FY 2003 Mainstem/Systemwide proposal 200310400
Contents
Section 1. General administrative information
Section 2. Past accomplishments
Section 3. Relationships to other projects
Section 4. Budgets for planning/design phase
Section 5. Budgets for construction/implementation phase
Section 6. Budgets for operations/maintenance phase
Section 7. Budgets for monitoring/evaluation phase
Section 8. Budget summary
Reviews and Recommendations
Additional documents
| Title | Type |
|---|---|
| 35055 Narrative | Narrative |
| 35055 Powerpoint Presentation | Powerpoint Presentation |
| 35055 Sponsor Response to the ISRP | Response |
Section 1. Administrative
| Proposal title | Role of Bacteria as Indicator Organisms for Watershed Assessment and in Determining Fish Pathogen Relationships with Fauna of Abernathy Creek |
| Proposal ID | 200310400 |
| Organization | U.S. Fish and Wildlife Service - Abernathy Fish technology Center (USFWS) |
| Proposal contact person or principal investigator | |
| Name | Richard Glenn |
| Mailing address | 1440 Abernathy Creek Road Longview, WA. 98632 |
| Phone / email | 3604256072 / richard_glenn@fws.gov |
| Manager authorizing this project | Carl Burger |
| Review cycle | Mainstem/Systemwide |
| Province / Subbasin | Mainstem/Systemwide / |
| Short description | The purpose of this project is to develop techniques to assess watershed health and fish health using bacteria as system indicator organisms. |
| Target species | Steelhead Trout (Onchorhynchus mykiss), Cutthroat Trout (Onchorhynchus clarki), Aquatic Ecosystem |
Project location
| Latitude | Longitude | Description |
|---|---|---|
| 46.1825 | -123.1367 | Headwater of Abernathy Creek |
| 46.3075 | -123.225 | Mouth of Abernathy Creek |
| 46.22 | -123.1375 | Abernathy Fish Technology Center |
Reasonable and Prudent Alternatives (RPAs)
Sponsor-reported:
| RPA |
|---|
| Action 1 |
| Action 152 |
| Action 155 |
| Action 198 |
Relevant RPAs based on NMFS/BPA review:
| Reviewing agency | Action # | BiOp Agency | Description |
|---|
Section 2. Past accomplishments
| Year | Accomplishment |
|---|
Section 3. Relationships to other projects
| Project ID | Title | Description |
|---|---|---|
| 30008 | The use of small stream PIT tag monitoring methods to evaluate movements, life history charachteristics and survival of salmonid. | Will collect fish tissue samples from sacrificed fish. |
| RPA Action 1 | Is a USFWS proposed project which provides research, monitoring, and evaluation of hydro resources and habitat. | |
| RPA Action 152 | Federal agency proposed project that will aid in water quality and biological monitoring information for subbasin and watershed assessments. | |
| RPA Action 155 | Project will aid to determine cause and effect relationships and identify research needs for improvement plans. | |
| RPA Action 198 | Is a USFWS project that will provide data for management of water quality and habitat use and restoration. |
Section 4. Budget for Planning and Design phase
Task-based budget
| Objective | Task | Duration in FYs | Estimated 2003 cost | Subcontractor |
|---|---|---|---|---|
| 1. Determine bacterial species found in the water column that are of particular interest. | a. Collect water samples, plate, and isolate specific bacteria. | 1 | $9,000 | |
| b. Send isolates to Microbial ID, Inc. for fatty-acid analysis and positive identification. | 1 | $2,000 | Yes | |
| 2. Develop 16s rDNA PCR primers | a. Use PCR techniques to cut out the 16s rDNA segment. b. Sequence 16s rDNA to determine areas where species specific primers can be developed. | 1 | $17,000 | |
| c. Production of primers at Genosys Biotechnologies. | 1 | $2,000 | Yes | |
| 3. Determine which bacterial species found in the water column are associated with mayfly, stone fly larvae and crawfish | a. Capture representative samples of invertebrates. b. Isolate bacteria from their intestines and body cavities and process specific bacteria. | 1 | $9,650 | |
| 4. Determine which bacterial species found in the water column and associated with invertebrates are associated with fish populations | a. Capture a representative sample of fish of each species of interest and sample intestinal tract and other body cavities and surfaces and process specific bacteria for isolation. | 1 | $9,650 |
Outyear objectives-based budget
| Objective | Starting FY | Ending FY | Estimated cost |
|---|
Outyear budgets for Planning and Design phase
Section 5. Budget for Construction and Implementation phase
Task-based budget
| Objective | Task | Duration in FYs | Estimated 2003 cost | Subcontractor |
|---|
Outyear objectives-based budget
| Objective | Starting FY | Ending FY | Estimated cost |
|---|
Outyear budgets for Construction and Implementation phase
Section 6. Budget for Operations and Maintenance phase
Task-based budget
| Objective | Task | Duration in FYs | Estimated 2003 cost | Subcontractor |
|---|
Outyear objectives-based budget
| Objective | Starting FY | Ending FY | Estimated cost |
|---|
Outyear budgets for Operations and Maintenance phase
Section 7. Budget for Monitoring and Evaluation phase
Task-based budget
| Objective | Task | Duration in FYs | Estimated 2003 cost | Subcontractor |
|---|---|---|---|---|
| 1. Obtain overall view of specific bacteria presence in the creek and watershed | a. Take water samples at predetermined locations to determine presence of specific indicator bacteria by PCR analysis with species-specific primers. | 3 | $11,000 | |
| b. Produce species-specific primers at Genosys Biotechnologies, Inc. | 3 | $1,000 | ||
| 2. Determine the bacterial relationships between bacteria, invertebrates, and fish species of interest. | a. Take tissue samples of invertebrates and fish at the beginning and end of test periods by PCR analysis with species-specific primers. | 3 | $11,000 | |
| b. Produce species-specific primers at Genosys Biotechnologies, Inc. | 3 | $1,000 | ||
| 3. Relate bacterial presence with water quality and environment data | a. At sites and in the lab, run water quality analysis and obtain water environment data | 3 | $2,500 | |
| 4. Relate bacterial presence and environment data to land uses. | a. Use survey maps to assess land uses and environment changes. | 3 | $200 |
Outyear objectives-based budget
| Objective | Starting FY | Ending FY | Estimated cost |
|---|---|---|---|
| 1. Obtain an overall view of specific bacteria and their presence in the creek. | 2004 | 2005 | $59,300 |
| 2. Determine the bacterial relationships between bacteria, invertebrates, and fish species of interest. | 2004 | 2005 | $59,300 |
| 3. Relate bacterial presence with water quality and land use data. | 2004 | 2005 | $500 |
Outyear budgets for Monitoring and Evaluation phase
| FY 2004 | FY 2005 |
|---|---|
| $59,400 | $61,200 |
Section 8. Estimated budget summary
Itemized budget
| Item | Note | FY 2003 cost |
|---|---|---|
| Personnel | FTE: GS-5 | $25,700 |
| Fringe | GS-5 health/dental/life/retirement | $8,500 |
| Supplies | Laboratory and Sampling Supplies | $13,450 |
| Travel | Seminars and conferences | $2,000 |
| Indirect | Overhead costs | $18,350 |
| Subcontractor | Microbial ID, Inc. | $2,000 |
| Subcontractor | Genosys Biotechnologies, Inc | $2,000 |
| Other | Sequencer Training | $4,000 |
| $76,000 | ||
Total estimated budget
| Total FY 2003 cost | $76,000 |
| Amount anticipated from previously committed BPA funds | $0 |
| Total FY 2003 budget request | $76,000 |
| FY 2003 forecast from 2002 | $0 |
| % change from forecast | 0.0% |
Cost sharing
| Organization | Item or service provided | Amount | Cash or in-kind |
|---|---|---|---|
| US Fish and Wildlife Service | 0.75 FTE, GS-7/9 | $30,600 | in-kind |
Reviews and recommendations
This information was not provided on the original proposals, but was generated during the review process.
Fundable only if response is adequate
Aug 2, 2002
Comment:
The objective of this project is to identify bacterial fish pathogens as indicator species for fish and watershed health. This proposal will use polymerase chain reaction (PCR) and species-specific primers to show the presence of aquatic bacteria in water and tissues of living organisms to determine their relationships to aquatic life. The idea is to identify bacteria species that can serve as indicators of aquatic ecosystem health. The technical background to this problem is adequate, as is the relationship to regional programs and other projects. It would help the project to place this work in the context of RPAs under the FCRPS BiOp: the presentation had these listed; they should be added to the proposal?Tasks and methods to meet these objectives are described in a fair amount of detail. However, detail about the sample design is absent. What is the reason for sampling in 10 locations? How did you derive this number of sites? The project proponents will consult with a biostatistician regarding data analysis: this consultation should be done in advance of sampling to ensure that the resulting data analysis has the appropriate statistical power. This comment also applies to the choice of the number of sample sites, which appears to already have been determined to be 10. How many samples will be taken from the ten sample sites, over which period of time?
The proposal could be clearer on how presence of bacteria types will be linked to the level of ecosystem health. Without a control, this work will be limited to establishing a description of the presence of ecosystem conditions in association with certain groups of bacteria, but the study will not generate understanding of processes by which these bacteria/conditions associations work.
The ISRP completed a review of this proposal very recently under the Lower Columbia/Estuary province (June 7, 2002 below). We note that the investigator did not provide further evidence of progress on development of the statistical design; consequently, we again request a response describing a statistically sound study design. This design needs to be in place before the project is started because the design will effect selection of sampling sites.
June 7, 2002 Province Review - ProjectID: 30013 Role of Bacteria as Indicator Organisms for Watershed Assessment and in Determining Fish Pathogen Relationships with Fauna of Abernathy Creek
Sponsor: USFWS
Province: Columbia Estuary
Subbasin: Elochoman
FY03 Request: $71,100
5YR Estimate: $189,690
Short Description: The purpose of this project is to develop techniques to assess watershed health and fish health using bacteria as system indicator organisms.
ISRP Final Recommendation: Fundable (Qualified - see comments)
CBFWA Category: Recommended Action
ISRP Comparison with CBFWA: Agree - Fundable (Qualified)
ISRP Final Review Comments: FundableThe research is interesting and the question is important in regard to non-point source pollution, but the proposal has a strong personal development aspect to its benefits. The ISRP had a number of comments that the author did try to address and did seek the statistical advice suggested. Our principal concern was that the PI did not have the statistical background required by this investigation but the PI has sought consultation on this issue. A requirement of funding for this project should be that the PI is required to submit a completed experimental design developed with full collaboration of a statistician and agreed with by more senior USFWS staff. A design developed in advance of the sampling will assist in interpretation of results and will likely reveal sampling issues before the project begins. The ISRP acknowledges that the idea being examined in this proposal is both different and challenging but we are also recommending funding as a developmental step for a young researcher who impressed the review committee with his presentations and abilities to answer our questions.
CBFWA Review Comments:
This project should be considered under the innovative category (or in the Mainstem and Systemwide Province).
Comment:
This project would appropriately be submitted in the Innovative category if unsuccessful in getting funded in the Systemwide "Province".Comment:
Not Fundable. Disagree with CBFWA's Recommended Action ranking. The ISRP's earlier recommendation of Fundable (qualified) in the Lower Columbia/Estuary Province was contingent upon submission of a completed experimental design developed with full collaboration of a statistician. The Mainstem and Systemwide solicitation and response provided an opportunity to complete an experimental design, but the proposal and response does not provide this.The objective of this project was to identify bacterial fish pathogens as indicator species for fish and watershed health. This proposal would use polymerase chain reaction (PCR) and species-specific primers to show the presence of aquatic bacteria in water and tissues of living organisms to determine their relationships to aquatic life. The idea was to identify bacteria species that can serve as indicators of aquatic ecosystem health. The technical background to this problem is adequate, as is the relationship to regional programs and other projects. The response placed this work in the context of RPAs under the FCRPS BiOp.
Tasks and methods to meet these objectives are described in a fair amount of detail. However, detail about the sample design is absent. The response to the question about sampling design takes the approach of sampling within the constraints of time and personnel, and seems to miss the point that a sampling scheme is determined by the requirements of the statistical analysis necessary to answer the research questions. We are not sure the principal investigator is aware that some analysis may not be better than none if the data are inadequate, and were confused at the process he describes for determining the power of the test etc. after he has sampled. These are the things that determine sample size.
The proposal could be clearer on how presence of bacteria types will be linked to the level of ecosystem health. Without a control, this work will be limited to establishing a description of the presence of ecosystem conditions in association with certain groups of bacteria, but the study will not generate understanding of processes by which these bacteria/conditions associations work. The ISRP does note that the use of bacteria as an indicator of watershed health is a topic worthy of consideration. This proposal though is technically inadequate.
Comment:
Statement of Potential Biological BenefitIndirect. Monitor bacterial indicator species which may make it possible to detect the onset of habitat degradation and predict harmful pathogen growth.
Comments
This proposal may provide some links between aquatic health and microbial communities. However, explicit links to fish survival, or population response appear to be lacking (i.e. it is unclear what the impact that the presence of various microbes or environmental indicators with which they might be associated have on fish population status), somewhat lessening the utility of these metrics. In addition, determining some of the environmental variables (e.g. logging, housing, etc.) may be more challenging than the proposers believe.
Already ESA Required?
No
Biop?
No
Comment:
Category:3. Other projects not recommended by staff
Comments: