FY07-09 proposal 200500100

Jump to Reviews and Recommendations

Section 1. Administrative

Proposal titleEcology of Yearling and Subyearling Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta in the Lower Columbia River
Proposal ID200500100
OrganizationPacific Northwest National Laboratory
Short descriptionThis study addresses juvenile salmonid use of shallow water habitats (0-5 m) in Columbia R. tidal freshwater between Portland and Bonneville (RM 110-146).
Information transferInformation from this study will be transferred via a web-based data sharing link, inter-project work group coordination meetings, a biennial conference for the lower Columbia River and estuary, annual project reports, and peer-reviewed publications.
Proposal contact person or principal investigator
Form submitter
Gary Johnson Pacific Northwest National Laboratory gary.johnson@pnl.gov
All assigned contacts
Gary Johnson Pacific Northwest National Laboratory gary.johnson@pnl.gov

Section 2. Locations

Province / subbasin: Lower Columbia / Columbia Lower

[none] Sandy River delta and vicinity

Section 3. Focal species

primary: Chinook Snake River Fall ESU
primary: Chinook Snake River Spring/Summer ESU
primary: Chinook Upper Columbia River Spring ESU
secondary: All Anadromous Salmonids

Section 4. Past accomplishments

2005 The FY05 contract was executed in August 2005. In FY05, we started the following project activities: collection permit applications, sampling deigns, estuary conference planning, FY06 proposal, FY05 annual report, and inter-project coordination. •

Section 5. Relationships to other projects

Funding sourceRelated IDRelated titleRelationship
BPA 200311400 Acoustic Tracking For Survival We will inform these researchers of our findings, and vice versa. They are using a different and incompatible (at this time) acoustic telemetry system than we propose.
Other: USACE unk Crims Is. Monitoring We will integrate our results with those from Crims Is.
Other: USACE EST-P-04-04 Cumulative Ecosystem Effects of Habitat Restoration We will inform this study of our telemetry monitoring protocols for action effectiveness research and vice versa.
BPA 200301000 Historic Hab Food Web Link Sal We will integrate our results with these. Dr. Casillas and Mr. Johnson agreed to collaborate (July 10, 2006).
Other: USACE EST-P-02-02 Monitoring Current and Historic Biophysical Linkages in the Estuary We will integrate our results with these.
BPA 200300700 Lwr Col River/Est Eco Monitor We will coordinate and integrate our study with this one; it may be possible to have some of the same habitat sampling sites.
BPA 200207700 Estuary/Ocean Rme Support We will provide monitoring data to help design sampling for the Estuary RME Plan and we will implement applicable elements of the Estuary RME Plan when it is revised in 2006
Other: USACE unk Juvenile Salmon Stranding from Ship Traffic We will integrate our results with these.
Other: USACE EST-P-02-01 Juvenile Salmon Survival in the Estuary We will sample tagged fish from this study, if present at our study area.
BPA 200201200 Lower Columbia Habitat Mapping We will consult maps from this project.
BPA 200301100 Columbia R/Estuary Habitat We will inform this project of our findings.
BPA 200400200 PNAMP Funding We will inform this effort of our work.
BPA 200301700 Integrated Status/Effect Progr We will consult with these researchers regarding pilot RME.
BPA 199902500 Sandy River Delta Habitat We will coordinate, integrate, and inform this key project about our work.

Section 6. Biological objectives

Biological objectivesFull descriptionAssociated subbasin planStrategy
Acoustic Telemetry Monitoring Monitor the residence time in shallow, tidal freshwater habitats of fish acoustically tagged as part of other projects.. Lower Columbia same as below, E.S5 and Sa.PO.7
Habitat Usage Understand yearling and subyearling salmonid usage of shallow tidal freshwater habitats in the Lower Columbia River between Portland, Oregon and Bonneville Dam. Lower Columbia E.S5. Improve understanding..salmonids utilize estuary & lower mainstem habitats... develop scientific basis for estimating responses to habitat quantity & quality. Sa.PO.7. Develop understanding.. salmonid...habitat use...lower mainstem...

