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 | 30013 |
| 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 / [email protected] |
| Manager authorizing this project | Carl Burger |
| Review cycle | Columbia Estuary |
| Province / Subbasin | Columbia Estuary / Elochoman |
| 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 |
| 46.2225 |
-123.1465 |
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 |
|---|
| NMFS |
Action 152 |
NMFS |
The Action Agencies shall coordinate their efforts and support offsite habitat enhancement measures undertaken by other Federal agencies, states, Tribes, and local governments by the following: |
| NMFS |
Action 155 |
NMFS |
BPA, working with BOR, the Corps, EPA, and USGS, shall develop a program to 1) identify mainstem habitat sampling reaches, survey conditions, describe cause-and- effect relationships, and identify research needs; 2) develop improvement plans for all mainstem reaches; and 3) initiate improvements in three mainstem reaches. Results shall be reported annually. |
| BPA |
Action 152 |
NMFS |
The Action Agencies shall coordinate their efforts and support offsite habitat enhancement measures undertaken by other Federal agencies, states, Tribes, and local governments by the following: |
Section 2. Past accomplishments
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 |
$8,850 |
|
|
b. Send isolates to Microbial ID, Inc. for fatty-acid analysis and positive identification. |
1 |
$1,000 |
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 |
$18,000 |
|
|
c. Production of primers at Genosys Biotechnologies. |
1 |
$450 |
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 |
$11,300 |
|
|
b. Produce species-specific primers at Genosys Biotechnologies, Inc. |
3 |
$450 |
Yes |
| 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 |
$11,300 |
|
|
b. Produce species-specific primers at Genosys Biotechnologies, Inc. |
3 |
$450 |
Yes |
| 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 |
$2,350 |
|
| 4. Relate bacterial presence and environment data to land uses. |
a. Use survey maps to assess land uses and environment changes. |
3 |
$0 |
|
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 environment data. |
2004 |
2005 |
$500 |
Outyear budgets for Monitoring and Evaluation phase
| FY 2004 | FY 2005 |
|---|
| $58,690 | $60,400 |
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 |
$13,000 |
| Travel |
Seminars and conferences |
$2,000 |
| Indirect |
Overhead costs |
$17,900 |
| Subcontractor |
Microbial ID, Inc. |
$1,000 |
| Subcontractor |
Genosys Biotechnologies, Inc |
$1,350 |
| Other |
Sequencer Training |
$4,000 |
| $73,450 |
Total estimated budget
| Total FY 2003 cost | $73,450 |
| Amount anticipated from previously committed BPA funds | $0 |
| Total FY 2003 budget request | $73,450 |
| FY 2003 forecast from 2002 | $0 |
| % change from forecast | 0.0% |
Cost sharing
| Organization | Item or service provided | Amount | Cash or in-kind |
|---|
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:
Mar 1, 2002
Comment:
A response is needed. The test proposed will not likely provide the intended relationship between watershed health and microbial community structure. Further detail needs to be provided on this subject. It is unclear whether the PI is qualified to do this work (BS in Chemistry, limited research experience); it's unlikely that a GS5 Technician, however capable, would be able to fulfill the responsibilities of a PI.
Recommendation:
Recommended Action
Date:
May 17, 2002
Comment:
This project should be considered under the innovative category (or in the Mainstem and Systemwide Province).
Recommendation:
Fund
Date:
Jun 7, 2002
Comment:
The 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.
Recommendation:
Date:
Jul 19, 2002
Comment:
Statement of Potential Biological Benefit to ESU
Uses indicator bacteria species found in the water and in other aquatic life to assess and monitor the health of the system, and attempt to determine the relationship of fish pathogens to other aquatic bacteria. Monitoring bacterial indicator species 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 Req? No
Biop? No
Recommendation:
C
Date:
Jul 23, 2002
Comment:
Defer to development of RM&E plan to identify research priorities (has some overlaps with 30003, 3008, and 30013); see comment on proposal number 30003.
Recommendation:
Do Not Fund
Date:
Oct 30, 2002
Comment: