FY 2003 Mainstem/Systemwide proposal 198740100

Additional documents

TitleType
198740100 Narrative Narrative
198740100 Powerpoint Presentation Powerpoint Presentation
198740100 Sponsor Response to the ISRP Response

Section 1. Administrative

Proposal titleAssessment of Smolt Condition: Biological and Environmental Interactions
Proposal ID198740100
OrganizationU.S. Geological Survey-Biological Resouces Division, Columbia River Research Lab (USGS)
Proposal contact person or principal investigator
NameRobin M. Schrock Or Alec G. Maule
Mailing addressUSGS, Columbia River Research Laboratory, 5501A Cook-Underwood Road Cook, WA
Phone / email5095382299 / Robin_Schrock@usgs.gov
Manager authorizing this projectDr. James G. Seelye
Review cycleMainstem/Systemwide
Province / SubbasinMainstem/Systemwide /
Short descriptionProvide research support to regional hatchery and fishery managers to determine interactions between juvenile salmonid physiological development and the environment that affect smoltification,disease resistance and smolt-to-adult returns.
Target speciessalmon and steelhead
Project location
LatitudeLongitudeDescription
Mainstem/Systemwide Columbia River Basin
Reasonable and Prudent Alternatives (RPAs)

Sponsor-reported:

RPA
184
141
182
188
187

Relevant RPAs based on NMFS/BPA review:

Reviewing agencyAction #BiOp AgencyDescription
NMFS Action 184 NMFS The Action Agencies and NMFS shall work within regional prioritization and congressional appropriation processes to establish and provide the appropriate level of FCRPS funding for a hatchery research, monitoring, and evaluation program consisting of studies to determine whether hatchery reforms reduce the risk of extinction for Columbia River basin salmonids and whether conservation hatcheries contribute to recovery.
NMFS Action 141 NMFS The Action Agencies shall evaluate juvenile fish condition due to disease in relation to high temperature impacts during critical migration periods. This evaluation should include monitoring summer migrants at lower Columbia and lower Snake river dams to clarify the possible link between temperature and fish disease and mortality. This information will be used to assess the long-term impacts of water temperature on juvenile fish survival.

