FY 2003 Mainstem/Systemwide proposal 200303300

Additional documents

35024 Narrative Narrative
35024 Powerpoint Presentation Powerpoint Presentation
35024 Sponsor Response to the ISRP Response
Narrative for project proposal 35024 (revised) Narrative

Section 1. Administrative

Proposal titleEvaluating the sublethal impacts of current use pesticides on the environmental health of salmonids in the Columbia River Basin.
Proposal ID200303300
OrganizationNational Marine Fisheries Service/Northwest Fisheries Science Center (NMFS)
Proposal contact person or principal investigator
NameNathaniel Scholz
Mailing address2725 Montlake Blvd. E Seattle, WA 98112
Phone / email2068603454 / nathaniel.scholz@noaa.gov
Manager authorizing this projectDr. John Stein, Director, ECD
Review cycleMainstem/Systemwide
Province / SubbasinMainstem/Systemwide /
Short descriptionScreen for the effects of a broad range of current use pesticides on a model species (zebrafish). Evaluate the effects of specific pesticides on the physiology and fitness of at-risk chinook. Incorporate data into a model of chinook population viability.
Target speciesChinook Salmon
Project location
NWFSC, Seattle, WA
NWFSC, Manchester Research Station, Manchester, WA
Reasonable and Prudent Alternatives (RPAs)


Section 9 Action 39

Relevant RPAs based on NMFS/BPA review:

Reviewing agencyAction #BiOp AgencyDescription
NMFS Action 39 NMFS BOR shall evaluate the water quality characteristics of each point of surface return flows from the Columbia Basin Project to the Columbia River and estimate the effects these return flows may have on listed fish in the Columbia River and in the wasteways accessible to listed fish. By June 1, 2001, BOR shall provide NMFS with a detailed water quality monitoring plan, including a list of water quality parameters to be evaluated. If the water quality sampling reveals enough water quality degradation to adversely affect listed fish, BOR shall develop and initiate implementation of a wasteway water quality remediation plan within 12 months of the completion of the monitoring program.
NMFS/BPA Action 183 NMFS Initiate at least three tier 3 studies (each necessarily comprising several sites) within each ESU (a single action may affect more than one ESU). In addition, at least two studies focusing on each major management action must take place within the Columbia River basin. The Action Agencies shall work with NMFS and the Technical Recovery Teams to identify key studies in the 1-year plan. Those studies will be implemented no later than 2003.

Section 2. Past accomplishments

new applicant

Section 3. Relationships to other projects

Project IDTitleDescription

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
1. Evaluate impacts of pesticides on fish a. Phenotypic screening in zebrafish 3 $166,900 Yes
b. Survival and homing in chinook salmon 3 $197,205 Yes
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
1. Evaluate impacts of pesticides on fish 2004 2005 $650,000
Outyear budgets for Operations and Maintenance phase
FY 2004FY 2005

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
1. Evaluate impacts of pesticides on fish b. Survival and homing in chinook salmon 1 $0
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
1. Evaluate impacts of pesticides on fish 2005 2005 $39,870
Outyear budgets for Monitoring and Evaluation phase
FY 2005

Section 8. Estimated budget summary

Itemized budget
ItemNoteFY 2003 cost
Personnel FTE: PI @ 0.5 $39,800
Fringe included in Personnel $0
Supplies Physiological and laboratory equipment $63,005
Travel one national meeting and regional for two $7,000
Indirect SLUC and NOAA TDL $19,400
Subcontractor Senior Post-doctoral fellow $80,000
Subcontractor NRC Post-doctoral associate $57,000
Subcontractor Cell and Molecular Biology Technician $58,700
Subcontractor Laboratory Technician $39,200
Total estimated budget
Total FY 2003 cost$364,105
Amount anticipated from previously committed BPA funds$0
Total FY 2003 budget request$364,105
FY 2003 forecast from 2002$0
% change from forecast0.0%
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.

Fundable only if response is adequate
Aug 2, 2002


A response is needed. The quality of this proposal is extremely high. This is an exceptionally thorough proposal for research on a topic that needs attention. The investigators are highly knowledgeable of the techniques and literature. The proposed research is scientifically sound; it is consistent with the FWP; it has clearly defined objectives and related tasks. And it has a monitoring component. It is well connected to other pesticide studies in the basin. The staff seems exceptionally well qualified for the type of work proposed. Some very good science is likely to be done under this proposal. Thus, the expectations from the authors to implement the program and obtain results are not questioned.

But a key question is whether the research is likely to lead to useful results and implementable mitigation? Do pesticides in question exist in sufficient quantities in the environment such that those concentrations are likely to have measurable effects and can be partitioned and separated from other large and known sources of salmon mortality. Although a variety of pesticides are used and detectible in the environment, what are the concentrations and identities that are expected at levels in which salmon would be affected. If there is evidence, it should be cited.

Is the model realistic? The use of a copper based model and surrogate for organic pesticides seems convenient but not necessarily realistic. No evidence was provided to show copper concentrations exist in the Columbia River or most tributaries of the levels likely to be toxic or have sub-lethal impacts. Copper does exist in the Clarkfork River in high concentrations. There the homing instincts of rainbow trout and bull trout, two potradromous species, seem extremely well developed (Schmetterling, personal communication, MDFWP) in this extremely copper contaminated system. Milltown Dam is one of the most studied and evaluated cleanup sites on EPA's superfund list.

Is the work directly applicable to salmon? The proposed work is physiological research (driven by good ecological issues). The question arises is what is the actual relevance of the studies to the real world of salmon. For example, how applicable is the zebrafish model to salmon and what evidence is there that the rapid development rate of zebrafish embryos (a tropical species) represents much slower development of coldwater salmon embryos?

Are natural concentrations and mortalities significantly detectable to warrant the research? The discovery of microscopic anatomical or physiological anomalies after exposure to high concentrations of a toxin in a rapid developing model (zebrafish) in vitro may present unrealistic results and lead to unwarranted conclusions (Type 2 statistical error- i.e. find problems that don't actually exist for example, that pesticides from lab data extrapolated to the wild indicate a mortality component for wild salmon when there may be none). Response?

Are there potential affects on other species of fish and if so, what would be consequences to salmon? The authors hypothesize that predators may gain some advantage over smolts with impaired olfactory senses; however, should such a pesticide condition occur, why wouldn't the predators species have similar impairment?

Does evidence exist in nature that shows any unusual patterns of straying that might be connected with pesticides? The authors hypothesize olfactory impairment from pesticides may be a source of straying. Is there even anecdotal evidence that specific basins, sub-basins or tributaries with higher levels of pesticides (even use, if not data) show higher rates of straying than other basins?

Can we really get at the question of genetic consequences of pesticides? The authors hypothesize that genetic integrity of certain weak stock ESU's may be compromised by straying. The introduction of artificial selection to 95% of the salmon migrants via various artificial propagation (hatchery) techniques and selective harvest of the past 50 years seems gargantuan compared to the potential problem of incremental straying from a pesticide source. A simpler hypothesis is that if pesticides are entering the salmon's life cycle, it is likely that those individuals and populations are carrying an additional genetic or environmental load. If this is true, a more direct approach to warrant the physiological studies proposed herein would be to find at least one watershed that has physiological detectable concentrations of copper (or other toxins) and then emulate that condition in the lab. At the same time, the problem of toxicity can be addressed as a preventative measure while research confirms the extent of the mechanism and the extent of the problem in the lab.

If any results suggested that pesticides were an additive component of lifecycle mortality, how would such a finding be extrapolated over all populations and with all other causes of mortality? This becomes statistically daunting when in even a healthy system, 95-98% of the smolts do not return, mostly for unknown causes.

Alternative Research Designs. Is there any possibility of an alternative experiment that would use salmon, perhaps in populations known to be exposed to certain toxins; e.g. are there known exposed and control populations in nature that could be used as subjects of this study? The current approach asks us to extrapolate from zebrafish to salmon and do theoretical population modeling using a large suite of hypothetical variables about olfactory impairment and gene flow. The ISRP would be more enthusiastic if the model were with salmon and in a location where pesticide is actually found in known concentrations of concern in the environment?


  1. Please address the basic evidence that pesticides in the environment are having a measurable and detectable impact on the return rates of salmon. Of the 100 pesticides identified, how many exist at concentrations are physiologically affecting sub-populations of salmon. Please identify evidence of specific impairment or straying or genetic or environmentally detectable load on any population. Address the concern that the model of zebrafish in the lab has several limitations to direct application to salmon in the wild. Address alternative approaches using salmon, potentially in nature.
  2. If a potential connection between copper and salmon is found, how significant is this source of mortality versus dozens of other sources not only of other pesticides, but also of dams, harvest, predation, ocean losses etc. Normal mortality rates are already above 95%. This speaks to the previously defined experiment, as the treatment and control will be exposed to all these cumulative impacts.
  3. The research seems extremely interesting to basic science, but please elaborate more directly on the likelihood that results will be directly applicable to the management of the FCRPS and salmon recovery. For example, hypothesize some expected and quantifiable impact, and what might be done about it. Wouldn't it be simpler to keep concentrations of harmful chemicals at sub-physiological impairment levels? This is EPA's mission and the toxicological research is usually in the realm of EPA chemical use and approval domains. Shouldn't this research wait for more details about natural concentrations of toxins? Some fascinating observations were cited by the authors about physiological and behavioral responses to predator alarm pheromones. What types of research can be done to develop more wild-like traits in hatchery reared smolts? Does this area of physiological research hold potential large benefits to salmon?

Oct 24, 2002


Are other funding sources available for this project? This proposal addresses a very important issue. The Water Quality Planning Group (WQP) recognizes the long term nature of fish research projects involving fish and toxic chemicals, e.g., current use pesticides. However, the WQP group could not reach a consensus recommendation on this project. Following are a range of comments provided by group members: • The impacts of sublethal concentrations of pesticides on salmonid survival in the Columbia River is a large gap in our current knowledge base. If the impacts are significant, as current research suggests, then this knowledge needs to be factored into our overall approach to salmon recovery. For that reason, it is important to know the significance of this issue as soon as possible so that appropriate measures can be developed, i.e., this is an urgent project. • The project proposal addresses key technical information needs and some critical uncertainties that are identified in the Mainstem and Systemwide Province Water Quality Summary, specifically, item III.D.2., Comprehensive Water Quality Knowledge in the Columbia River Basin; III.D.3. Scientific Uncertainties Associated with Water and Sediment Quality Evaluations; and III.D.4. CRITFC View of Salmon Recovery and Toxic Contaminants. • Projects involving toxics and effects on fish often require extensive time and effort. This fact alone suggests that delaying the initiation of projects such as this can only be detrimental, i.e., the longer these projects are deferred, the longer this type of information will be unavailable to the region and salmon recovery efforts. • Based on results recently released by EPA regarding fish tissue contamination (EPA Columbia River Basin Fish Contamination Survey, July 2002), the information these projects can provide is especially valuable to the protection of both fish and human health. As the EPA results indicate, contaminants such as dioxin, PCB's, DDT, arsenic, and mercury were present in the tissues of both resident and anadromous fish, with higher concentrations occurring in bottom feeding resident fish, such as sturgeon. Surveys have indicated that average fish consumption by CRITFC member tribes is nine times greater than that of the average American. Studies involving anadromous fish and current use pesticides (#35024) would not only be pertinent, but also timely. For the above three reasons, this is a high priority project. • Although the Water Quality Planning Group believes that projects investigating the fate and biological effects of current-use pesticides and other toxic chemicals found in the environment are important to the region, further regional discussion is needed on what the next steps should be to develop an integrated, comprehensive research approach or work plan. In addition, topics and projects regarding toxic materials are scheduled to be addressed by the group in the next calendar year. The immediate emphases of this group are improvements in water temperature and total dissolved gas. For this reason, this project is a recommended action. • While this may be a good project technically, at least one member felt there would not be a significant loss that could be demonstrated by not funding this project this year, or in a limited budget condition. Moreover, it is difficult to determine how this study would contribute to the management of current use pesticides in the Columbia Basin.
Oct 24, 2002


This project only has two tasks, and the individual studies within each task are closely interrelated and interdependent. To ensure we can complete the work as originally proposed, we have increased the amount of cost sharing by NMFS/NWFSC. Specifically, we have removed salary support and associated overhead for the Principal Investigator from our request. This will result in a cost savings of $58,600 for each year of the three-year study. Thus, our revised request is for $876,375. The NWFSC will contribute salary support for the Principal Investigator ($175,800), the equipment necessary to conduct phenotypic screens (~$95,000), and facilities support for all project personnel as a cost share.
Nov 5, 2002


Fundable, we agree with CBFWA that this is fundable; however, it is not apparent that this project should be among the highest priority for BPA funding. This exceptionally high quality proposal contains well-designed scientific experiments on toxicological effects of pesticides on zebrafish physiology. The premise for the research is that pesticides exist in the environment at concentrations that are physiologically affecting sub-populations of salmon and have a measurable and detectable impact on the return rates of salmon. The investigators are highly knowledgeable of the physiological laboratory techniques and literature and well qualified for the type of work proposed. The proposed research is scientifically sound; it is consistent, albeit not directly or likely immediately useful to the FWP. It has clearly defined objectives and related tasks; and it has a monitoring component. It is well connected to other pesticide studies in the basin.

The response was thorough and provided convincing evidence that embryonic development is a highly canalized physiological phenomenon in all vertebrates and thus the zebrafish model is relevant; i.e. zebrafish are an accepted standard for such screening tests, and as such are logical to use. The proponents make a persuasive case for the rapidity of the zebrafish assay compared to salmon. They also clarified that copper is a primary ingredient of many pesticides and therefore relevant.

The ISRP's concern with the proposal is with the next step, that is, making the link to salmonids and other Columbia River basin fish, but this is not what they propose. The authors hypothesize olfactory impairment from pesticides may be a source of straying, but do straying, physiological, or behavioral anomalies exist differentially in the basin and could those be related to pesticide concentration? No data exist according to the authors; thus, the hypothesis that straying is affected by pesticide would need to be corroborated. Whether pesticides exist in quantities sufficient to affect salmon and especially salmon embryos in the wild remains hypothetical. The authors present evidence that some of the pesticides are detectable in agricultural basins at ppb levels of concentrations. Are these sufficient levels to raise concerns to warrant in vitro tests on zebrafish? The authors indicate that if, after three years of research on zebrafish, there is significant justification they will then proceed to transfer hypotheses directly to salmon. The ISRP would be more enthusiastic about the priorities of this research if there were field evidence for the hypothesized issue, i.e. observed data that the problem exists to which the proposed research might explain or mitigate the problem in salmonid populations

The research seems extremely interesting to basic science, but potentially a long shot, based on the likelihood that results will be directly applicable to the management of the FCRPS and salmon recovery. Near-term benefits to salmon are unlikely because of the long-term nature of the studies including the need for connections in the field.

Some fascinating observations were cited by the authors about physiological and behavioral responses by salmon to predator alarm pheromones. Although not the intended subject of this research, the ISRP would be interested in research that can be done to develop more wild-like traits in hatchery-reared smolts. Does this area of physiological research hold potential large benefits to salmon?

We agree with CBFWA's suggestion that this research should be funded through other sources like EPA.

Jan 21, 2003


Statement of Potential Biological Benefit
Indirect. This project will evaluate the sublethal impacts of pesticides on the health and performance of fish and, for salmon, relate sublethal toxicity in individual fish to the viability and genetic integrity of native populations in the Columbia River Basin.

NMFS proposal. Inappropriate to comment.

Already ESA Required?


Do Not Fund
Mar 24, 2003


Do not fund. This is a proposal to write a proposal. This proposal could definitely lead to a worthwhile project if it was focused and complete. The proposal provides a thorough and convincing description of the importance and the relative neglect (in a research/ mitigation context) of water quality. However, implementation of an undetermined plan is included in the outyear funding. As it stands, the proposal cannot be effectively reviewed or recommended.

This is no longer a focused “pesticide proposal” but a general water quality and land use proposal (the title is misleading). This change of focus is good in one sense, as it broadens the topic to other important features of water quality and the factors that affect them. The proposal further emphasizes salmon and drops zebra fish assays, which the ISRP had earlier questioned for relevance. However, in broadening the topics, the proposal lost clear focus and directed project planning. It lacks critical detail needed for evaluation of the soundness of its science and its likelihood of success. Even the water quality features to be analyzed are vague, and the proposal says that it is not going to be limited to those listed in the RPAs. The thrust is on two subbasins that partially match the three proposed for monitoring in the other proposals of this “integrated set.” If this collection of proposals is to be an integrated set, then why is this one proposing work in the Wenatchee and Yakima, when the others in the set propose work in the Wenatchee, John Day, and Upper Salmon? It is not clear how these proposals link together.

A working group including the RME group, EPA, State DEQs, etc., might be formed to plan and design a call for proposal on water quality before going forward with this proposal. The relationships of water quality to life history characteristics and life-cycle success of salmonids could be a good topic for a targeted solicitation.

The proposal lacks critical detail. As was commented upon by the ISRP for the first proposal, there is no evidence presented that pesticides (or any other water quality parameter) are actually a problem. We see only informed speculation. Are levels seen in the field within the range that cause mortalities, lowered growth, etc.? The ISRP recommends that a workgroup composed of state and federal agencies familiar with water quality problems be convened to scope work on water quality before a targeted solicitation for the work is advanced.

In Part I, the proposal does not make clear the relationship to RPA 183 (Part II cites RPAs 180, 181, 183, and 198, not just 183, as justification). This is critical for the context of the proposal, especially its urgency in the Action Effectiveness process. A seemingly excessive amount of funding is requested just to select sites ($370k). There are only very brief objectives provided in Part I, where the scope of the project should be clear through an outline of objectives. No cost sharing is anticipated in Part I, although Part II notes a large amount of cooperation with other agencies.

Part II notes that this proposal is tied to proposals 35019, 35020, and 35048 as a package, but there is no indication of what the linkages are. Is there an overall set of objectives for which each proposal has a part? If so, what parts do the other proposals play? As commented on for Part I, establishing a justification in RPAs and among related proposals is essential.

The ESUs selected for study are important, but the ISRP wonders whether they are the most appropriate for such a study. They have to be considered as pilot studies for the rest of the Columbia River basin.

Use of a life-cycle model is a good idea, as is attention to aspects of water quality that have not often been studied in the Fish and Wildlife Program. Use of specific quantitative models, parameterized with field-measured life-history data and linked to field-measured environmental characteristics (such as presence and levels of various pollutants or other determinants of water quality) could provide a powerful approach to better understanding the health of and threats to salmon in the Columbia River Basin. However, the strength of such a study would depend critically in details of sample design, measurement, and analytical details that are not given in the proposal.

The part of the proposal to “develop a new laboratory infrastructure for salmon health research” is not clear. It seems that the lab is to be funded for a major renovation of facilities. However, the amount of funds required is not carefully spelled out and contrasted with the funds for actual research and monitoring.

As an overall monitoring proposal, the CBFWA proposal (35033) is superior.

Jun 2, 2003


NPCC tier 3. BPA revised budget to reflect a change of scope to accommodate RME requirements consistent with ISRP review
Do Not Fund (Tier 3)
Jun 11, 2003


3. Other projects not recommended by staff