Crims Island Habitat Restoration proposal 200734600

FY07-09 proposal 200734600

Section 1. Administrative

Proposal title	Crims Island Habitat Restoration
Proposal ID	200734600
Organization	US Geological Survey (USGS) - Cook
Short description	The goal of this project is to describe the response of juvenile salmonids and biological productivity to tidal marsh restoration at Crims Island in the Columbia River Estuary.
Information transfer	Information will be disseminated in the form of project reports, peer reviewed jounals, and scientific presentations.
Proposal contact person or principal investigator

Contacts

Contact	Organization	Email
Form submitter
Kenneth Tiffan	U.S. Geological Survey	ken_tiffan@usgs.gov
All assigned contacts
Michele Beeman	U.S. Geological Survey	michele_beeman@usgs.gov
Kenneth Tiffan	U.S. Geological Survey	ken_tiffan@usgs.gov
Kenneth Tiffan	U.S. Geological Survey	ken_tiffan@usgs.gov

Section 2. Locations

Province / subbasin: Columbia Estuary / Columbia Estuary

Latitude	Longitude	Waterbody	Description
46.17163	123.14275	Columbia River	Crims Island, Columbia River Mile 56

Section 3. Focal species

primary: Chinook Lower Columbia River ESU
primary: Chum Columbia River ESU
secondary: All Anadromous Salmonids
secondary: Other Resident
Additional: Banded killifish

Section 4. Past accomplishments

Year	Accomplishments

Section 5. Relationships to other projects

Funding source	Related ID	Related title	Relationship
Other: USACE	[no entry]	Tiffan et al. 2003, 2004, 2006: Crims Island Habitat Restoration in the Columbia River Estuary-Fisheries Monitoring and Evaluation	The project sponsor has conducted 2 years of pre-restoration fisheries monitoring and data collection at Crims Island, and the first year of post-restoration data will be collected in 2006. The proposed project would be a continuation of these efforts and will result in data and information that can be used to better gage the success of Crims Island restoration beyond a single year of post-restoration monitoring.
Other: USACE	[no entry]	McComas et al. 2001-2003: A study to estimate salmonid survival through the Columbia River estuary using acoustic tags	This project tracks the survival of juvenile salmon from Bonneville Dam to the Pacific Ocean. An important component of this survival, especially for Chinook salmon, is an increased understanding of the importance and value of rearing habitat as is being restored and monitored at Crims Island
Other: USACE	[no entry]	Bottom et al. 2001-2003: Estuarine habitat and juvenile salmon – current and historic linkages in the lower Columbia River and estuary	The results of the proposed research and monitoring at Crims Island will be directly comparable to data collected for this study. Our approach and methodologies are similar to those used for this project
BPA	200301000	Historic Hab Food Web Link Sal	The results of the proposed research and monitoring at Crims Island will be directly comparable to data collected for this study. Our approach and methodologies are similar to those used for this project. Food web linkages are an important aspect of the proposed work
Other: USACE	[no entry]	Thom et al. 2003-2005: Evaluating the Cumulative Ecosystem response to Restoration Projects in the Columbia River Estuary	Methodologies developed from this project will be incorporated into monitoring activities at Crims Island
BPA	200301100	Columbia R/Estuary Habitat	Crims Island is the first of six priorities for this project
BPA	200300800	Pres/Restore Col R/Est Willapa	This is the specific project to purchase and restore Crims and Walker Islands for juvenile salmon and Columbian white tailed deer
BPA	200300700	Lwr Col River/Est Eco Monitor	The project sponsor has kept LCREP informed of monitoring activities at Crims Island

Section 6. Biological objectives

Biological objectives	Full description	Associated subbasin plan	Strategy
Evaluate biological productivity	Determine if habitat restoration at Crims Island increases biological productivity of salmonid rearing habitats and detrital export	Lower Columbia	EH.S5. EH.M4.
Juvenile salmon residence, growth, and seasonality	Determine if restoration of Crims Island benefits juvenile salmon by increasing their growth, residence time, and seasonal use of restored habitats	Lower Columbia	EH.S5. EH.M4.

Section 7. Work elements (coming back to this)

Work element name	Work element title	Description	Start date	End date	Est budget
Produce Environmental Compliance Documentation	Secure sampling permits	Secure ESA Section 10 scientific research permit and Oregon and Washington fish collection permits in place prior to sampling	1/1/2007	2/15/2009	$3,000
Biological objectives Evaluate biological productivity Juvenile salmon residence, growth, and seasonality			Metrics
Manage and Administer Projects	Manage project	The Principal Investigator will be responsible for project management and organizational responsibilities	1/1/2007	12/31/2009	$6,000
Biological objectives Evaluate biological productivity Juvenile salmon residence, growth, and seasonality			Metrics
Produce/Submit Scientific Findings Report	Produce Annual Report	Annual reports to BPA’s COTR will be prepared by the USGS. Reports will summarize the results obtained that year. Reports will follow standard scientific format and include an executive summary, introduction, methods, results, discussion, recommendation, and literature cited section, as well as tables, figures and data appendices	6/15/2007	1/31/2010	$500
Biological objectives Evaluate biological productivity Juvenile salmon residence, growth, and seasonality			Metrics
Produce/Submit Scientific Findings Report	Produce article(s) for submission to peer-reviewed journals	After the final year of data collection, or sooner if the data warrants, the principal investigator will prepare and submit one or more scientific manuscripts to Transactions of the American Fisheries Society, North American Journal of Fisheries Management, and/or other appropriate outlets	6/15/2009	1/31/2010	$8,000
Biological objectives Evaluate biological productivity Juvenile salmon residence, growth, and seasonality			Metrics
Produce/Submit Scientific Findings Report	Produce project completion report	In the final year of the project, the principal investigator will prepare a project completion report for the project which will summarize all years of data collected for the project and will include the final year’s data. The completion reports will follow standard scientific format and include an executive summary, introduction, methods, results, discussion, recommendation, and literature cited section, as well as tables, figures and data appendices	6/15/2009	1/31/2010	$4,000
Biological objectives Evaluate biological productivity Juvenile salmon residence, growth, and seasonality			Metrics
Produce/Submit Scientific Findings Report	Produce quarterly reports	Quarterly reports to BPA’s COTR will be prepared by the USGS every three months. These reports will summarize significant results and activities from the quarter, problems or schedule deviations, and activities and schedule for the upcoming quarter. A quarterly report will not be produced for the last quarter	3/29/2007	10/1/2007	$3,000
Biological objectives Evaluate biological productivity Juvenile salmon residence, growth, and seasonality			Metrics
Analyze/Interpret Data	Calculate and compare benthic invertebrate diversity indices in restored and reference habitats	Benthic invertebrates will removed from samples enumerated, identified to the lowest practical taxon, and dried and weighed. The mean number of taxa, mean number of individuals per taxa (organisms m-2), and standard deviation (SD) for each sampling site will be calculated. Community structure indices will be used to evaluate benthic invertebrate densities at the T-channel, mainstem river site, and the tidal marsh reference site. We will use two community structure indices to measure diversity between sampling sites: the Shannon-Weaver index for Diversity (H) and Evenness (J). Diversity (H) is expressed as: k H= -S pi log10 pi I=1 where k = number of categories (taxa) and pi = the number of observations in a category/sample. The second index, Evenness (J), expresses the observed diversity as a proportion of the total possible diversity, ranging from 0 to 1, with 1 being the highest possible diversity given the total number of taxa present in the study area. Evenness is expressed as: J= H/log10 k where H=Shannon-Weaver index and k=number of categories (taxa). ANOVA will be used to compare invertebrate density and diversity within and between sites. Invertebrate densities will be tested for normality and, if necessary, transformed prior to performing the ANOVAs. We expect that over time restored habitat will support a more diverse benthic community than existed prior to restoration. Greater benthic invertebrate production should translate to higher growth opportunity for juvenile salmon.	2/15/2007	7/15/2009	$27,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Monitoring Secondary R, M, and E Type: Uncertainties research Secondary R, M, and E Type: Status and Trend Monitoring
Analyze/Interpret Data	Calculate and compare drift invertebrate diversity indices in restored and reference habitats	See Work Element 2.2 – ‘Calculate and compare benthic invertebrate diversity indices in restored and reference habitats’ for methods.	2/15/2007	7/15/2009	$28,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Status and Trend Monitoring
Analyze/Interpret Data	Calculate and compare residence times of juvenile salmon in restored and reference habitats	We will construct recapture distributions and determine median residence times for each site. We will qualitatively compare median residence times in reference and restored habitats to determine if they are similar or different. Mean fish size at recapture will be calculated for each sampling time and compared between sampling times to determine if fish size differs over time. Recapture distributions will be graphically compared to tidal cycle data to determine if recapture rate is related to the incoming or outgoing tide. Finally, recapture distributions will be compared between the reference tidal marsh and the restoration area using the Kolomogorov-Smirnov test (alpha=0.05).	2/15/2007	7/15/2009	$32,000