Section 2. Past accomplishments

YearAccomplishment
2002 23rd Smolt Workshop. The Role of Smoltification in an Ecosystem-based Life History Symposium at the international conference: Toward Ecosystem-based Management: Breaking Down the Barriers in the Columbia Basin and Beyond. Spokane, WA April 27.
2002 Odeh, M., R. M. Schrock, and A. L. Gannam. (accepted). Comparative hydraulics of two fishery research circular tanks and recommendations for control of experimental bias. Journal of Applied Aquaculture.
2001 Gannam, A. L. and R. M. Schrock. 2001. Immunostimulants in Fish Diets. In "Nutrition and Fish Health" (C. Lim and C. D. Webster, eds.). The Haworth Press, New York.
2001 Schrock, R.M., S.D. Smith, A.G. Maule, S.K. Doulos, and J.J. Rockowski. 2001. Mucous lysozyme levels in hatchery coho salmon (Oncorhynchus kisutch) and spring chinook salmon (O. tshawytscha) early in the parr-smolt transformation. Aquaculture 198:169-17
2001 Schrock, R. M., R. E. Reagan, and T. E. Batt. 2001. BIGSAM: A Biologically Integrated Geospatial Salmonid data Access and Management tool. Compact disk prototype data access tool. National Biological Information Infrastructure, U. S. Geological Survey
2000 22nd Smolt Workshop. Salmon and Steelhead in the 21st Century. October 30-31. 2000. Boise, Idaho. (Bonneville Power Administration funded, Idaho Department of Fish and Game co-sponsored).
2000 Schrock, R. M., S. P. VanderKooi, A. G. Maule, J. W. Beeman, R. E. Reagan, and K. M. Hans. 2000. Assessment of Smolt Condition for Travel Time Analysis. Summary Report 1999. Report (Contract number DE-A179-87BP35245) to Bonneville Power Administration
1999 Schrock, R. M., R. E. Reagan, P. A. Petrusso and J. Coyle. 1999. Assessment and Analysis of Smolt Condition in the Columbia River Basin. Technical Report, Volume 1. Evaluation of a Modified Feeding Strategy on Growth and Smoltification of Summer Steel
1999 21st Smolt Workshop. Smoltification: changing perspectives in research and management. December 6, 1999. University of Washington, Seattle, WA. (Bonneville Power Administration funded, Oregon Department of Fish and Wildlife and U.W. School of Fisheries
1999 Schrock, R. M., P. V. Haner, K. M. Hans, J. W. Beeman, S. P. VanderKooi, J. D. Hotchkiss, P. A. Petrusso, S. G. Smith and A. G. Maule. 1999. Assessment of smolt condition for travel time analysis. Annual report . (Contract DE-A179-87BP3524
1999 Gannam, A. L. and R. M. Schrock. 1999. Immunostimulants in Fish Diets. Journal of Applied Aquaculture 9(4):53-89.
1999 VanderKooi, S. P. and A. G. Maule. 1999. Incidence of Renibacterium salmoninarum in juvenile spring chinook salmon at Columbia and Snake River hatcheries: 1993-1996. Journal of Aquatic Animal Health 11: 162-169.
1999 Martinelli-Liedtke, T. L., R. S. Shively, G. S. Holmberg, M. B. Sheer, and R. M. Schrock. 1999. Nonlethal gill biopsy does not affect juvenile chinook salmon implanted with radio transmitters. North American Journal of Fisheries Management 19:856-859.
1999 20th Smolt Workshop. February 1-2, 1999. Olympia, Washington. (Bonneville Power Administration funded, Washington Department of Fish and Wildlife co-sponsored).
1998 Schrock, R. M., J. W. Beeman, P. V. Haner, K. M. Hans, J. D. Hotchkiss, S. T. Sauter, S. P. VanderKooi, W. L. Gale, P. A. Petrusso and A. G. Maule. 1998. Assessment of smolt condition for travel time analysis. Project review 1987-1997. Report (Co
1996 Maule, A.G., D.W. Rondorf, J W. Beeman, and P.V. Haner. 1996. Epizootiology of Renibacterium salmoninarum in juvenile hatchery spring chinook salmon in the Columbia and Snake rivers. Journal of Aquatic Animal Health 8:37-46.
1996 Maule, A.G., R.M. Schrock, C. Slater, M.S. Fitzpatrick, and C.B. Schreck. 1996. Immune and endocrine responses of adult spring chinook salmon during freshwater migration and sexual maturation. Fish and Shellfish Immunology 6:221-233.
1995 Project reports and products from 1987 - 1995 can be viewed by searching 1987401 at http://www.efw.bpa.gov/cgi-bin/ws.exe/websql.dir/FW/PUBLICATIONS/QueryPublications.pl

Section 3. Relationships to other projects

Project IDTitleDescription
199005200 Performance/productivity impacts of hatchery supplementation Provide smolt assessment for project.

Section 4. Budget for Planning and Design phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Planning and Design phase

Section 5. Budget for Construction and Implementation phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Construction and Implementation phase

Section 6. Budget for Operations and Maintenance phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Operations and Maintenance phase

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
1. Provide science support and technical assistance to federal, state, and Tribal fishery agencies to determine if juvenile salmonid condition is determined by biological and environmental interactions that are distinguishable from genetic effects. Task 1.1 Prioritize research stocks and select from at-risk species based on HGMP results (RPA 169). 1 $2,000
cost estimate only Task 1.2 Verify genetic origin analysis or conduct genetic sampling/analysis in cooperation with regional genetics programs. ongoing $2,000 Yes
Task 1.3 Develop research design based on site specific environmental variables relevant to ecology of local natural or wild spawning population, and [proximate] hatchery stock. 1 $5,000
Task 1.4 Cooperate with regional management agencies to coordinate juvenile rearing investigations with measures of adult reproductive success. ongoing $0
Task 1.5 Provide analytical support to regional juvenile salmonid projects, complete ongoing analysis and reporting. ongoing $242,000
Task 1.6 Organize annual smolt workshop. 3 $5,000
2. Determine if juvenile salmonids of the same genetic origin show differential growth and condition under varied controlled environmental conditions. Task 2.1 Rear fish of the same genetic origin indifferent environmental regimes from the time of spawning through the time of release. 2 $0
Task 2.2 Use controlled immunostimulant exposures to determine differences in response of fish reared in different environmental regimes. 2 $0
Task 2.3 Analyze physiological and immunological samples from different treatment groups. 2 $0
cost estimate only Task 2.4 Genetic sampling and analysis. ongoing $0 Yes
Task 2.5 Data analysis. 3 $0
Task 2.6 Report preparation. 1 $0
3. Determine if juvenile salmonids of the same species of different genetic origin show differential growth and condition under similar environmental conditions. Task 3.1 Rear fish of known genetic origin in similar environmental regimes from the time of spawning through the time of release. 2 $0
Task 3.2 Use controlled immunostimulant exposures to determine differences in response of fish reared in similar environmental regimes. 2 $0
Task 3.3 Analyze physiological and immunological samples from different treatment groups. 2 $0
Task 3.4 Genetic sampling and analysis. ongoing $0 Yes
Task 3.5 Data analysis. 3 $0
Task 3.6 Report preparation 1 $0
4. Determine if juvenile salmonids of the same genetic origin show differential emigration behavior or seawater survival when reared in different, controlled rearing environments. Task 4.1 PIT tag fish of the same genetic origin reared in different environmental regimes (coordinate PIT tagging with CWT and other PIT tag programs). 2 $0
Task 4.2 Monitor PIT tagged fish during outmigration. 2 $0
Task 4.3 Collect PIT tag/CWT information on adult returns. ongoing $0
cost estimate only Task 4.4 Genetic sampling and analysis of adult returns. 3 $0 Yes
Task 4.5 Data analysis. 3 $0
Task 4.6 Report preparation. 1 $0
5. Determine if juvenile salmonids of the same species of different genetic origin show differential emigration behavior or seawater survival after rearing in similar environmental regimes. Task 5.1 PIT tag fish of different genetic origin reared in similar environmental regimes (coordinate PIT tagging with CWT and other PIT tag programs). 2 $0
Task 5.2 Monitor PIT tagged fish during outmigration. 2 $0
Task 5.3 Collect PIT tag/CWT information on adult returns. ongoing $0
cost estimate only Task 5.4 Genetic sampling and analysis of adult returns. 3 $0 Yes
Task 5.5 Data analysis. 3 $0
Task 5.6 Report preparation. 1 $0
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
1. Provide science support and technical assistance to federal, state, and Tribal fishery agencies to determine if juvenile salmonid condition is determined by biological and environmental interactions that are distinguishable from genetic effects. 2003 2005 $702,000
2. Determine if juvenile salmonids of the same genetic origin show differential growth and condition under varied controlled environmental conditions. 2004 2005 $120,000
3. Determine if juvenile salmonids of the same species of different genetic origin show differential growth and condition under similar environmental conditions. 2005 2006 $120,000
4. Determine if juvenile salmonids of the same genetic origin show differential emigration behavior or seawater survival when reared in different, controlled rearing environments. 2004 2005 $128,000
5. Determine if juvenile salmonids of the same species of different genetic origin show differential emigration behavior or seawater survival after rearing in similar environmental regimes. 2005 2006 $128,000
Outyear budgets for Monitoring and Evaluation phase
FY 2004FY 2005FY 2006FY 2007
$347,550$550,000$365,000$262,500

Section 8. Estimated budget summary

Itemized budget
ItemNoteFY 2003 cost
Personnel FTE: 3.0 $125,000
Fringe 0.3 $32,000
Supplies includes workshop $21,000
Travel $10,000
Indirect 0.38 $68,000
$256,000
Total estimated budget
Total FY 2003 cost$256,000
Amount anticipated from previously committed BPA funds$0
Total FY 2003 budget request$256,000
FY 2003 forecast from 2002$199,821
% change from forecast28.1%
Reason for change in estimated budget

The budget will increase incrementally during the projected period as tasks outlined in the proposed objectives are addressed based on the previous years results. Because of the asynchrony of the spring chinook life history with the funding process, and the uncertainty of permit review timelines, the first major experiment would begin with spawning in the fall of 2003. The major juvenile sampling periods will be in the spring 2004 and 2005, with analysis during the summer and fall. However, during the early implementation period in 2003, genetic information will be gathered, locations for instream smolt sampling will be determined, and coordination with juvenile tagging and adult monitoring programs will be finalized.

Reason for change in scope

The on-going project objectives allow response to manager needs on an as-need basis. New regional priorities, based on the NWPPC Fish and Wildlife Program, and the All-H goal to meet recovery standards have suggested additional project objectives. Based on our 15-year project research, monitoring and evaluation experience with hatchery and wild stocks, we have developed new objectives to address specific RPAs related to differential reproductive success between wild and hatchery-origin fish over the entire life-cycle. Our project expertise is smolt physiology; therefore we are focusing on the long-term effects of the early rearing environment on condition, smoltification and emigration as measures of reproductive success. We will implement associated genetic testing only if that information is not available from other projects, and will coordinate with existing tagging and spawning evaluation projects to insure full life-history data for the proposed work..

Cost sharing
OrganizationItem or service providedAmountCash or in-kind
USGS specific funds for preliminary early rearing research 2001-2003 $149,000 cash

Reviews and recommendations

This information was not provided on the original proposals, but was generated during the review process.

Recommendation:
Fundable only if response is adequate
Date:
Aug 2, 2002

Comment:

Response required, this is a technically inadequate proposal. This proposal is difficult to really understand. The research topic is interesting and the researchers have a long history of working with smolt monitoring in the basin. They are well qualified to conduct this research but the descriptions of methods and tasks are inadequate. This proposal is putatively developed from a continuing task in the basin but appears largely to be about developing a new research topic. If the proponents wish to continue to provide smolt assessments on "an as needed basis" then that should be clearly separated from a new research proposal.

The new topic is to "determine if basic water chemistry and background levels of natural immunostimulants in rearing water sources affect early development of immune response, disease resistance, and long-term survival of eggs, fry, and smolts in relation to adult returns." If during early development, biotic and abiotic characteristics of the aquatic rearing environment determine immune competence and disease resistance, then this innovative research could be very important to the basin. However, it is not possible to assess the research proposed from this proposal. The method isn't well described here--a preliminary study design is given, but no data from that study are presented. No design for statistical analysis is presented. The intention and value of the genetic screening are not clear.

Annual ongoing tasks concerning smolt condition should be clearly identified in a separate proposal. It should be designed to directly assist facility managers throughout the program.


Recommendation:
High Priority
Date:
Oct 24, 2002

Comment:

There appears to be a significant change in scope for this ongoing project. There was some question whether this project should be viewed as a new proposal, rather than an ongoing, planned study as originally proposed. The proposal is taking on a new path in developing it's own study design and research plan. The ISRP has raised significant concerns regarding the study design. Some of the CBFWA reviewers agree with their concerns and will provide additional comment.
Recommendation:
High Priority
Date:
Oct 24, 2002

Comment:

2003 budget revision includes use of part-time personnel, limiting technical assistance to two ongoing projects, running smolt workshop locally to eliminate travel, and limiting site visits and meetings for coordination and set-up of 2004 and 2005 tasks. 2004 revision includes using wild/natural stock that is already part of the Upper Columbia River PIT tagging effort and elimination of seawater survival evaluation at the marine field station. 2005 revision assumes a reduction in number of sample dates, samples and number of analyses run based on 2004 results; genetic analysis by other BPA project; coordination of PIT tagging with basin-wide effort; sampling by hatchery and field crews; and elimination of seawater survival experiment at the marine field station. Additional information was provided by the project sponsor including a response to CBFWA's review. This information is available on request from CBFWA.
Recommendation:
Fund
Date:
Nov 5, 2002

Comment:

Fund in part (qualified). Agree in part with CBFWA's High Priority ranking. The annual ongoing tasks concerning smolt condition or quality, clearly identified in a project designed to directly assist facility managers, appear fundable. However, regional support needs to be demonstrated that this is a needed ongoing required task. The sponsor's proposal to begin a major new project on environmental determinants of early development of the immune system may be valuable; but the Council should understand what it is supporting. A well-designed experiment on this issue could have significant scientific value, but an adequate design is not provided in the proposal or response.

The research topic is interesting and the researchers have a long history of working with smolt monitoring in the basin. They are well qualified to conduct this research but the descriptions of methods and tasks are inadequate. This proposal is putatively developed from a continuing task in the basin, but appears largely to be about developing a new research topic.

It is worth noting that the CBFWA reviewers raised many of the same concerns as the ISRP about whether this represented evolving ongoing work, or a new proposal.

CBFWA: There appears to be a significant change in scope for this ongoing project. There was some question whether this project should be viewed as a new proposal, rather than an ongoing, planned study as originally proposed. The proposal is taking on a new path in developing its own study design and research plan. The ISRP has raised significant concerns regarding the study design. Some of the CBFWA reviewers agree with their concerns and will provide additional comment.
The ISRP's preliminary comments noted that the new portion of the proposal needed to be separated from the ongoing portion of the proposal, the new portion needed to be justified as to why it was appropriate as an extension of "smolt condition", and it needed to be supported by an appropriate experimental design (including clarification of the genetic issues). The response failed to provide adequate detail on the ISRP preliminary concerns about study methods, statistical design, and additional information on the intention and value of the genetic screening. Also in their response, project sponsors strongly disagreed with the ISRP and CBFWA assessment that the proposed research is new, and should be separated from their continuing provision of smolt assessments.
Recommendation:
Date:
Jan 21, 2003

Comment:

Statement of Potential Biological Benefit
Indirect. Investigates the fundamental biological questions related to developmental differences between wild, natural, and hatchery salmonids specifically if exposure to different water sources affects physiological condition, immunological factors, and survival and if fish from different stocks demonstrate different ranges of immunological response and disease resistance based on the rearing environment.

Comments
The proposal clearly lacks rigor in the description of the experimental design. The different treatments are fairly well presented, but the response variables are not well-defined. First, what are the specific physiological and immunological tests to be performed? This may be the most easily-obtained information from the study, but the proposal provides no details. The most glaring weakness is the lack of any statistical design. For instance, “long-term survival” is mentioned several times as a response variable but never clearly defined. Because of this, no power analysis was conducted to determine sample sizes. If one of the goals is to assess delayed mortality, then it is clear that adult return rate will need to be measured. To distinguish among treatments, thousands of fish will need to be tagged per treatment. Is this the scale the researchers envisioned? Also, it is doubtful if enough wild fish will be available to extend the analysis to wild populations. Finally, the statement that the survival of hatchery fish is suppressed relative to wild stocks is not necessarily true. In recent years, smolt-to-adult return rates of hatchery and wild PIT-tagged fish have been nearly equivalent.

Already ESA Required?
No

Biop?
Yes


Recommendation:
Do Not Fund (Tier 3)
Date:
Jun 11, 2003

Comment:

Category:
3. Other projects not recommended by staff

Comments:


Recommendation:
Date:
Sep 20, 2003

Comment: