FY 2002 Innovative proposal 34001

Additional documents

TitleType
34001 Narrative Narrative

Section 1. Administrative

Proposal titlePilot Study: Spatial and Temporal Occurrence of Salmonid Pathogens in the Upper Middle Mainstem Subbasin of the Columbia Cascade Province
Proposal ID34001
OrganizationWashington State University (WSU)
Proposal contact person or principal investigator
NameFrank Loge
Mailing addressP.O. Box 642910 Pullman, WA 99164-2910
Phone / email5093353227 / floge@wsu.edu
Manager authorizing this projectFrank Loge
Review cycleFY 2002 Innovative
Province / SubbasinColumbia Cascade / Columbia Upper Middle
Short descriptionMonitor the occurrence of salmonid pathogens and assess sources, fate, and transport throughout the subbasin.
Target speciesSalmonids
Project location
LatitudeLongitudeDescription
47.53 -119.91 Entire region of the Columbia Upper Middle Mainstem Subbasin
Reasonable and Prudent Alternatives (RPAs)

Sponsor-reported:

RPA

Relevant RPAs based on NMFS/BPA review:

Reviewing agencyAction #BiOp AgencyDescription

Section 2. Past accomplishments

YearAccomplishment

Section 3. Relationships to other projects

Project IDTitleDescription

Section 4. Budget for Planning and Design phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2002 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 2002 costSubcontractor
Objective 1: Develop a DNA microarray coupled with PCR for multiplex detection of salmonid pathogens 3 $35,058
Objective 2: Characterize the spatial and temporal occurrence of Salmonid pathogens and associated fluctuations in selected water quality parameters within the Upper Middle Mainstem Subbasin of the Columbia Cascade Province. Task 2.1: Identify sample sites 3 $7,250
Objective 2 Task 2.2: Sample collection 12 $62,585
Objective 2 Task 2.3: Analysis of water quality 12 $29,258
Objective 2 Task 2.4: Pathogen analysis 12 $44,016
Objective 3: Identify possible sources of Salmonid pathogens and relationships between the occurrence of pathogens and selected water quality parameters. 3 $21,294
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 2002 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 2002 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Monitoring and Evaluation phase

Section 8. Estimated budget summary

Itemized budget
ItemNoteFY 2002 cost
Personnel FTE: 2.375 $79,621
Fringe Calculated by the Office of Grant and Research Development (OGRD) at WSU $26,451
Supplies Filters for sample collection; expendables for DNA microarray, PCR, and water quality analyses $17,504
Travel Truck rental from WSU motor pool $8,980
Indirect 45% of MTDC Base of $130,900 $58,905
Capital None $0
PIT tags $0
NEPA Proposed research is categorically excluded as per Nancy Weintraub $0
Subcontractor None $0
Other Gas/Oil and Insurance for boat owned and operated by the Washington Water Research Center $8,000
$199,461
Total estimated budget
Total FY 2002 cost$199,461
Total FY 2002 budget request$199,461
Cost sharing
OrganizationItem or service providedAmountCash or in-kind

Reviews and recommendations

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

Recommendation:
Fund - Rank 7
Date:
May 24, 2002

Comment:

This seventh ranked proposal is technically excellent, fundable, and innovative. The idea is so new, however, that it is difficult for the ISRP to evaluate its potential importance to fish or its practical implementation until results are seen (this fits the purpose of the innovative process). While some skepticism is probably warranted about the significance and potential use of these assays for ultimately improving the survival of fish, results should help quantify pathogen loads to which fish are exposed within the basin and should be a valuable tool for observing effects of hatchery practices on pathogen concentrations. For example, results could provide specific information that might inform hatchery managers about suitable timing and locations for releases of hatchery-produced fish to minimize exposures to waterborne pathogens. The proposal allays some skepticism by planning to demonstrate levels of exposure that are effective in inducing example diseases. Thus, when the quantitative distribution of potential pathogens is described, the significance of the findings for disease initiation can be estimated. The ultimate question of whether or not significant losses of fish result from disease, and at what life-stages and locations, may be more readily answered if this rapid assay is available. Reviewers thought the pilot study would be better tested on the Snake River, which appears to be more pathogen prone.

The ISRP reviewed this proposal in the preliminary Columbia Cascade Provincial review and found it to be a good proposal, saying it also would be acceptable as an innovative proposal. However, that proposal was for four years at budgets of ~220K, 255K, 263K, and 68K. This pilot version retains the scientific elements that were viewed favorable in the Columbia Cascade but for a more limited study.

This proposal would use innovative DNA-based detection techniques to assay selected waters of the upper middle Columbia River basin (Columbia Cascade Province) for presence and relative abundance of several fish pathogens. Synoptic information on the occurrence of pathogens in broad regions has been hampered by lack of rapid detection techniques (reliance on standard culture approaches). This project would develop for fish pathogens a recently developed DNA-based detection system that has already been demonstrated successfully for human pathogens. The work is broken down into three explicit phases: methods development, pilot survey of selected waters, and search for sources of pathogen contamination. The detection technique would first be adapted for specific fish pathogens. The technique would then be applied to detection of fish pathogens in water samples collected from representative sites throughout the upper middle basin. The analyses would be quantitative. They can process great amounts of water and have fine scale detection rate -- 0.002 organisms per liter. They would quantify the significance of the presence of pathogens in the environment to actual infection of fish, using quantitative exposure-response equations. A dose-response relationship would be evaluated to suggest whether the quantities of pathogens per unit of water are sufficient to be an infectious problem for fish. Initial efforts would be made to locate the source(s) of pathogens in the water (e.g., hatchery effluents, polluted waters).

This proposal describes the new technique in appropriate detail to be persuasive that it is something worth pursuing for both its technique development and for the pathogen characterization it would provide. The proposed work is certainly innovative (has not been used for fish projects in the Northwest) and meets the ISRP criteria of sound science, consistency with the FWP, has potential benefit to fish, has clear objectives and expected outcomes, and has appropriate monitoring and evaluation in the form of quality assurance. The proposal goes through a rationale for regional relevance. There is a good attempt to integrate the proposed work with other pathogen projects (few) and other regional assessments. There are good hypotheses, objectives, tasks, and a good timeline. The presentation for the province review noted that initial samples will be taken from hatchery outfalls where pathogens could be expected to be most easily detected. Methods are presented in detail. Expected benefits overall, and benefits to fish are explicitly described. Facilities appear to be excellent and suitable (since the sort of work has already been done for human pathogens). The authors cite abundant, relevant scientific literature. There is an excellent set of resumes for well-qualified staff. The project meets ISRP evaluation criteria.


Recommendation:
High Priority
Date:
Jun 28, 2002

Comment:


Recommendation:
Date:
Jul 12, 2002

Comment:

Statement of Potential Biological Benefit
Indirect benefits. This proposal describes the development and use of a multiplex method coupling PCR and DNA microarray analysis to detect infectious salmonid pathogens in water samples, and to use the method to characterize spatial and temporal occurrences of these pathogens in selected areas of the Columbia Cascade Province. This information would then be used in an attempt to identify possible sources of the pathogens, and determine the possible relationships between pathogen occurrence and specific water quality parameters. If successful, it has the potential to reduce disease in listed fish.

Comments
The methodology is well thought out, can be highly specific and extremely sensitive, and has been used for detection of human pathogens in environmental samples. The method has great advantages over standard microbiological culturing methods, and its multiplex nature is much more flexible than other sample concentration and PCR methods, allowing simultaneous detection of multiple pathogens in a single reaction. The strength of the proposed method and the data to be collected by it lies in the determination of the spatial and temporal relationships between the presence of a particular pathogen in different aquatic habitats, as outlined in Phase 3. Such information, when combined with future epizooilogical data on disease outbreaks in a specific location or habitat, will help in the determination as to whether certain habitat conditions, man-made or natural, contribute to infectious disease outbreaks that impact threatened and endangered salmon runs.

Already ESA Required?
No

Biop?
No


Recommendation:
Date:
Jul 12, 2002

Comment:

Statement of Potential Biological Benefit to ESU
Indirect benefits. This proposal describes the development and use of a multiplex method coupling PCR and DNA microarray analysis to detect infectious salmonid pathogens in water samples, and to use the method to characterize spatial and temporal occurrences of these pathogens in selected areas of the Columbia Cascade Province. This information would then be used in an attempt to identify possible sources of the pathogens, and determine the possible relationships between pathogen occurrence and specific water quality parameters. If successful, it has the potential to reduce disease in listed fish.

Comments
The methodology is well thought out, can be highly specific and extremely sensitive, and has been used for detection of human pathogens in environmental samples. The method has great advantages over standard microbiological culturing methods, and its multiplex nature is much more flexible than other sample concentration and PCR methods, allowing simultaneous detection of multiple pathogens in a single reaction. The strength of the proposed method and the data to be collected by it lies in the determination of the spatial and temporal relationships between the presence of a particular pathogen in different aquatic habitats, as outlined in Phase 3. Such information, when combined with future epizootilogical data on disease outbreaks in a specific location or habitat, will help in the determination as to whether certain habitat conditions, man-made or natural, contribute to infectious disease outbreaks that impact threatened and endangered salmon runs.

Already ESA Req? No

Biop? No