Using the Diet Composition of Adult Chinook Salmon to Understand the Regional Structure of Salish Sea Forage Communities

Accurate determination of adult salmon spawner abundance is key to the assessment of recovery actions for wild Snake River spring/summer Chinook salmon (Onchorynchus tshawytscha), a species listed as 'threatened' under the Endangered Species Act (ESA). As part of the Bonneville Power Administration Fish and Wildlife Program, the Nez Perce Tribe operates an experimental project in the South Fork of the Salmon River subbasin. The project has involved noninvasive monitoring of Chinook salmon escapement on the Secesh River between 1997 and 2000 and on Lake Creek since 1998. The overall goal of this project is to accurately estimate adult Chinook salmon spawning escapement numbers to the Secesh River and Lake Creek. Using time-lapse underwater video technology in conjunction with their fish counting stations, Nez Perce researchers have successfully collected information on adult Chinook salmon spawner abundance, run timing, and fish-per-redd numbers on Lake Creek since 1998. However, the larger stream environment in the Secesh River prevented successful implementation of the underwater video technique to enumerate adult Chinook salmon abundance. High stream discharge and debris loads in the Secesh caused failure of the temporary fish counting station, preventing coverage of the early migrating portion of the spawning run. Accurate adult abundance information could not be obtained on the Secesh with the underwater video method. Consequently, the Nez Perce Tribe now is evaluating advanced technologies and methodologies for measuring adult Chinook salmon abundance in the Secesh River. In 2003, the use of an acoustic camera for assessing spawner escapement was examined. Pacific Northwest National Laboratory, in a collaborative arrangement with the Nez Perce Tribe, provided the technical expertise to implement the acoustic camera component of the counting station on the Secesh River. This report documents the first year of a proposed three-year study to determine the efficacy of using an acoustic camera to count adult migrant Chinook salmon as they make their way to the spawning grounds on the Secesh River and Lake Creek. A phased approach to applying the acoustic camera was proposed, starting with testing and evaluation in spring 2003, followed by a full implementation in 2004 and 2005. The goal of this effort is to better assess the early run components when water clarity and night visibility preclude the use of optical techniques. A single acoustic camera was used to test the technology for enumerating adult salmon passage at the Secesh River. The acoustic camera was deployed on the Secesh at a site engineered with an artificial substrate to control the river bottom morphometry and the passage channel. The primary goal of the analysis for this first year of deployment was to validate counts of migrant salmon. The validation plan involved covering the area with optical video cameras so that both optical and acoustic camera images of the same viewing region could be acquired simultaneously. A secondary test was contrived after the fish passage was complete using a controlled setting at the Pacific Northwest National Laboratory in Richland, Washington, in which we tested the detectability as a function of turbidity levels. Optical and acoustic camera multiplexed video recordings of adult Chinook salmon were made at the Secesh River fish counting station from August 20 through August 29, 2003. The acoustic camera performed as well as or better than the optical camera at detecting adult Chinook salmon over the 10-day test period. However, the acoustic camera was not perfect; the data reflected adult Chinook salmon detections made by the optical camera that were missed by the acoustic camera. The conditions for counting using the optical camera were near ideal, with shallow clear water and good light penetration. The relative performance of the acoustic camera is expected to be even better than the optical camera in early spring when water clarity and light penetration are limited. Results of the laboratory tests at the Pacific Northwest National Laboratory facility indicated that the detection rate for the acoustic camera system was essentially 100% across all levels of turbidity in the experiments. Overall, the acoustic camera outperformed the optical camera at detecting fish, both in the laboratory tank and at the Secesh River fish counting station. However, the optical camera approach still offers some advantages over the acoustic camera under certain limited circumstances. The primary advantages are better species, gender and condition determination and better separation of debris from fish moving downstream. Using both systems in parallel will provide the most robust and accurate platform for counting fish in the field by exploiting the relative strengths of both systems through the season.

Dynamic prey resources influence foraging opportunities for consumers. In coastal food webs, forage fish abundance and seasonal reproduction mediate foraging opportunities for mobile consumers. Recent declines in Chinook salmon productivity have prompted efforts to determine whether poor marine survival is caused by limited feeding opportunities. To establish the importance of phenological diversity in Pacific herring for Chinook salmon, we used genetic stock identification to assign individual herring collected from the guts of juvenile and adult Chinook salmon to populations with distinct spawning phenologies. The majority of herring in the guts of adult Chinook salmon across seasons and geographic areas were dominated by the March–April herring spawn group, but juvenile Chinook salmon diets varied seasonally, with a higher proportion of January–February spawners in summer than in spring. Our results suggest that (1) population diversity of Pacific herring is used by juvenile Chinook salmon and thus contributes to their growth, and (2) stock-specific distribution of Pacific herring extends well beyond documented spawning grounds. Herring population diversity may therefore support foraging opportunities for Chinook salmon during a critical period and highlights the need for future research to quantify seasonal distribution and abundance of phenologically distinct groups of Pacific herring within Salish Sea.

A hyperiid amphipod acts as a trophic link between a scyphozoan medusa and juvenile Chinook Salmon

Ceratomyxa shasta (Myxozoa) is a common gastrointestinal pathogen of salmonid fishes in the Pacific Northwest of the United States. We have been investigating this parasite in adult Chinook salmon ( Oncorhynchus tshawytscha ) in the Willamette River, Oregon. In prior work, we observed differences in the pattern of development of C. shasta in adult salmon compared to juvenile salmon. Adult salmon consistently had large numbers of prespore stages in many of the fish that survived to spawn in the fall. However, myxospores were rarely observed, even though they were exposed and presumably infected for months before spawning. We evaluated the ability of C. shasta to sporulate following fish death because it is reported that myxosores are common in carcasses of Chinook salmon. We collected the intestine from 30 adult salmon immediately after artificial spawning and death (T0). A total of 23 fish were infected with C. shasta based on histology, but only a few myxospores were observed in 1 fish by histology. Intestines of these fish were examined at T0 and T7 (latter held at 17 C for 7 days) using quantified wet mount preparations. An increase in myxospore concentrations was seen in 39% of these fish, ranging between a 1.5- to a 14.5-fold increase. The most heavily infected fish exhibited a 4.6-fold increase from 27,841 to 129,352 myxospores/cm. This indicates, supported by various statistical analyses, that under certain conditions presporogonic forms are viable and continue to sporulate after death in adult salmon. Considering the life cycle of C. shasta and anadromous salmon, the parasite may have evolved 2, non-mutually exclusive developmental strategies. In young fish (parr and smolts), the parasite sporulates shortly after infection and is released into freshwater from either live or dead fish before their migration to seawater, where the alternate host is absent. The second strategy occurs in adult salmon, particularly spring Chinook salmon, which become infected upon their return to freshwater in the spring or early summer. For several months throughout the summer, only prespore stages are observed in most fish, even at the time of spawning. But once the fish dies, environmental conditions experienced by C. shasta change and viable presporogonic stages are induced to sporulate. As the post-spawned fish occur in the upper reaches of rivers, the myxospores would be released in a freshwater environment that would provide a reasonable opportunity for them to encounter their freshwater polychaete hosts, which reside downstream.

Objective Our overarching objective was to better understand how river environment affects the migration phenology and behavior of adult Chinook Salmon Oncorhynchus tshawytscha in a watershed (Oregon’s Willamette River basin) where climate warming and other habitat impacts threaten the spring-run population. Methods We analyzed migration phenology of annual spring runs using a 23-year time series of daily adult Chinook Salmon counts at Willamette Falls (river kilometer 42, measuring from the Willamette River–Columbia River confluence) in relation to river discharge and temperature data at a nearby gauge site. We also examined stock-specific phenology and upstream migration rates with general linear models using monitoring data from 909 radio-tagged Willamette River Chinook Salmon to explore the effects of river environment and fish traits on movement through 13 main-stem and tributary reaches. Results Willamette River Chinook Salmon runs migrated earlier in warm, low-flow years. Mean annual river conditions in May were the best predictors of median run timing dates, which ranged from early May to mid-June. Radio-tagged salmon moved upstream faster when river temperatures were higher and discharge was lower. Tagged salmon moved much faster (∼25–50 km/d) in low-gradient main-stem reaches than in the steeper tributary reaches (mostly <10 km/d). Individual fish traits, including stock of origin, were generally not statistically associated with migration rate after statistically accounting for water temperature and discharge. Phenology and migration rate results from the Yukon, Columbia, and Snake River basins broadly aligned with those from the Willamette River basin. Conclusions Our study results offer a mechanistic explanation for why adult salmon migrations occur earlier in warmer years across a broad geographic range. The results also suggest that some spring-migrating populations may continue to trend earlier, a behaviorally plastic response with uncertain implications. Of particular concern are the risks presented by increased adult freshwater residency for spring-migrating populations like upper Willamette River spring-run Chinook Salmon.

Underwater time-lapse video technology has been used to monitor adult spring and summer chinook salmon (Oncorhynchus tshawytscha) escapement into the Secesh River and Lake Creek, Idaho, since 1998. Underwater time-lapse videography is a passive methodology that does not trap or handle this Endangered Species Act listed species. Secesh River chinook salmon represent a wild spawning aggregate that has not been directly supplemented with hatchery fish. The Secesh River is also a control population under the Idaho Salmon Supplementation study. This project has demonstrated the successful application of underwater video adult salmon abundance monitoring technology in Lake Creek in 1998 and 1999. Emphasis of the project in 2000 was to determine if the temporary fish counting station could be installed early enough to successfully estimate adult spring and summer chinook salmon abundance in the Secesh River (a larger stream). Snow pack in the drainage was 93% of the average during the winter of 1999/2000, providing an opportunity to test the temporary count station structure. The temporary fish counting station was not the appropriate technology to determine adult salmon spawner abundance in the Secesh River. Due to its temporary nature it could not be installed early enough, due to high stream discharge, to capture the first upstream migrating salmon. A more permanent structure used with underwater video, or other technology needs to be utilized for accurate salmon escapement monitoring in the Secesh River. A minimum of 813 adult chinook salmon spawners migrated upstream past the Secesh River fish counting station to spawning areas in the Secesh River drainage. Of these fish, more than 324 migrated upstream into Lake Creek. The first upstream migrating adult chinook salmon passed the Secesh River and Lake Creek sites prior to operation of the fish counting stations on June 22. This was 17 and 19 days earlier than the first fish arrival at Lake Creek in 1998 and 1999 respectively. Peak net upstream adult movement at the Secesh River site occurred June 28 and at the Lake Creek site on June 27. Peak of total movement was August 16 at Secesh River and August 7 at Lake Creek. The last fish passed through the Lake Creek fish counting station on August 31 and on September 8 at the Secesh River site. Migrating salmon in the Secesh River and Lake Creek exhibited two behaviorally distinct segments of fish movement. The first segment of movement was characterized, mainly, by upstream movement only. The second segment consisted of upstream and downstream movement with very little net upstream movement. The fish counting stations did not impede salmon movements, nor was spawning displaced downstream. Fish moved freely upstream and downstream through the fish counting structures. Fish movement was greatest between the period of 5:00 p.m. and 4:00 a.m. There appeared to be a segment of ''nomadic'' males that moved into and out of the spawning area, apparently seeking other mates to spawn with. The downstream movement of salmon allowed by this fish counting station design may be an important factor affecting reproductive success as male salmon seek other females to spawn with. Traditional weirs operated for broodstock collection do not allow for downstream movement of adults. This methodology has the potential to provide more consistent and accurate salmon spawner abundance information than single-pass and multiple-pass spawning ground surveys. Accurate adult abundance would allow managers to determine if recovery actions were benefiting these salmon spawning aggregates and if recovery goals were being met.

Low levels of heterozygosity can have detrimental effects on life history and growth characteristics of organisms but more subtle effects such as those on trade-offs of expensive tissues and morphological laterality, especially of the brain, have not been explicitly tested. The objective of the current study was to investigate how estimated differences in heterozygosity may potentially affect brain-to-body trade-offs and to explore how these heterozygosity differences may affect differential brain growth, focusing on directional asymmetry in adult Chinook salmon (Oncorhynchus tshawytscha) using the laterality and absolute laterality indices. Level of inbreeding was estimated as mean microsatellite heterozygosity resulting in four ‘inbreeding level groups’ (Very High, High, Medium, Low). A higher inbreeding level corresponded with a decreased brain-to-body ratio, thus a decrease in investment in brain tissue, and also showed a decrease in the laterality index for the cerebellum, where the left hemisphere was larger than the right across all groups. These results begin to show the role that differences in heterozygosity may play in differential tissue investment and in morphological laterality, and may be useful in two ways. Firstly, the results may be valuable for restocking programmes that wish to emphasize brain or body growth when crossing adults to generate individuals for release, as we show that genetic variation does affect these trade-offs. Secondly, this study is one of the first examinations to test the hypothesized relationship between genetic variation and laterality, finding that in Chinook salmon there is potential for an effect of inbreeding on lateralized morphology, but not in the expected direction.

Innate and adaptive immune responses in migrating spring-run adult chinook salmon, Oncorhynchus tshawytscha.

Handling-induced delay and downstream movement of adult chinook salmon in rivers

To characterize the marine distribution of New Zealand adult chinook salmon Oncorhynchus tshawytscha, we analyzed data on chinook salmon taken off the South Island east coast as a bycatch of a commercial fishery dominated by bottom trawling on the continental shelf and slope in depths up to 1,000 m. Chinook salmon, widely but sparsely distributed out to depths of 100 m throughout most of the year, showed a strong tendency to concentrate off Banks Peninsula (latitude 43°45′S) in midsummer (December–February). Of 161 metric tons taken between 1984 and 1988, 151 metric tons were taken by larger trawlers capable of towing nets with 6-m headline heights at speeds of up to 6.5 km/h. Most chinook salmon caught at sea were maturing adults returning to nearby rivers, such as the Rakaia, rather than immature fish associated with the oceanic phase of their life cycle. The low incidence of immature fish and the lack of data for offshore waters preclude any definitive conclusions about the extent to which chinook salmon travel offshore, but our results are consistent with their northern distribution being bounded by subtropical water north of about latitude 43°S and their eastern distribution being bounded by cold, low-productivity sub-Antarctic waters.

Spawning migration of adult male chinook salmon Oncorhynchus tshawytscha was monitored by radio telemetry to determine their response to the presence of metals contamination in the South Fork of the Coeur d'Alene River, Idaho. The North Fork of the Coeur d'Alene River is relatively free of metals contamination and was used as a control. In all, 45 chinook salmon were transported from their natal stream, Wolf Lodge Creek, tagged with radio transmitters, and released in the Coeur d'Alene River 2 km downstream of the confluence of the South Fork and the North Fork of the Coeur d'Alene River. Fixed telemetry receivers were used to monitor the upstream movement of the tagged chinook salmon through the confluence area for 3 weeks after release. During this period, general water quality and metals concentrations were monitored in the study area. Of the 23 chinook salmon observed to move upstream from the release site and through the confluence area, the majority (16 fish, 70%) moved up the North Fork, a...

Temperature‐sensitive transmitters and archival tags allowed precise measurement of adult Chinook salmonOncorhynchus tshawytscharesponses to high water temperatures and other environmental variables in the Klamath River basin during 2004 and 2005. Mean daily river temperatures upon initiation of upriver migration by adult Chinook salmon after a period of thermally induced migration inhibition ranged from 21.8°C to 24.0°C (mean = 22.9°C). During the first week (168 h) of migration, mean average body temperature was 21.9°C, mean average minimum daily body temperature was 20.6°C, and mean average maximum daily body temperature was 23.1°C. Temperatures above these levels appeared to completely block migration in almost all circumstances. Migration was inhibited at lower mean daily river temperatures during periods of increasing river temperatures than during periods of declining river temperatures. The ability of adult Chinook salmon to correctly gauge the onset of periods of declining or inclining river temperature is a vital mechanism for taking advantage of brief thermal windows for upriver migration. Weather fronts were responsible for periods of declining river temperature, but no precipitation or consistent drops in atmospheric pressure were associated with these weather fronts or with fish movements. The associated decrease in light levels, however, appeared to serve as an indicator of impending reductions in river temperatures for adult Chinook salmon. Changing river discharge had a negligible influence on migration behavior, and hypoxia sufficient to inhibit upriver migration (i.e., dissolved oxygen < 5 mg/L) never occurred during the study. The upper thermal limits to adult Chinook salmon migration as indicated by results from the Klamath River basin are substantially higher than previously reported in the literature and approached or exceeded the highest ultimate upper incipient lethal values determined for any life stage of this species.

Histology is often underutilized in aquatic animal disease screening and diagnostics. The agreement between histological classifications of infection and results using diagnostic testing from the American Fisheries Society's Blue Book was conducted with 4 common salmon pathogens: Aeromonas salmonicida, Renibacterium salmoninarum, Ceratomyxa shasta, and Nanophyetus salmincola. Adult Chinook salmon (Oncorhynchus tshawytscha) in Oregon were evaluated, and agreement between tests was calculated. Live and dead (both pre- and postspawning) salmon were collected from the Willamette River, Oregon, its tributaries, the Willamette Hatchery, and after holding in cool, pathogen-free water during maturation at Oregon State University. Sensitivity and specificity of histology compared to Blue Book methods for all fish, live fish only, and dead (pre- and postspawned combined) fish only were, respectively, as follows: A. salmonicida (n = 105): specificity 87.5%, 87.5%, 87.5% and sensitivity 38.6%, 14.8%, 60.0%; R. salmoninarum (n = 111): specificity 91.9%, 85.7%, 97.7% and sensitivity 16.0%, 7.1%, 27.2%; C. shasta (n = 136): specificity 56.0%, 63.3%, 28.6% and sensitivity 83.3%, 86.2%, 71.4%; N. salmincola (n = 228): specificity 68.2%, 66.7%, not possible to calculate for dead fish and sensitivity 83.5%, 80.5%, 87.3%. The specificity was good for bacterial pathogens. This was not the case for C. shasta, likely due to detection of presporogenic forms only by histology. Sensitivity of histology for bacterial pathogens was low with the exception of dead fish with A. salmonicida. Kappa analysis for agreement between Blue Book and histology methods was poor to moderate. However, histological observations revealed the presence of other pathogens that would not be detected by other methods.

We assessed upstream migration rates of more than 12,000 radio-tagged adult Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss past a series of dams and reservoirs on the Columbia and Snake rivers. Most fish passed each dam in less than 2 d. Migration behavior in reservoirs and through multiple dam–reservoir reaches varied within and between years and between species. Within years, spring–summer Chinook salmon migrated more rapidly as water temperature and date of migration increased; between years, spring–summer Chinook salmon migrated fastest in low-discharge years. Steelhead migrations slowed dramatically when summer water temperatures peaked within each year, then increased as rivers cooled in fall. Mean summer temperatures explained more between-year variation in steelhead passage rates than did differences in discharge. Fall Chinook salmon migration rates also slowed during periods of warm water. Protracted passage times within the hydrosystem were most likely for fish from all...

We reviewed current methods used to estimate survival of adult chinook salmon (Oncorhynchus tshawytscha) as they migrate upstream past hydroelectric projects in the Columbia and Snake rivers, evaluated known and unaccounted-for loss factors, and assessed how adult survival estimates could be improved. Dam counts and associated passage conversion rates do not always provide accurate estimates of adult survival between hydroelectric projects. Expansion techniques for reconstructing run size and harvest rates also contribute to variability in estimates of run size and potential loss between hydroelectric projects. Use of passage conversion rates to estimate in-river survival of adult spring chinook salmon had less uncertainty than for estimates of other runs. Fixed-run cutoff dates for migration timing result in a high uncertainty for monitoring relative numbers of summer chinook salmon. We also found it difficult to reconstruct run size to spawning areas or to estimate interdam survival for fall chinook in lower Snake River dams because of straying and high incidence (e.g., up to 40% at some projects) of fallback behavior. In-river survival estimates of adult chinook salmon would be improved by factoring adult fallback percentages into passage estimates, combining spring and summer runs for accounting purposes, and reassessing harvest accounting methods.