Section 7. Work elements (coming back to this)

Work element nameWork element titleDescriptionStart dateEnd dateEst budget
Produce Environmental Compliance Documentation Fish collection permits State and federal scientific collection permits 10/1/2006 9/30/2009 $28,446
Biological objectives
Acoustic Telemetry Monitoring
Habitat Usage
Coordination Coordination and information exchange Project meetings, regional meetings, Estuary Conference, etc. (WE 118 was recently replaced by a new WE for Regional Coordination) 10/1/2006 9/30/2009 $67,633
Biological objectives
Acoustic Telemetry Monitoring
Habitat Usage
Manage and Administer Projects Project Management Project management plan, PISCES, budget tracking, scheduling, etc. 10/1/2006 9/30/2009 $42,445
Biological objectives
Acoustic Telemetry Monitoring
Habitat Usage
Produce Annual Report Annual Report Technical report to document project objectives, methods and results 10/1/2006 9/30/2009 $124,750
Biological objectives
Acoustic Telemetry Monitoring
Habitat Usage
Analyze/Interpret Data Data analysis Data management, reduction, and analysis of the field data collected for habitat usage 10/1/2006 9/30/2009 $233,895
Biological objectives
Habitat Usage
Collect/Generate/Validate Field and Lab Data Data Collection Field and laboratory data collection for habitat usage, genetic analysis, diet, etc. 10/1/2006 9/30/2009 $1,470,360
Biological objectives
Habitat Usage
Develop RM&E Methods and Designs Acoustic telemetry protocols Acoustic telemetry protocols for action effectiveness research on tidal/hydrologic reconnection restoration project in shallow, tidal freshwater of the LCRE 10/1/2006 9/30/2009 $154,266
Biological objectives
Acoustic Telemetry Monitoring
Disseminate Raw/Summary Data and Results Disseminate data Data dissemination via the internet, reports, scientific information exchanges, peer-reviewed publications, etc. 10/1/2006 9/30/2009 $56,893
Biological objectives
Acoustic Telemetry Monitoring
Habitat Usage

Section 8. Budgets

Itemized estimated budget
Personnel approx. 3 FTE per yr $281,924 $296,208 $310,795
Fringe Benefits sick leave, vacation, etc. $54,911 $60,624 $65,701
Supplies sample jars, PIT tags, hardware, etc. $11,193 $10,890 $10,890
Travel Sequim/Portland, NBON/Port., Seattle/Port. $91,350 $91,350 $91,350
Capital Equipment acoustic nodes, work boat, PIT reader, YSI meter, etc. $65,340 $0 $0
Overhead general and administrative, and overhead $232,580 $246,368 $257,214
Totals $737,298 $705,440 $735,950
Total estimated FY 2007-2009 budgets
Total itemized budget: $2,178,688
Total work element budget: $2,178,688
Cost sharing
Funding source/orgItem or service providedFY 07 est value ($)FY 08 est value ($)FY 09 est value ($)Cash or in-kind?Status
Corps of Engineers JSATS tags and nodes $250,000 $250,000 $250,000 In-Kind Confirmed
NOAA Fisheries genetic baseline $200,000 $200,000 $200,000 In-Kind Confirmed
PNNL field equipment, e.g., seines and meters $50,000 $50,000 $50,000 In-Kind Confirmed
Totals $500,000 $500,000 $500,000

Section 9. Project future

FY 2010 estimated budget: $500,000
FY 2011 estimated budget: $500,000
Comments: Coninued monitoring

Future O&M costs:

Termination date: None
Comments: n/a

Final deliverables: n/a

Section 10. Narrative and other documents

[Attached Document] Jul 2006
[Attached Document] Jul 2006

Reviews and recommendations

FY07 budget FY08 budget FY09 budget Total budget Type Category Recommendation
NPCC FINAL FUNDING RECOMMENDATIONS (Oct 23, 2006) [full Council recs]
$0 $0 $0 $0 Expense ProvinceExpense Do Not Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$0 $0 $0 $0 ProvinceExpense


