Juvenile Fall-run Chinook Salmon Research Articles

Responses to pathogen exposure in sentinel juvenile fall-run Chinook salmon in the Sacramento River, CA.

This study investigated how the deployment of juvenile Chinook salmon in ambient river conditions and the subsequent exposure to and infection by pathogens was associated with the changes in the expression of genes involved in immune system functioning, general stress and host development. Juvenile fish were deployed in sentinel cages for 21days in the Sacramento River, CA, USA. Gill, kidney and intestinal tissue were sampled at 0, 7, 14 and 21days post-deployment. Pathogen detection and host response were assessed by a combination of molecular and histopathological evaluation. Our findings showed that fish became infected by the parasites Ceratonova shasta, Parvicapsula minibicornis and Ichthyophthirius multifiliis, and to a lesser extent, the bacteria Flavobacterium columnare and Rickettsia-like organisms. Co-infection was common among sentinel fish. Expression of investigated genes was altered following deployment and was often associated with pathogen abundance. This study provides a foundation for future avenues of research investigating pathogens that affect out-migrating Chinook salmon in the Sacramento River, and offers crucial knowledge related to conservation efforts.

The effect of temperature on specific dynamic action of juvenile fall-run Chinook salmon, Oncorhynchus tshawytscha.

Juvenile fall-run Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento-San Joaquin River Basin experience temporally and spatially heterogenous temperature regimes, between cool upper tributaries and the warm channelized Delta, during freshwater rearing and outmigration. Limited water resources necessitate human management of dam releases, allowing temperature modifications. The objective of this study was to examine the effect of temperature on specific dynamic action (SDA), or the metabolic cost associated with feeding and digestion, which is thought to represent a substantial portion of fish energy budgets. Measuring SDA with respect to absolute aerobic scope (AAS), estimated by the difference between maximum metabolic rate (MMR) and standard metabolic rate (SMR), provides a snapshot of its respective energy allocation. Fish were acclimated to 16°C, raised or lowered to each acute temperature (13°C, 16°C, 19°C, 22°C or 24°C), then fed a meal of commercial pellets weighing 2% of their wet mass. We detected a significant positive effect of temperature on SMR and MMR, but not on AAS. As expected, there was no significant effect of temperature on the total O2 cost of digestion, but unlike other studies, we did not see a significant difference in duration, peak metabolic rate standardized to SMR, time to peak, percent of meal energy utilized, nor the ratio of peak O2 consumption to SMR. Peak O2 consumption represented 10.4-14.5% of AAS leaving a large amount of aerobic capacity available for other activities, and meal energy utilized for digestion ranged from 5.7% to 7.2%, leaving substantial remaining energy to potentially assimilate for growth. Our juvenile fall-run Chinook salmon exhibited thermal stability in their SDA response, which may play a role in maintaining homeostasis of digestive capability in a highly heterogeneous thermal environment where rapid growth is important for successful competition with conspecifics and for avoiding predation.

Effect of release timing on apparent survival of juvenile fall run Chinook Salmon from Coleman National Fish Hatchery

Hatchery production of Pacific salmon for release into the environment is a common tool for conservation and supplementation of depleted stocks. Hatchery conditions are controlled to support high survival rates; however, once released into the environment, managers have little control over conditions experienced by juveniles. Thus, release timing is a critical decision in hatchery operations. This 3-year study used acoustic telemetry to estimate release timing effects on migration survival of fall run Chinook Salmon from the largest hatchery in California: the Coleman National Fish Hatchery. Juvenile Chinook Salmon implanted with JSATS transmitters were released in two or more groups each year, concomitant with the regular hatchery production. Arrays of acoustic monitors were deployed at six locations within the 517 km migration route to estimate reach-specific survival of each release. Mark-recapture models identified both year and release timing effects on reach-specific survival. In years when release effects were well-supported, survival was higher in the earlier release group. Survival in subsequent releases was similar or significantly lower indicating that conditions in the river may decline or stay the same but improvement was not observed. Survival was consistently high in the first 92 km of the migration route and may be related to predator swamping from the release of millions of hatchery fish. Survival declined, and became more variable, within the lower 425 km of the river with the lowest rates observed in the tidal bay-delta. These results indicate that both year and release timing can strongly influence survival and that time between releases likely influences the magnitude of the effect.

Relating survival of fall-run Chinook Salmon through the San Joaquin Delta to river flow

Survival of juvenile fall-run Chinook Salmon Oncorhynchus tshawytscha from the San Joaquin River (SJR) during their migration through the Sacramento-San Joaquin Delta of California has been low in recent years, and there is uncertainty about the role of river flow on survival. Five years (2010–2014) of acoustic telemetry data from juvenile hatchery-reared salmon offer spatially detailed survival information through this region. Multinomial regression and generalized linear models were used to relate survival to river flow in the SJR and its distributary, Old River (OR), on various spatial and temporal scales. Higher survival to Delta exit (rkm 77 from Golden Gate Bridge) was associated with higher root mean square of OR flow in the strongly tidal interior Delta (rkm 123; P < 0.0001), but not with higher SJR flow either entering the Delta from upstream (rkm 196; P = 0.2795) or measured in the Delta near the riverine/tidal interface (rkm 150; P = 0.3845). Survival in the upstream, more riverine region of the Delta was positively associated with SJR flow measured at rkm 150 and average net flow in the interior Delta (P ≤ 0.0001 for each), suggesting different mechanisms driving survival in the upstream versus downstream reaches of the Delta. The spatial complexity of the survival-flow relationship suggests that efforts to maximize total Delta survival should focus on a sequence of smaller regions, tailoring management strategies to each region rather than a single strategy for the Delta as a whole. Highly variable environmental conditions in this region combined with very low survival require more data to fully address the complex survival-flow relationship, both more years of data on various spatial scales and larger sample sizes of acoustic-tagged fish.

Evaluation of Long-Term Mark-Recapture Data for Estimating Abundance of Juvenile Fall-Run Chinook Salmon on the Stanislaus River from 1996 to 2017

Conservation and management of culturally and economically important species rely on monitoring programs to provide accurate and robust estimates of population size. Rotary screw traps (RSTs) are often used to monitor populations of anadromous fish, including fall-run Chinook Salmon (Oncorhynchus tshawytscha) in California’s Central Valley. Abundance estimates from RST data depend on estimating a trap's efficiency via mark-recapture releases. Because efficiency estimates are highly variable and influenced by many factors, abundance estimates can be highly uncertain. An additional complication is the multiple accepted methods for how to apply a limited number of trap efficiency estimates, each from discrete time-periods, to a population’s downstream migration, which can span months. Yet, few studies have evaluated these different methods, particularly with long-term monitoring programs. We used 21 years of mark-recapture data and RST catch of juvenile fall-run Chinook Salmon on the Stanislaus River, California, to investigate factors associated with trap efficiency variability across years and mark-recapture releases. We compared annual abundance estimates across five methods that differed in treatment of trap efficiency (stratified versus modeled) and statistical approach (frequentist versus Bayesian) to assess the variability of estimates across methods, and to evaluate whether method affected trends in estimated abundance. Consistent with short-term studies, we observed negative associations between estimated trap efficiency and river discharge as well as fish size. Abundance estimates were robust across all methods, frequently having overlapping confidence intervals. Abundance trends, for the number of increases and decreases from year to year, did not differ across methods. Estimated juvenile abundances were significantly related to adult escapement counts, and the relationship did not depend on estimation method. Understanding the sources of uncertainty related to abundance estimates is necessary to ensure that high-quality estimates are used in life cycle and stock-recruitment modeling.

Incorporating thermal requirements into flow regime development for multiple Pacific salmonid species in regulated rivers

It has long been recognized that altered flow regimes and warm water temperature are among major stressors that have contributed to the precipitous decline of salmonid populations in California’s Central Valley, resulting in many of them being listed as endangered or threatened pursuant to the U.S. Endangered Species Act. While it is widely acknowledged that water temperature affects all freshwater life stages of salmonids, it has not been a focus when developing instream flow requirements. In this study, we developed a framework that incorporates water temperature requirements into flow regime development for multiple Pacific salmonid species. We applied this framework to Clear Creek, an upper Central Valley stream that supports three salmonid species and has been regulated by reservoir releases for instream flow since 1963 when Whiskeytown dam was built. The analysis of flow data indicated that from the pre-project (i.e., pre-dam) period to post- project period, flow magnitude was reduced by 45–76% for flood flows, 43% for spring pulse flows, and 27–53% for monthly average flows from January through May. Water temperature from 1996 to 2013 exceeded the U.S. Environmental Protection Agency recommended criteria for salmonids from May to October, with most exceedances occurring in September, followed by May and October. Statistical analyses suggested that the abundances of both adult and juvenile salmonids in Clear Creek were strongly correlated to flow magnitude, water temperature, or both. Higher flows that coincided with adult immigration were correlated to higher numbers of adults spawning in Clear Creek, which in turn produced a higher number of juveniles; however, higher flows that occurred during the early life stages (e.g., fry) appeared to reduce the number of outmigrating juveniles. Higher water temperatures in the immigration, spawning, and juvenile rearing periods were correlated with reduced numbers of both adult and juvenile spring-run Chinook salmon in Clear Creek. High water temperatures in June and July were correlated with reduced number of outmigrating juvenile steelhead. Adult or juvenile fall-run Chinook salmon showed either a curvilinear or linear relationship with water temperature during their immigration, spawning, and rearing periods. Based on the pre-project flow and strong correlation between fish abundance and flow or water temperature, we developed a flow regime that incorporates water temperature requirements and other needs of different life stages of salmonids. The flow regime includes the following elements: winter and spring base flow, summer and fall water temperature sustaining flow, winter floodplain inundation flow, and spring pulse flow. This approach can be applied to other regulated streams for developing flow regimes to conserve and recover listed salmonid species.

Ecomorphological plasticity of juvenile fall-run chinook salmon (Oncorhynchus tshawytscha) in perennial and ephemeral streams

In the Central Valley of California, environmental characteristics differ between perennial and ephemeral stream types and therefore present different challenges for rearing salmonids with respect to water discharge, water temperature, food availability, and habitat complexity. Body shape of juvenile fall-run Chinook salmon (Oncorhynchus tshawytscha) reared in a perennial stream environment was compared to juveniles reared in an ephemeral stream environment. Using geometric morphometrics and multivariate analyses, this study presents morphological differences of rearing juvenile Chinook salmon both within and between ephemeral and perennial stream types. We found that shape differences between stream types were primarily associated with expansion of the mid-body region relative to differences in body length. Specifically, juvenile Chinook salmon reared in the ephemeral stream expressed increased body depth dominated by dorsal-ventral elongation of the dorsal, adipose, and anal fins. Eye position and gill opercula-body insertion points also were anteriorly shifted in the juvenile body shape of the ephemeral stream. Our findings support that juvenile Chinook salmon are morphologically flexible and can express habitat-specific developmental differences.

Size, growth, and origin-dependent mortality of juvenile Chinook salmon Oncorhynchus tshawytscha during early ocean residence

Selective mortality during early life history stages can have significant population- level consequences, yet critical periods when selective mortality occurs, the strength of selection, and under what environmental conditions can be difficult to identify. Here, we used otolith microstructure and chemistry to examine the factors potentially linked to selective mortality of juvenile fall-run Chinook salmon Oncorhynchus tshawytscha from California's Central Valley during early ocean residence. Back-calculated size and growth rates of the population were com- pared across 3 sample periods: as juveniles exited the San Francisco Bay estuary (estuary-exit), after their first month at sea (summer-ocean) and 5 mo after ocean entry (fall-ocean). We com- pared mortality dynamics during years of exceptional recruitment (addition of individuals to har- vestable population; 2000 and 2001) to a year of poor recruitment (2005). Otoliths from 2005 were also analyzed for sulfur isotopes to discern hatchery from naturally spawned stock. Significant size and growth-rate selective mortality were detected during the first month at sea in the low recruit- ment year of 2005, but not in 2000 and 2001. Individuals that were larger and growing faster dur- ing freshwater and estuarine rearing were more likely to survive to summer and fall in the low recruitment year. There was a slight, but insignificant, increase in the proportion of hatchery to naturally spawned individuals from estuary-exit to fall-ocean, suggesting that fish from neither origin were overwhelmingly favored. Our results suggest that Central Valley Chinook salmon can be subject to significant size and growth-rate selective mortality resulting in low adult abundance, and this mortality appears independent of origin.

Dietary lipid composition affects the gene expression of gill Na+/K+-ATPase α1b but not the α1a isoform in juvenile fall chinook salmon (Oncorhynchus tshawytscha)

We assessed the effects of dietary fatty acid composition on sodium-potassium ATPase (Na(+)/K(+)-ATPase) activity and isoform expression in the gills of juvenile fall chinook salmon, Oncorhynchus tshawytscha by supplementing diets with either anchovy oil (AO) or AO blended with canola oil (CO) so that CO comprised 0% (0CO), 11% (11CO), 22% (22CO), 33% (33CO), 43% (43CO), or 54% (54CO) of the measured dietary lipid content. The effects of diet were assessed in freshwater (FW) following 104 days of diet manipulation, in response to 24-h seawater (SW) transfer at this time, and following an additional 35 days of SW acclimation. Gill Na(+)/K(+)-ATPase activity was not significantly affected by diet at any sampling time, and there were no consistent effects of diet on the expression of the Na(+)/K(+)-ATPase alpha1a isoform. As dietary CO increased, Na(+)/K(+)-ATPase alpha1b mRNA decreased in fish held in FW, with the 43CO and 54CO diet groups having significantly lower levels than fish fed the 0CO and 11CO diets. Twenty-four-hour SW challenge did not affect the expression of the Na(+)/K(+)-ATPase alpha1a isoform in any diet group, but this isoform was down-regulated in all diet groups following 35 days of SW acclimation. Na(+)/K(+)-ATPase alpha1b expression levels increased in response to 24-h SW transfer and SW acclimation only in fish fed the 54CO diet. The effects of the two extreme diets (0CO and 54CO) were also assessed at various time points during 104 days of rearing in FW. Na(+)/K(+)-ATPase alpha1b mRNA levels were greater in fish fed diet 0CO versus those fed diet 54CO at all times during the FW culture period. These data demonstrate that dietary fatty acid composition can influence the gill Na(+)/K(+)-ATPase isoform physiology of juvenile fall-run chinook salmon prior to SW transfer.

Comparison of Diets of Prickly Sculpin and Juvenile Fall-Run Chinook Salmon in the Lower Mokelumne River, California

I compared diets of prickly sculpin, Cottus asper, and juvenile fall-run chinook salmon, Oncorhynchus tshawytscha, in the lower Mokelumne River, California, from January through June during 1998 and 1999. Prickly sculpin fed primarily on chironomid (Diptera) larvae and hydroptilid and hydropsychid (Trichoptera) larvae. Juvenile chinook salmon fed on zooplankton, plus chironomid, hydroptilid, and hydropsychid pupae. Both supplemented their diets with several other prey items, including larval Sacramento suckers, Catostomus occidentalis. Their diets did not overlap significantly any time during the study. Each species fed more as time progressed in both years. A significant relationship between prey item and fish size was observed for juvenile chinook salmon in 1998 and for both species in 1999. The pattern of growth for chinook salmon and prickly sculpin suggests increased feeding might be more related to water temperature than increase in size. I observed no predation by prickly sculpin on juvenile chinook salmon during this study, although sculpin eggs and larvae were infrequently observed in salmon stomachs.