Biological objectives Juvenile salmon residence, growth, and seasonality			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Analyze/Interpret Data	Create yearly post restoration maps using a GIS	Elevation and position data will be input into ArcInfo GIS software to create topographic coverages for Crims Islands. We will create color contour plots of the post-restoration island for comparison to pre-restoration data collected in 2003. Additional data layers (e.g., terrestrial vegetation type and coverage) can be added for future use by those involved in the Crims Island restoration project.	2/18/2007	1/31/2010	$990
Biological objectives Evaluate biological productivity			Metrics
Analyze/Interpret Data	Describe seasonal use and abundance of salmonids in restored and reference habitats	Fish catch data will be used to create seasonal frequency distributions of abundance for each salmonid species. Date of peak abundance will be determined from each distribution as well as the dates of first and last observation. Catch data will be related to physical habitat variables at the different sites through correlation analyses to determine the habitat conditions most preferred at each site. Abundances will also be examined in relation to water temperature to determine at what temperature salmonids no longer use tidal marsh habitats at Crims Island.	2/15/2007	7/15/2009	$27,000
Biological objectives Juvenile salmon residence, growth, and seasonality			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Analyze/Interpret Data	Measure and compare detrital export from restored and reference habitats	Collected detritus will be identified to the lowest practical taxon, dried, and weighed. Composition and dry weight will be compared between sites using percent occurrence and percent of total weight to determine the source of organic material making the greatest contribution to detrital drift. All data will be standardized to the amount of water strained by the drift net during sampling. We expect that as restored habitats recover from the construction process and begin to support a tidal marsh vegetation community and a mature riparian forest that organic input will increase. Consequently, greater export of detritus to the estuary should occur.	2/15/2007	7/15/2009	$27,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Analyze/Interpret Data	Measure and compare prey consumption indices of juvenile salmon and banded killifish in restored and reference habitats	Organisms from fish stomachs will be identified and enumerated to the lowest practical taxon. The number, weight, and frequency of occurrence of prey items will be used to determine the importance of prey items, using the Index of Relative Importance (IRI) (Pinkas et al. 1971). IRI values will be converted to percentages (McCabe et al. 1986; Muir and Emmett 1988) with high percent IRI values indicating greater importance of a food group. An Index of Feeding (IF) (McCabe et al. 1986) will measure the amount of food eaten by juvenile salmon. The IF is the weight of the stomach contents divided by the weight of the fish. High IF values indicate a greater amount of food in the stomach at the time the sample was collected and will serve as an indicator of the relative condition of fish. Our sample sizes for food habits are similar to than those used by Bottom and Jones (1990). IRI and IF values will be compared using ANOVA with sampling location and sampling period as the main effects. Normal probability plots of residuals vs. predicted values will be used to assess normality and constant variance and IRI values will be transformed as necessary. Interactive effects between sampling period and sampling location will be examined prior to main effects differences. Mean IRI and IF values will also be compared for juvenile Chinook salmon and banded killifish to determine the degree of overlap between their diets.	2/15/2007	7/15/2009	$30,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Reseach Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Analyze/Interpret Data	Measure and compare productive capacity and sediment characteristics in restored and reference habitats	We will measure dissolved total organic carbon (mg L-1) from whole water samples collected at each site and particulate total organic carbon (mg L-1) from sediment samples at each site using a CHN analyzer (Small et al. 1990). Sediment samples will also be analyzed for median grain size and percent sand/silt/clay. Mean total organic carbon levels will be calculated for water and sediments samples for each site and sampling date. Differences in mean total organic carbon will be compared between sites and sample dates using two-way ANOVA. Normal probability plots of residuals vs. predicted values will be used to assess normality and constant variance and total organic carbon values will be transformed as necessary. Interactive effects between sampling period and sampling location will be examined prior to main effects differences.	2/15/2007	7/15/2009	$7,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Collect/Generate/Validate Field and Lab Data	Collect benthic invertebrates in restored and reference habitats	Invertebrate samples will be collected to compare the relative productivity of the benthic invertebrate community in restored and reference habitats. We will collect ten benthic samples from each site using a 174.6-cm3 PVC coring device (McCabe and Hinton 1996) every other week from February through July. Ten samples will be collected and treated as replicates for subsequent analyses of the benthic community. Collected organisms will be preserved in 95% ethanol.	2/15/2007	7/15/2009	$60,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Reserach Secondary R, M, and E Type: Uncertainties research
Collect/Generate/Validate Field and Lab Data	Collect drift invertebrates in restored and reference habitats	Because of the importance of drift invertebrates to juvenile salmon at Crims Island, we will collect three replicate drift invertebrate samples at each site to describe the relative abundance and diversity of invertebrates in the drift. Drift samples will be collected using a metered 150-micron mesh drift net with a mouth opening of 35 x 50 inches (Haskell et al. 2005a). Samples will be collected every other week. A boat mounted net will be moved through the water for a period of 5 min. A General Oceanics flow meter attached inside the mouth of the net will be used to calculate the amount of water strained for each sample. Captured organisms will be preserved in 95% ethanol.	2/15/2007	7/15/2009	$30,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Collect/Generate/Validate Field and Lab Data	Collect juvenile salmonid and banded killifish stomach contents in restored and reference habitats	Every other week, 10 juvenile Chinook and 10 banded killifish will have their stomach contents removed using non-lethal lavage in both the restoration area and the tidal reference marsh to compare metrics of feeding activity between the two sites. The lavage instrument will be a 30 ml syringe with a 100µL pipette tip affixed to the end. Each fish will be anesthetized and the pipette tip will be inserted to the head of the stomach. Distilled water will be used to flush the contents of the stomach into a Whirl-Pak, which will be frozen on dry ice for subsequent analyses. USGS personnel have used this technique to successfully remove up to 93% of the stomach contents of Chinook salmon as small as 42 mm in both the Snake and Columbia rivers.	2/15/2007	7/15/2009	$30,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Collect/Generate/Validate Field and Lab Data	Collect macro detritus from restored and reference habitats	Since tidal marsh habitat restoration at Crims Island has the potential to increase detrital export to the estuary, we will collect and compare detrital export between restore and reference habitats. We will sample particulate organic matter (>150 um) every other week by collecting three replicate drift samples in restored and reference habitats concurrent with Work Element 2.3. Samples will be collected during outgoing tides. The net will be walked upstream for a period, or held stationary for a period of 5 min depending the flow and morphology of each site. A General Oceanics flow meter attached inside the mouth of the net will be used to calculate the amount of water strained for each sample. Collected organic material will be stored in bags and frozen for subsequent analysis.	2/15/2007	7/15/2009	$30,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Collect/Generate/Validate Field and Lab Data	Collect position and elevation data in the restored area at Crims Island	Habitat restoration at Crims Island resulted in substantial topographic changes. The elevation of the restoration area was lowered by 2 ft, new channels were created, and existing banks re-sloped. To quantify these changes and monitor changes over time, position and elevation data will be collected using a survey grade, real-time kinematic (RTK) GPS to construct a topographic map of the study area. A high density of points (1 point/4m2) will be collected in primary restoration areas, and fewer points will be collected elsewhere depending on topographical complexity. The accuracy for the RTK is +2.45 cm on the vertical plane and +1.45 cm on the horizontal plane.	2/15/2007	2/17/2009	$750
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Collect/Generate/Validate Field and Lab Data	Collect salmonids, other fishes, and habitat data in restored and reference habitats	Fish assemblages at Crims Island will be sampled to document seasonal fish abundance, timing of habitat use, and life history. Data collection will focus on juvenile salmon, however other fishes will also be identified, measured, and enumerated. We will sample fish every week from February through July each year at the T-channel (restoration area), Reference Tidal Marsh, and the Columbia River Mainstem (Figure 1). We will use beach seines and fyke nets with 4.7 mm mesh to capture fish. Beach seines (15.2 m x 6 m) will be used at the Reference Tidal Marsh, Columbia River Mainstem sites, and in the main inlet channel to the T-channel. Beach seine sites will be sampled by pulling the seine parallel to shore for a distance of roughly 50 m. Smaller stick seines and fyke nets will also be used in the secondary and tertiary channels in the restoration area. The T-channel will also be sampled with dual fyke nets; one facing upstream and the other facing downstream. Fyke nets will be suspended from a wooden beam support system and raised and lowered with the flood and ebb tide with pulleys and a hand crank mounted on both shores. Floats will be attached to the frame of the fyke nets for use in the deeper water of the channel. Each fyke net has additional netting on the bottom of each wing because of the greater depths in the channel and 3/16” chain is attached to the bottom of the wings to insure that the nets remain on the channel bottom. This configuration will enable us to simultaneously collect fish moving in either direction in the T-channel and to raise and lower the nets with changes in tide. We will collect fish from both nets at 1-h intervals. Forty juvenile salmonids of each species and life history type will be measured to the nearest millimeter fork length, weighed to the nearest 0.1 g, and released. Forty individuals of all other species will be measured and released. When large numbers of non-salmonid juveniles are present, total numbers for these species will be estimated before release. Concurrent with fish collections, data will be collected at each site to describe the physical habitat following the methods of Key et al. (1994). The following information will be collected at each beach-seine and fyke-net site: water depth, water velocity, and water temperature measured at a distance of 1, 7.5, and 15 m from shore. Turbidity was measured to the nearest 0.1 Nepholometric Turbidity Unit (NTU).	2/15/2007	7/31/2009	$120,000
Biological objectives Juvenile salmon residence, growth, and seasonality			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Staus and Trend Monitoring
Collect/Generate/Validate Field and Lab Data	Collect sediment and water samples in restored and reference habitats	The construction process to restore tidal marsh habitat had the potential to greatly affect the productive capacity of the underlying soil since the top 2 ft of topsoil was removed in areas that will be inundated and used by fish. We will measure total organic carbon in both water and soil samples in both the restoration area and at the Reference Tidal Marsh to determine the effect of soil removal on productive capacity. We will collect five whole water and sediment samples every month from February through July at each site. Sediment samples will be collected using a 174.6-cm3 PVC coring device (McCabe and Hinton 1996) and frozen on dry ice for subsequent analysis. Water samples will be kept on ice or refrigerated until analysis.	2/15/2007	7/15/2009	$6,000
Biological objectives Evaluate biological productivity			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Collect/Generate/Validate Field and Lab Data	Compare growth of juvenile salmon in restored and reference habitats	Weekly length frequency histograms will be constructed to calculate changes in relative growth over time within and between sites. Because there will be a continual influx of smaller fish and efflux of larger fish into rearing habitats over time, changes in fork length over time will only represent growth in a relative sense. Mean weekly fork lengths will be compared within and between sites using analysis of variance (ANOVA; alpha=0.05). All data will be tested for normality and transformed, if necessary, prior to performing the ANOVAs.	2/15/2007	7/15/2009	$27,000
Biological objectives Juvenile salmon residence, growth, and seasonality			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Collect/Generate/Validate Field and Lab Data	Recapture marked fish for residence time analysis	After release, fish will be recaptured using beach seines or fyke nets every 4 hours for a period of 5 days, then daily thereafter until recapture rates drop to less than 5% of the number released. All captured fish will be examined with a Calcein detector for presence of a mark. Marked fish will be enumerated, measured, and released.	2/15/2007	7/15/2009	$90,000
Biological objectives Juvenile salmon residence, growth, and seasonality			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring
Mark/Tag Animals	Capture and mark juvenile salmonids for residence time analysis	We propose to capture, mark, and release juvenile salmon monthly from February through June in restored and reference habitats. We will attempt to mark and release 500 fish each in the restoration area and the tidal reference marsh. This number of fish represents the best compromise between obtaining adequate numbers of recaptures and the effort and handling required to obtain fish for marking. Half of the fish will be randomly assigned to and released in the reference tidal marsh site and the other half will be released into the restoration area. Fish will be captured and marked with Calcein monthly. Because conventional marking techniques (PIT tagging, telemetry) are inappropriate for marking fry, we will use a fluorochrome dye, Calcein, to batch mark Chinook salmon fry and juveniles at Crims Island. This innovative technique leaves a permanent mark on bony structures and scales and is easily detectable under the proper ultraviolet light conditions, but is otherwise undetectable. Furthermore, large numbers of small salmon can be batch marked with minimal handling while remaining in water. Because this technique can be used to mark very small fish and is detectable through the life of a fish, it may be an important, non-lethal monitoring tool for Pacific salmon. Calcein has already been successfully used with Atlantic salmon fry and laboratory trials indicated no increased predation risk to marked fish (Mohler 1997; Mohler et al. 2002). This drug is still awaiting FDA approval; however the USGS is registered as a member of an INAD (Investigational New Animal Drug) for initial use of this product. Using Calcein in 2004, the USGS successfully marked and released over 2,300 fish smaller than 60 mm at Crims Island. We propose to mark subyearling Chinook salmon for residence time estimation because they are the most abundant salmonid in the study area. Fish will be collected with beach seines or fyke nets and held in net pens attached to a floating dock in Bradbury Slough for 1-3 d prior to marking. Methods used in marking followed those developed by Mohler (1997) for juvenile Atlantic salmon. Prior to marking, a 1.5% (15g L-1) salt solution and a 0.5% Calcein solution will be prepared in separate plastic basins using fresh river water. Subyearling Chinook salmon will be marked by placing about 150 fish in a plastic basin with a mesh bottom that will be stacked in another unmodified plastic basin of the same size, which will contain fresh river water. Fish will be marked by first placing them into the salt solution for 3.5 min followed by brief draining and then immediately placing them into the Calcein solution. Fish will be kept in the Calcein solution for 3.5 min. before being returned to fresh river water for recovery. After marking, fish will be held in net pens over night prior to release.	2/15/2007	6/15/2009	$30,000
Biological objectives Juvenile salmon residence, growth, and seasonality			Metrics Focal Area: Estuary Primary R, M, and E Type: Action Effectiveness Research Secondary R, M, and E Type: Uncertainties Research Secondary R, M, and E Type: Status and Trend Monitoring

Section 8. Budgets

Itemized estimated budget

Item	Note	FY07	FY08	FY09
Personnel	[blank]	$90,009	$90,009	$90,009
Fringe Benefits	[blank]	$27,003	$27,003	$27,003
Travel	20 days	$7,200	$7,200	$7,200
Overhead	[blank]	$68,720	$68,720	$68,720
Supplies	Nets, Sample Jars, Ethanol, Dry Ice, Sediment Analysis	$5,820	$5,820	$5,820
Other	Vehichle and Boat	$10,328	$10,328	$10,328
Totals		$209,080	$209,080	$209,080

Total estimated FY 2007-2009 budgets

Total itemized budget:	$627,240
Total work element budget:	$627,240

Cost sharing

Funding source/org	Item or service provided	FY 07 est value ($)	FY 08 est value ($)	FY 09 est value ($)	Cash or in-kind?	Status
Totals		$0	$0	$0

Section 9. Project future

FY 2010 estimated budget: $92,000
FY 2011 estimated budget: $92,000

Comments: For continued monitoring at a reduced effort

Future O&M costs:

Termination date: 9/30/2012
Comments:

Final deliverables: Final completion report and published journal articles

Section 10. Narrative and other documents

Reviews and recommendations

FY07 budget	FY08 budget	FY09 budget	Total budget	Type	Category	Recommendation
NPCC FINAL FUNDING RECOMMENDATIONS (Oct 23, 2006) [full Council recs]
$0	$0	$0	$0	Expense	ProvinceExpense	Do Not Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$0	$0	$0	$0		ProvinceExpense

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Fundable (Qualified)

NPCC comments: The Crims Island restoration project in the lower Columbia River (LCR) is a major program, and monitoring and evaluation is clearly justified. In addition, little evaluation on habitat action effectiveness for restored tidal marshes in the Columbia is available and so the results of the evaluation will add valuable data to the Regional information base. A possible reference area is nearby on the same island and monitoring data were collected at the site prior to the onset of restoration actions. Both the reference and pre-restoration information can be compared to post-restoration information to assess effectiveness. The proposed work is consistent with Fish and Wildlife Program’s subbasin plans and elements of the Biological Opinion. The work will directly address monitoring requirements called for in the BiOp. The objectives relating to use of Crims Island by migratory salmonids, feeding, benthic community status and elevation analyses have clearly defined and measurable end points, which match objectives in the subbasin plans. However, the ISRP qualifies this “fundable” recommendation because further details on methods and design of the work would enhance the proposal: 1. The proposal would benefit by more details on how the Crims Island project is coordinated with the other restoration and evaluation projects in the lower Columbia River or Columbia River estuary (CRE) such as those being conducted by the Lower Columbia River Estuary Partnership (200300700) or by the USFS at the Sandy River delta (199902500). Has there been direct discussion between the various researchers to try and standard methods (e.g., fish marking techniques, vegetation analyses)? 2. More details on the suitability of Gull Island as a reference site and the rationale for sampling the main stem river would be helpful. Does the name “Gull Island” indicate there are large numbers of potential predators on the island relative to the restored site? Gull Island does not appear to have natural tidal channels which would provide the best “control” as an undisturbed habitat site. Is that why fyke net sampling is not proposed there? 3. The proposal would be clarified by an expansion of the concept that increasing detrital flow from Crims Island will lead to an increase in salmon survival. Is there empirical evidence for this linkage at the LCR or elsewhere? Will the results give data on incremental increase in detrital flow from Crims Island relative to other projects in the LCR or CRE? 4. Expansion or further detail on the following methods would be useful: a. Detrital sampling - Is it possible that benthic algal production from the tidal channels or imported from the main stem river is also important to support invertebrates? It would be helpful if the proponents explained why algae were not considered. b. Sediment organics – The proposal would be enhanced if the researchers explained what they mean by “productive capacity” (PC). It is not clear how organic carbon in sediments will provide an assessment of productive capacity. Has this methodology been used elsewhere? c. Invertebrate sampling - A power analysis to clarify within site variation for core (n=10) and drift (n=3) sampling would be useful. The proponents should clarify how they are going to measure invertebrate productivity since the methods described only measure biomass. The methods used to sample benthic invertebrates (cores) will only partially provide data on fish food availability - the cores will work for Corophium but will not sample drift and surface organisms. Chinook feed from a variety of sites in the water column. The proposal would be improved by an explanation of why more specific methods such as emergent traps for chironomids were not considered. d. Fish abundance, growth, and residency – The proposal would be improved by better justification of attempts to relate habitat variables at the capture sites to fish abundance. Fish likely will be present at a capture sites for reasons other than just the characteristics at that site. The fish don’t have many choices as to where they enter the area and what routes they take once they have entered. Fish may be captured at a site simply because it is the only route of movement. The sponsors indicate that their measurements would only represent “growth in a relative sense.” It would be helpful if the proponents clarified this statement. The methods proposed to measure “growth” are only appropriate for measuring sizes of incoming and outgoing fish. Incoming fish may not necessarily be fish that egressed on the last tide and their residence time and growth attributable to marsh residence would not be known. Also, as the sponsors indicate, the sizes of incoming fish may change over the sampling season. The only reliable way to measure growth would be to mark fish. Even then, if fish move out of the area with the tide and spend time rearing in the mainstem, the increment of growth attributable to tidal marsh residence would be extremely difficult to determine. Will the fish used in the tagging study be those captured in the restored and reference areas? Have the proponents considered the use of scales to measure growth increments, which are correlated with seasonal growth rates? For example, see Fisher, Joseph P., and William G. Pearcy, 2005 Seasonal changes in growth of coho salmon (Oncorhynchus kisutch) off Oregon and Washington and concurrent changes in the spacing of scale circuli. Fisheries Bulletin 103:34-51. 5. The proposal would be improved by further explanation of other personnel/experts involved in the laboratory analyses of water and soil samples and identification of invertebrates, and detritus for this project. 6. The proposal would be enhanced by a discussion of animal care protocols and provisions for live release by catch in seines and fyke nets. The proposal would be improved if a subsample of marked and unmarked fish were held throughout the period of the study (through July) To assess delayed mortality effects due to handling and marking with Calcein have the proponents considered holding a subsample of marked and unmarked fish (to July)? 7. Embayments off mainstem rivers sometimes silt in after a few years. Could this happen with the tidal channels at Crims Island? If silting occurs will this study have to be repeated in the future to evaluate long term benefits to fish? 8. The proposal would be improved by better justification for studying killifish. The existence of diet overlap of salmon and killifish, while it is useful information, does not necessarily indicate that competition is occurring. To demonstrate competition, the sponsors would need to show that killifish actually reduce the density of salmon food organisms and that this reduction results in decreased growth.

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable (Qualified)