Recommendation: Not fundable

NPCC comments: With the exception of a change in sampling design, this proposal is similar to the FY06 proposal for this project that the ISRP recently reviewed; see ISRP 2006-2, www.nwcouncil.org/library/isrp/isrp2006-2.htm. This is understandable because the FY07-09 proposal was submitted by January 10, before the ISRP produced its final review of the revised FY06 proposal on January 26, 2006. On November 30, 2005, the ISRP reviewed an initial FY06 proposal and found it not fundable. The sponsors submitted a revised proposal, which the ISRP reviewed (January 26, 2006). The ISRP concluded that the sponsors had not addressed the ISRP’s previous concerns sufficiently in the revised proposal and again regarded the proposal as not fundable. This proposal contains many of the same deficiencies as the earlier proposals, particularly those related to methods and sampling design. Research and monitoring in the tidal freshwater estuary is badly needed. The ISRP recommends tendering a competitive Request for Proposals calling for research in the tidal freshwater portion of the estuary. Because this work is crucial, a competitive process will result in selection of the most scientifically rigorous proposal and the most qualified personnel to conduct the research. In lieu of a competitive RFP, work conducted under project # 200300700 may satisfy the need for research and monitoring in the tidal freshwater portion of the Columbia River estuary. Technical and scientific background: The problem being addressed by this proposal is adequately defined. The proposal does a good job of explaining why data on the ecology of subyearling salmon are required to assist in salmon recovery and river management. The possibility of finding overwintering chinook (possibly reservoir type) is mentioned, indicating the sponsors are thinking about this critical need. However, as per previous ISRP reviews, the rationale for the radio-tagging studies is weak. The proposal needs further justification for the use of the habitat classification scheme and the major habitat complexes need to be described in more detail. For example, what distinguishes the major types hydrologically and geomorphically? The difference between “river confluence floodplain” and “floodplain” should be explained. How does the classification scheme pertain to salmonid habitats and habitat requirements? Review of the technical literature is somewhat narrow, and not many papers are cited from the vast literature on the riverine ecology of salmonids. The study reaches proposed are more similar to rivers than to estuaries. Rationale and significance to subbasin plans and regional programs: The proposal directly responds to a number of plans that call for research and monitoring in the lower Columbia River estuary. These plans include the Fish and Wildlife Program, the Lower Columbia River and Estuary Subbasin Plan, and the 2000 Biological Opinion. There is a strong relation (although not specifically listed as a high priority) between the need for research on salmon in the tidal freshwater portion of the Columbia River and the objectives of the Fish and Wildlife Program and other subbasin plans. Relationships to other projects: The proposal cites relationships to a number of ongoing projects in the lower Columbia River estuary. A more complete description and evidence of close collaboration with other projects would improve this proposal. The juvenile salmon ecology work is put in context of the several other studies proposed in the lower estuary. The tie in with the Sandy River restoration project is weaker. There are 15 related projects listed in the proposal and, given that this proposal is the first substantial proposal to conduct research in the freshwater tidal part of the estuary, it would be prudent to integrate it with as many other projects as possible. Project history: A "desk" project was conducted from August 2005 to January 2006 which was primarily a planning study, permits were obtained, etc. The results of the desk project are reasonably well documented in the present proposal Objectives: The objectives generally address elements of the subbasin plans and the Fish and Wildlife Program. The objectives for understanding fish habitat use have measurable benefits for fish and wildlife; this is the strongest part of the proposal. The benefits from the acoustic telemetry work are harder to define and only generally tied into subbasin plans. Other tagging studies including PIT tagging, POST work etc. may be more relevant and more immediately applicable. Tasks (work elements) and methods: The methods are the same as those reviewed in the FY06 proposal. There were substantial technical objections raised in the ISRP review of that proposal, ranging from questions about beach seine methods, to tagging technology, to methods for choosing stations (EMAP was recommended, but the sponsors did not build this method into their response to initial ISRP comments). A number of specific questions about methods exist. Why were only six sampling sites selected? Accurately assessing presence/absence and relative abundance in a large, complex area like the delta could be very difficult with only six sites. The sponsors need to explain how the sampling sites in each major habitat type were chosen and why there are only one or two sites per major habitat. How is the major habitat type termed “shallows” different from shallow water areas that will be sampled in the other major habitats? Failure to make a clear distinction could confound interpretation of the data. Large wood tends to accumulate in the deltas of large rivers. Juvenile fish in the delta may congregate around and under aggregations of large wood and, in fact, these kinds of habitats could be some of the most important. How will fish use of large wood aggregations in the delta be determined, if the aggregations are present? It will be nearly impossible to sample the areas adjacent to and under large wood with seines. Systematic snorkeling may be the only means of determining fish presence and abundance in these kinds of habitat. An assumption in using the Latin-square design is that there is no interaction between the treatment and the row or column blocking factors. That is, the magnitude of differences between sites should be consistent from sampling trip to sampling trip (i.e., months). Also the magnitude of differences between sites should be consistent for each order within the cycle. It is not clear that both of these assumptions are valid because it is likely that differences between sites would change depending on the month, even within the same season. It is unclear how sampling for the mark-recapture study is related to the habitat use work. Will the sites selected for mark-recapture be among the six habitat-use sampling sites? It would seem that for a months-long study 500 tagged fish would be too few to obtain accurate M-R estimates. The sponsors need to justify why this number of tagged fish is adequate. What kind of precision can be expected? What method will be used produce abundance estimates from the M-R data? For the diet study, what are the size classes of fish that will be sampled and why will only ten fish be sampled for gut contents? The sponsors indicate that some fish will be euthanized and otoliths will be taken. Is this effort part of another study? If not, more details are needed. How will the decision be made as to the sites where invertebrate sampling will be conducted? How often will invertebrate sampling be done? Monitoring and evaluation: The project is intended to be M&E, but numerous concerns about methods make the success of the project uncertain. Facilities, equipment, and personnel: The facilities are adequate and the personnel appear to form a well-rounded and experienced team with good credentials, publication records, and track records of work in the lower estuary. Information transfer: The sponsors have identified several ways in which information will be transferred including conferences, participation in work groups, technical reports, and peer reviewed publications. Technology transfer to stakeholders and laypersons are not described. Benefits to focal and non-focal species: Numerous documents and several ISRP reports have emphasized that studies on the ecology of juvenile salmonids in the tidal freshwater Columbia River will benefit focal species. However, as stated in the ISRP review of the FY06 proposal, a pilot study of RM&E in the tidal freshwater Columbia River should be more comprehensive and extend beyond the Sandy River delta. This proposal would be improved if proponents could be more specific about significant benefits that will persist over the long-term as a result of this presence/absence monitoring study. Information on habitats and fish communities in the tidal Columbia River could benefit non-focal species. This project is not likely to have adverse effects on non-focal species, except for possible direct or indirect mortalities associated with fish sampling operations.

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable in part (Qualified)

NPCC comments: The sponsors have improved their proposal and adequately addressed many of the ISRP's comments. The proposal has a new name, and the scope is reduced. This project is no longer a pilot study for RME of juvenile salmon in tidal freshwater. Now, the study involves status and trends monitoring and testing monitoring protocols. The sponsors have done a lot of preparatory work and obviously a lot of thinking has been done on the proposal. The methodological concerns have been addressed as best they can be at this time. While it is certainly important to try and find out the habitat utilization of focal species such as Snake River Chinook in tidal freshwater habitats, it is not clear, however, why the work should be done at the Sandy River delta. There is no justification for choosing this particular area as a representative tidal freshwater reaches of the Lower Columbia River. Four habitat complexes will be sampled at six sites: river confluence floodplain (1 site), shallows (2 sites), floodplain (1 site), and mainstem island (2 sites). The catena method for classification is being developed through project #200300700. However, this work is not complete and, in the fact, the completion of the development of the method was a qualifying factor from the ISRP in the final recommendation of the latter project. The sponsors have added stream-type chinook and steelhead to the species that will be studied. They do not plan to sample channel habitats, although these may be the main habitats used by stream-type chinook and steelhead. The sponsors should seriously consider sampling channel habitats, especially since they have added stream-type Chinook and steelhead as target species. The sponsors propose to use a beach seine to sample shallow water (0-2 m) and a trawl for mid-depth water (2-5 m). The trawling still may miss many fish as the 2-5 m band will not extend very far offshore. The sponsors seem to be defining the depth intervals they will sample based on the gear they have available. Perhaps a Kvichak trawl (or similar) can be towed in the deeper water unless the current is too strong. Some references to cross channel distributions of Chinook can be provided by the ISRP. The connection with the Sandy River Delta Habitat Restoration project (BPA #project 199902500) is one of the strongest parts of this project, but the sponsors state in their revised proposal: “The tie in with the Sandy River restoration effort is limited at this time because restoration to date has concerned re-vegetation. If and when the tidal reconnection project happens, we will coordinate with the appropriate parties.” The sponsors state the Sandy River restoration is "only" dealing with re-vegetation, but re-vegetation is supposed to have benefits to fish (e.g., through increased terrestrial insect food supply, etc) and so there is a rationale of a linkage between # 19902500 and this project. Coordination with the restoration project should happen at the outset if both studies are funded. USACE studies in 2007 call for tagging (JSATS tags) over 15,000 juvenile salmonids. The sponsors will attempt to detect the tagged fish with listening nodes at two locations. More information on the species, life history types, and stock composition of the releases of JSATS-tagged fish, as well as release schedules, would have been useful. The sponsors mention VEMCO tags released by the Acoustic Tracking for Estimating Ocean Survival project (BPA project #200301400), but it's not clear if they can detect VEMCO tags using JSATS equipment. (Review and coordination of all acoustic telemetry studies in the Columbia Basin is needed to avoid duplication of efforts.) It will be cost-effective to take advantage of the USACE tags but the focus on detecting them for the Sandy River delta is not well defended, and the ISRP hopes that the findings are not extrapolated very widely. The Project History section notes that the sponsors convened a conference on the lower Columbia River estuary, including the ecology of juvenile salmonids, with FY 2006 funding. The proposal would have been improved if relevant results of the conference had been summarized. Qualifications: 1. The number of sampling sites is too small especially for a project that is essentially trying to find fish. Because so little is known about the types of habitat fish use in the tidal freshwater, the ISRP strongly recommends that the number of sites be expanded even if this requires not funding another part of the proposed work or at least delaying initiation until a better understanding of fish distribution is achieved. 2. Areas in the delta with large wood definitely should be sampled to determine if it is an important habitat for fish. The sponsors did not explain why acoustic camera surveys are necessary. Although snorkeling has its problems as a fish sampling method including limitations in murky water, it still may be a reasonably efficient means of detecting fish. 3. The ISRP strongly recommends that this project collaborate closely with projects #200300700 and #199902500. 4. The ISRP questioned use of the Latin square design; the proponents noted that they would address this concern when the project statistician returned to the office after July 24, 2006. This should be addressed before funding is approved. 5. While this project will likely provide hydrosystem managers with useful data on salmonid ecology in shallow habitats in the vicinity of Sandy River delta, it should not be viewed as a replacement for the original concept of a comprehensive RME pilot study. While the proponents state that a comprehensive (EMAP-type) project design is not feasible because of funding constraints and habitat complexity, this issue would best be determined through a competitive proposal process. The ISRP recommends issuing a new RFP for a comprehensive RME pilot study. Not Fundable: The sponsors do not provide sufficient justification for sampling invertebrates, and this part of the proposal is not fundable at this time. After more is known about fish habitat use invertebrate sampling may be more meaningful. Perhaps funds from this part of the work could help to augment funding for an increased number of sampling sites.