the factors that could be used in stratifying sites in a regional monitoring program.
Multivariate Fish Community and Habitat Associations. Using the expanded spatial sampling of the blitz sites (i.e., total of 9 + 8 = 17 sites), associations between fish community and habitat characterizations will be examined. Principal component analysis (PCA) will be used to identify the two principal components that most describe the variability in the fish community traits between sites. Bivariate principal component (PC) plots will be used to characterize the range in site variability for the fish.
Analysis of distance (ANODIS ) will be used to regress the habitat principal components against salmonid density based on PC1 and PC2 being orthogonal (i.e., independent). The result will be a bivariate regression line that can be superimposed on the bivariate PC plots.
WE 162, Sub-Objective 1e. Determine species composition, release locations, and distributions of JSATS-tagged fish from other studies and estimate run timing, residence times, and migration pathways for these fish in the study area. Acoustic-tag arrays upstream and downstream of Sandy River Delta (Figure 5) will be used to estimate average residence time for tagged fish in that reach. For fish known to have traversed the reach (i.e., those detected both upstream and downstream), average residence time will be computed as the arithmetic average. Mean travel times will be computed for different fish stocks (i.e., yearling, subyearling Chinook salmon) and over different periods of the outmigration. If the rechannelization of the old channel is performed during this monitoring program, mean residence time will be compared between pre- and post-mitigation periods. There will also be four single acoustic receivers located between the arrays to monitor fish activity. One of the receiver nodes is located in the vicinity of the old mouth of the Sandy River. This receiver node will be used to estimate an index of fish usage of the old channel environment. The index of usage will be calculated as the fraction of the number of unique tagged fish detected at one or both of the acoustic arrays and the number of the m fish that are detected at the channel node. Because the expected value of x is a function of both the probability of old Sandy River mouth usage and detections, the value I is only an index of proportional use. It will be important for the detection probability and location of the channel node to be constant over the course of the study in order to properly interpret trends in the value of I. The standard error for I is based on the binomial sampling. Again, in the case where rechannelization occurs during the course of the study, I can be compared between pre- and post-mitigation periods. The three single arrays will also be used jointly to calculate an activity index within the vicinity of the Sandy River Delta.
WE 162, Sub-Objective 2a. Analyze the diet of juvenile salmon captured for Objective 1.
Sample Processing. In the laboratory, up to 400 stomach content samples collected in Year 3 of the TFM Study will be removed from their sample bottles using a pipette or by straining through a 500-µm sieve. Entire stomach content samples will be weighed damp (blotted dry) then placed in a shallow glass dish containing a 70% ethanol solution and examined under a dissecting microscope. All prey items will be identified to the lowest classification possible using standard taxonomic keys (e.g., Merritt and Cummins 1996) and enumerated. Partially degraded organisms will be identified based on paired or individual characteristic structures. Prey items of the same taxon or generalized group will be placed in small polyethylene centrifuge vials. To preserve prey items for any subsequent analyses, vials will be filled with 70% ethanol and labeled with a fish identification number—corresponding to the original data sheet—and a letter identifying the site of capture. Unidentifiable prey appendages and insect exuviae will be returned to the original sample bottle and stored in 70% ethanol.
Samples collected in Year 3 and from all samples (n = 500) collected during Year 2 of the TFM Study will be weighed. Each prey taxa-life history group from these samples will also be weighed (blotted dry) to the nearest 0.0001 g. Unidentified material—comprised primarily of exuviae and sediment—will be weighed, but excluded from subsequent analyses. For quality assurance purposes, a second analyst will examine 1 of every 25 samples enumerated by the primary analyst. Counts for each taxon will be compared to ensure percent differences do not exceed 15%. Additionally, a daily calibration check will be performed on the balance using standard weights in the range of the samples to be weighed. A calibration log will be maintained to identify the weights used for the calibration check, and the balance deviations from the known and/or standard weight.
Data Analyses. We will calculate several metrics to compare differences over time and space between species and between hatchery and naturally produced Pacific salmon. An Index of Relative Importance (IRI) and Percent Index of Relative Importance (%IRIi, standardized IRI) will be calculated to quantify the contributions of specific taxa to diets of salmon sampled. These indices should be used in conjunction with single metrics (e.g., percent composition by biomass, percent composition by number), because IRI values can vary depending on taxonomic resolution (a result of the multiplicative effect that frequency of occurrence has on the index; %Oi; see Hansson 1998) and in this way may mask some of the information expressed by the individual components. Despite these limitations this metric may be useful in comparing our results to other studies in the region. We will evaluate the dietary diversity of salmon encountered in our monitoring activities by calculating a Shannon-Weiner Diversity Index.
WE 162, Sub-Objective 2b. Analyze the species composition and abundance of available prey from terrestrial, planktonic, and benthic sources.
Organisms collected in all gear types will be identified to the lowest possible taxonomic classification. Prior to inspection, rose bengal will be added to preserved samples to aid in the separation of invertebrates from detritus and other matter. Whenever possible, entire samples will be processed; however, samples containing large numbers of organisms (> 1,000 individuals) will be sub-sampled using procedures described below.
Benthos. Benthic samples containing high densities of prey will be sub-sampled according to procedures adapted from Boward and Freidman (2000). Prior to inspection, individual samples will be poured through a 500-µm sieve held over a collecting bucket to remove preservative and any remaining fine sediment. Sample contents remaining in the sieve will then be rinsed gently with tap water to remove any residual preservative. Large debris, including sticks and leaves, will be cleaned with a scrub brush to remove any clinging organisms; the debris will then be discarded appropriately.
The contents of the sieve will be rinsed into a sampling tray partitioned into 100 5-cm grids labeled 1 through 100. After the sample has been rinsed completely onto the tray, the contents will be homogenized and spread evenly over the entire bottom. One grid will be selected at random, and the contents of that grid will be placed in a watch glass. Organisms transferred to the watch glass will be identified and enumerated by taxon. If the total number of organisms encountered in the watch glass does not meet or exceed 120 organisms, further randomly selected grids will be processed until the target number of organisms has been met or the entire sample has been enumerated. The number of organisms within each taxon for the entire sample will then be estimated based on subsample counts and the total number of subsamples (i.e., grids) enumerated.
Insect Drift. When necessary, drift samples will be subsampled according to published protocols (Mills et al. 1992; Storch et al. 2006). Contents of sample bottles will be poured individually through a 500-µm sieve to remove preservative. Samples will then be rinsed into a graduated beaker with filtered water and further diluted to a whole volume. Two 1-mL aliquots will be withdrawn from the known-volume dilution of organisms and placed in separate watch glasses. Organisms in the two aliquots will be identified and enumerated, after which counts will be compared to ensure a difference equal to or less than 10%. If necessary additional aliquots will be removed until the 10% benchmark has been achieved. Total numbers of prey items in the sample will then be estimated by direct proportion.
Settling Organisms. To avoid pseudoreplication, each multiple plate sampler array (see Field Sampling) will be considered one sampling unit. In the laboratory, samples will be poured through a 500-µm sieve and rinsed gently with filtered tap water to remove fine sediment and residual preservative. The filtered sample will then be subsampled using the procedures outlined for benthic samples.
WE 162, Sub-Objective 2c. Model the bioenergetics of juvenile salmon in shallow tidal freshwater and compare results among species, seasons, and habitat types.
Using species-specific physiological parameters, the bioenergetics model balances consumption with growth and losses from metabolic processes. In this modeling approach, energy is allocated hierarchically to various compartments: consumed energy is first allocated to catabolism (maintenance and activity metabolism), then to losses from waste (urine, feces, and specific dynamic action), and lastly remaining energy is allocated to somatic storage (body growth and gonad development; Hanson et al. 1997). Given these rules for energy allocation, by inputting observed diet (WE 162, Sub-Objective 2a), water temperature (WE 157, Sub-Objective 1d), and salmon and prey energy densities (literature) we will evaluate effects of variability in environmental parameters (i.e., diet and temperature) on growth among species, seasons, and habitat types in shallow tidal freshwater areas of the Columbia River.
WE 162, Sub-Objective 2d. Perform a pilot study to estimate residence time through mark-recapture of juvenile Chinook salmon during winter months.
The analysis methods for the mark-recapture of acoustic tagged fish will be the same as previously described in WE 162, Sub-Objective 1f. The basic difference between the two efforts is that we will rely on fish tagged as part of other studies for Sub-Objective 1f whereas in Sub-Objective 2e we will be tagging fish captured in our beach seine.
WE 162, Sub-Objective 2f. Determine fish condition using specimens captured in the beach seine.
We will calculate Fulton Condition Factors (K) using lengths and weights collected under WE 157, Sub-Objective 1a. Fulton Condition Factors are calculated as follows:
K = (W/L3) X 100,000
where,
W = weight of fish in grams
L = fork length of fish in millimeters.
Limitations, such as an inability to examine interspecies differences and differences between the sizes of the same species, exist with Fulton-type condition factors; however, we should be able to examine the differences between habitat types among species. | $104,083 | 14.14% | 05/01/2009 | 12/31/2010 |
| E | 72605 | 165 | Produce Environmental Compliance Documentation | Environmental compliance | Work Element 165: Environmental Compliance Documentation
Confirm the specific documentation BPA requires.
Prepare and submit a scientific collection permit application to the Oregon Department of Fish and Wildlife.
Prepare and submit a scientific collection permit application to the NOAA Fisheries.
Submit environmental compliance documents to BPA. | $12,102 | 1.64% | 05/01/2009 | 05/08/2009 |
| F | 72606 | 185 | Produce CBFish Status Report | Periodic Status Reports for BPA | The Contractor shall report on the status of milestones and deliverables in Pisces. Reports shall be completed either monthly or quarterly as determined by the BPA COTR. Additionally, when indicating a deliverable milestone as COMPLETE, the contractor shall provide metrics and the final location (latitude and longitude) prior to submitting the report to the BPA COTR. | $6,255 | 0.85% | 07/01/2009 | 12/31/2010 |
| G | 72607 | 189 | Coordination-Columbia Basinwide | Project coordination | Work Element 189: Coordination
Help convene and participate in a biennial conferences covering juvenile salmonid and related relevant research in the LCRE. The concept of a RME project involves coordination across multiple projects such that the integrated whole is greater than the sum of the individual parts. A workshop and/or conference is a useful forum for coordinating, exchanging information, and integrating across projects. In 2006, we coordinated with the BPA, USACE, Columbia River Estuary Study Taskforce, Estuary Partnership, NMFS, and others to convene the Columbia Estuarine Research Conference in Astoria, Oregon, in April 2006. We propose to coordinate and participate in a similar event during 2010.
Consider development of a joint research manuscript. We will consider developing a manuscript for submittal to a peer-reviewed journal. It would cover research and monitoring of subyearling salmon migration characteristics from studies by Ducks Unlimited, NOAA, PNNL, US Geological Survey, and others. This would expedite information dissemination by publishing new data the peer-reviewed literature.
Participate in regional technical groups. We will participate in regional groups such as the Action Agencies’ Estuary/Ocean RME subgroup, the Estuary Partnership’s science workgroup, and the Anadromous Fish Evaluation Program’s science review workgroup. | $14,505 | 1.97% | 05/01/2009 | 12/31/2010 |
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