Young Salmon Research Articles

Assessing genotype-environment interactions in Atlantic salmon reared in freshwater loch and recirculating systems.

The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices. In a commercial setting, we explore the genetic structure of growth characteristics, measure genotype-environment interactions (GxE) in salmon smolts, and examine genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net-pens and RAS. After an 8-week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re-ranking for whole-body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented.

Monitoring and predicting the presence and abundance of juvenile Atlantic salmon in tributaries according to habitat characteristics using environmental DNA

AbstractConservation of the Atlantic salmon Salmo salar requires to monitor the spatial distribution and abundance of juveniles at a local scale in tributaries. However, tributaries are rarely accounted for in monitoring programs despite their importance for juvenile life stages. This is mainly because inventories of young salmon populations in tributaries can be technically challenging with traditional methods, as the number of tributaries in a watershed can be important and their access limited compared to the main stem. In this study, we tested the use of environmental DNA (eDNA) to quantify the abundance of juvenile Atlantic salmon in tributaries. We successfully detected eDNA of juvenile Atlantic salmon in 19 tributaries of three main rivers of the Gaspé Peninsula (Québec, Canada) using quantitative real‐time PCR analyses. By comparing the eDNA approach with electrofishing surveys conducted in parallel to water sampling, we found that eDNA concentrations positively correlated with juvenile abundance, total biomass, and body surface area. The use of the allometrically scaled mass (ASM) instead of abundance improved the correlation. Furthermore, we demonstrated that the levels of eDNA molecules detected for juvenile Atlantic salmon were also correlated with water temperature and canopy cover measured in each tributary. Finally, we tested if eDNA concentrations measured in a tributary could be used as a reliable indicator of juvenile abundance or biomass in that tributary. We found that our models slightly better predicted juvenile biomass than juvenile abundance. The use of ASM did not improve model prediction, suggesting that further refinement would be required in the future. Our method will facilitate the implementation of conservation practices appropriate to the ecology of juvenile Atlantic salmon in tributaries.

Young Salmon in British Columbia Are Getting Bigger

A rediscovered catalog of sockeye scales gave researchers access to century-old fish DNA.

Lipid profile of parr and smolts of Atlantic salmon (Salmo salar L.) reared in aquaculture under various lighting regimes

The study of the biochemical mechanisms of the effect of additional lighting on the growth and early development of salmonids in aquaculture allows to identify patterns of slow or accelerated growth, as well as the onset of the smoltification. In this study, the results of changes in lipid status in parr and smolts of Atlantic salmon after the “winter window” (December-January) are presented. These results were obtained from three experimental groups exposed to different lighting and feeding regimes at the fingerlings stage. The changes in lipid composition of the studied young salmon indicate the onset of smoltification in all experimental groups. However, this effect is the most pronounced in the fish previously reared under continuous lighting during the summer-autumn season.

ISOTHERMAL RECOMBINANT POLYMERASE AMPLIFICATION AND CRIPSR(CAS12A) ASSAY DETECTION OF RENIBACTERIUM SALMONINARUM AS AN EXAMPLE FOR WILDLIFE PATHOGEN DETECTION IN ENVIRONMENTAL DNA SAMPLES.

Improving rapid detection methods for pathogens is important for research as we collectively aim to improve the health of ecosystems globally. In the northern hemisphere, the success of salmon (Oncorhynchus spp.) populations is vitally important to the larger marine, aquatic, and terrestrial ecosystems they inhabit. This has led to managers cultivating salmon in hatcheries and aquaculture to bolster their populations, but young salmon face many challenges, including diseases such as bacterial kidney disease (BKD). Early detection of the BKD causative agent, Renibacterium salmoninarum, is useful for managers to avoid outbreaks in hatcheries and aquaculture stocks to enable rapid treatment with targeted antibiotics. Isothermal amplification and CRIPSR-Cas12a systems may enable sensitive, relatively rapid, detection of target DNA molecules from environmental samples compared to quantitative PCR (qPCR) and culture methods. We used these technologies to develop a sensitive and specific rapid assay to detect R. salmoninarum from water samples using isothermal recombinase polymerase amplification (RPA) and an AsCas12a RNA-guided nuclease detection. The assay was specific to R. salmoninarum (0/10 co-occurring or closely related bacteria detected) and sensitive to 0.0128 pg/µL of DNA (approximately 20-40 copies/µL) within 10 min of Cas activity. This assay successfully detected R. salmoninarum environmental DNA in 14/20 water samples from hatcheries with known quantification for the pathogen via previous qPCR (70% of qPCR-positive samples). The RPA-CRISPR/AsCas12a assay had a limit of detection (LOD) of >10 copies/µL in the hatchery water samples and stochastic detection below 10 copies/µL, similar to but slightly higher than the qPCR assay. This LOD enables 37 C isothermal detection, potentially in the field, of biologically relevant levels of R. salmoninarum in water. Further research is needed to develop easy-to-use, cost-effective, sensitive RPA/CRISPR-AsCas12a assays for rapidly detecting low concentrations of wildlife pathogens in environmental samples.

Optimum timing and size at release of chum salmon: Improving survival by modifying hatchery practices

AbstractAn existing conceptual model that assessed the timing of and size at release of juvenile Japanese chum salmon in Japanese waters is modified using data obtained from young salmon collected in coastal waters off Kombumori, eastern Hokkaido, Japan. The early life histories of Tokachi River late‐migrating chum salmon are estimated based on microstructural analysis of thermally marked otoliths from recaptured fish. A revised model is presented that reveals the optimal timing of and size at release of chum salmon juveniles to be dependent upon their size at sea entry and sea surface temperature (SST) near Tokachi River mouth. Juvenile salmon are assumed to grow at a fixed rate after sea entry and to reach a target fork length upon arrival in Kombumori waters when SST conditions are within a specific optimal range. However, because of annual variation in SST, the size at and timing of juvenile chum salmon sea entry following their release from hatcheries represents a moving target, which flexible hatchery release practices are required to meet. Return rates of adult chum salmon to Tokachi River correlate positively with the number of days elapsed between the period when SST is suitable near the river mouth where they enter the sea, and SST conditions in Kombumori waters, which suggests that in years when SST increases rapidly the survival of salmon tends to decline. Windows of optimal times of and sizes at release are proposed for juvenile chum salmon to improve their survival and hatchery success.

To the question of the efficiency young pacific salmon at fish farms of the Sakhalin region

Effectiveness of the salmon juveniles feeding was examined during six cycles of fish breeding for pink salmon Oncorhynhus gorbuscha, chum salmon O. keta, cherry salmon O. masou, and coho salmon O. kisutsh at 12 fish hatcheries belonged to the Sakhalin branch of FBSI Glavrybvod with using of different starter feeds produced by Aller Aqua (Denmark) and Aquatech (Russia). All hatcheries worked in the coldwater regime of rearing. Both feeds were rather effective for all species that was evidenced by low feeding coefficients, usually 0.6–0.8. Anyway, average value of the feeding coefficient was lower for the starter feed Aquatech at all factories. Beyond a high quality of this feed, its availability in two variants of flotation was important, as the slowly sinking and floating forms. The floating food was found to be more suitable for the growing juvenile pink salmon at all farms. On the other hand, both starter feeds were suitable for chum salmon, their priority for this species depended on fish farm and obviously was determined by combination of many factors, such as temperature conditions, configuration of canals and ponds, their hydrodynamics, feed dispensers, etc.

Fish Love Floods: Benefits of Floodplains in San Francisco Estuary

Lots of rain can make rivers rise, causing them to spill into low-lying areas called floodplains. Floodplains protect cities from flooding and provide food-rich, safe habitats for freshwater creatures. The largest floodplain of the San Francisco Estuary is the Yolo Bypass. The Yolo Bypass is connected to the Sacramento River and protects Sacramento and surrounding areas from flooding. A twenty-plus year scientific monitoring program in the Yolo Bypass has documented many benefits that this floodplain provides to the Estuary. For example, the Yolo Bypass is a nursery area for baby fish such as young Chinook salmon and Sacramento splittail, and it is an important food bank that transports fish food to the rest of the Estuary. This article discusses some of the benefits that floodplains provide for fish species, and it highlights the importance of long-term monitoring to help scientists and managers make decisions for the benefit of fishes and ecosystems.

Estimating target strength of young chum salmon (Oncorhynchus keta)

Although chum salmon (Oncorhynchus keta) is an important fishery resource in Japan, acoustic methods cannot be applied to biomass estimation because the target strength (TS) is unknown. This study clarified the TS for each fork length (FL: 5.5–33.5 cm) of young chum salmon inhabiting the Japanese coastal area to the Bering Sea by measuring free-swimming fish. The size dependences of the TS values were TSmean = 20 log10 FL – 68.0, for both 38 and 120 kHz. This facilitated the estimation of biomass of young salmon using acoustic methods.

Juvenile Chinook salmon use of sandbar willows in a large-scale, simulated riparian floodplain: microhabitat and energetics

Outmigrating, juvenile Chinook salmon Oncorhynchus tshawytscha, with access to floodplains (e.g., Yolo Bypass California, USA), grow faster than those restricted to the main channel of the Sacramento River. How these young salmon might use rooted, vegetative structure (e.g., to decrease energy expenditures) while holding positions in flowing water on floodplains and flooded riparian zones is unknown. We conducted daytime experiments in a large (24.4 m long) flume containing a planted area (9.76 m × 1.22 m) of sandbar willows, Salix interior. Flume water was maintained at 1.5 m depth and 16 °C over a 15–90 cm s−1 test velocity range. Fish were videoed using 19 cameras to determine positional behavior, including their depth, use of vegetation, and tail-beat (body-undulation) frequencies (TBFs). These TBFs were replicated with similarly-sized salmon in a calibrated, Brett-type swimming respirometer, where oxygen consumption rates were measured. Using these laboratory measurements, we estimated their swimming velocities and energetic costs associated with occupying sandbar willow habitats in the flume. As flume velocities increased and the leafy canopies of the willows were bent over from the flow, salmon occupied deeper water, among the thick stems of the willows, and maintained their positions. Even at the highest (90 cm s−1) nominal flume velocities, their estimated swimming velocities were only 35.6 cm s−1, within the bottom 15 cm of the water column. This resulted in unchanged energetic costs, compared with those estimated at lower nominal water velocities. The use of vegetated (e.g., with sandbar willow common to the riparian zone) floodplains, rather than non-vegetated ones, can potentially provide energy-saving, growth-promoting daytime habitat for migrating juvenile salmonids during river-flow periods that include floodplain inundation.

Coldwater fish in a warm water world: Implications for predation of salmon smolts during estuary transit.

Predator–prey systems face intensifying pressure from human exploitation and a warming climate with implications for where and how natural resource management can successfully intervene. We hypothesized young salmon migrating to the Pacific Ocean face a seasonally intensifying predator gauntlet when warming water temperature intensifies a multiple predator effect (MPE) from Striped Bass Morone saxatilis and Largemouth Bass Micropterus salmoides. We evaluated this hypothesis using data synthesis and simulation modeling.Contemporary studies based on acoustically tagged fish reaffirmed older observations that Chinook Salmon smolts must transit the Delta before water temperature reaches 20°C or mortality will be nearly 100%. Striped Bass attack rates on tethered smolts were insensitive to distance from shore and water temperature, whereas Largemouth Bass attack rates were highest near shorelines in warm water, supporting the temporal aspect of the hypothesis. Whether the combined effects of the two predators produce an MPE remains unconfirmed due to limitations on quantifying salmon behavior.We used multiple simulation models to try to reconstruct the empirical relationship between smolt survival and water temperature. Simulations reinforced attack rate results, but could not recreate the temperature dependence in smolt survival except at higher than observed temperatures. We propose three hypotheses for why and recommend discerning among them should be a focus of research.We found significant linear relationships between monthly mean inflow to the Delta from each of its two largest tributaries and monthly mean water temperatures along associated salmon migration routes, but these relationships can be nonlinear, with most of the correlation occurring at low inflows when water temperature is largely controlled by air temperature and day length. As the global climate warms, changed circumstances in predator–prey relationships may present important challenges when managing species vulnerable to extinction in addition to presently more abundant species.

Artificial lights with different spectra do not alter detrimental attraction of young Chinook salmon and sockeye salmon along lake shorelines

Tabor RA, Perkin EK, Beauchamp DA, Britt LL, Haehn R, Green J, Robinson T, Stolnack S, Lantz DW, Moore ZJ. 2021. Artificial lights with different spectra do not alter detrimental attraction of young Chinook salmon and sockeye salmon along lake shorelines. Lake Reserv Manage. XX:XXX–XXX. Artificial light at night (ALAN) is common in lakes with developed shorelines, especially prevalent in the nearshore areas where juvenile fishes, including salmonids, are present. One concern is that fishes may be attracted to ALAN and become more vulnerable to predators. The use of longer wavelength lights has been suggested to reduce the effects of ALAN; however, the response in juvenile salmonids is not well known. We tested the hypothesis that longer wavelength lights would attract fewer subyearling Chinook salmon (Oncorhynchus tshawytscha) and sockeye salmon (O. nerka) than shorter wavelength lights. Test lights included 4 LED lights, an incandescent light, and a high-pressure sodium light (HPS). In total, 13 experimental trials were conducted in 2017 and 2018, and in total 1769 Chinook salmon and 870 sockeye salmon were collected with beach seines. The mean catch rate (number per beach seine set) of subyearling salmonids was 51.0 for lighted treatments but only 6.6 for control treatments (no light). In both years, we did not find any significant difference in catch rates for either species between either of the longer wavelength lights (red-filter and yellow-filter LED lights) and other lights, and thus we rejected the hypothesis that longer wavelength light would attract fewer subyearling salmonids. For these early life stages of salmon in shallow shoreline habitats, reducing the intensity of light present is likely more important than altering the spectral composition when trying to minimize maladaptive attraction to ALAN.

Phenological mismatch, carryover effects, and marine survival in a wild steelhead trout Oncorhynchus mykiss population

Climate-driven changes in the oceans, such as shifts in prey timing and abundance, could influence variability in population productivity of marine fishes. For example, according to the match/mismatch hypothesis, the temporal matching of the young salmon outmigration from freshwater to the ocean relative to the timing of availability of their prey could influence their marine survival. Indeed, understanding patterns and processes of marine survival is particularly pressing in many salmon and steelhead trout populations due to recent declines. To determine whether phenological mismatches between juvenile salmonids and their prey could contribute to low ocean survival, we analyzed the migration timing and ocean survival of 22,116 tagged juvenile steelhead trout Oncorhynchus mykiss over 12 years from the Wind River, Washington State, USA. We used a Bayesian multilevel modelling approach with variable selection to assess how survival was associated with body size, river exit date, the biological spring transition date (the day when northern zooplankton first appeared in the coastal region near the Columbia River estuary), and the degree of mismatch (the effect of the interaction between individual outmigration timing and biological spring transition date). The variables with the highest probability of contributing to individual survival were fish size (100%), river exit date (99%), the interaction between year and river exit date (91%), and the biological spring transition date (64%). Fish that were larger than average at outmigration had higher ocean survival, providing further evidence that freshwater growing conditions have carryover effects on marine survival. Years with greater annual phenological mismatches such as those years with late biological spring transition dates (i.e., occurring after June 1st), or warm sea surface temperatures, had sufficiently low marine survival to compromise recovery goals. Substantial intra-annual variation in outmigration timing buffered the population from inter-annual variation in optimal outmigration timing. Collectively these findings indicate that freshwater growing conditions, migration timing, and the timing of high-quality food availability in the nearshore coastal environment work in concert to influence individual survival and annual smolt-to-adult returns.

Effect of parental phenotype on dispersal, growth and maturation of offspring in wild masu salmon (Oncorhynchus masou)

Offspring traits are influenced by complex interactions among parent genotypes and phenotypes. However, ecological studies of these effects have tended to focus on one of either maternal or paternal influences. In this study, we investigated the effects of both parental phenotypes on offspring dispersal, growth and early sexual maturity in masu salmon. We used wild-caught parental fish in a half-sib mating design that allowed comparison of offspring from males of two different life-history types (precocious males that had lived only in fresh water and anadromous males that had migrated to the sea). These males were mated with anadromous females and the eggs planted in natural streams in three different years. Natal dispersal distance depended on offspring sex, body size and paternal life history: female offspring moved further downstream than males, whilst daughters of precocious fathers tended to move further downstream than those of anadromous sires. There was a maternal effect on offspring growth, with larger eggs resulting in larger offspring at least until these became precociously mature at the end of the first summer. However, while faster growing male offspring were more likely to become precociously mature, there was no evidence that the probability of precocious maturation was influenced by parental life history. We conclude that, although body size of young salmon was significantly influenced by egg size and there were sex differences in dispersal, their growth rate and divergence in life history types were mainly environmentally driven.

Farm to Fish: Lessons from a Multi-Year Study on Agricultural Floodplain Habitat

Large areas of California’s historic floodplain have been separated from adjacent river channels by levee construction, allowing the development of an extensive agricultural industry. Based on successful partnerships between agriculture and conservation groups to support migrating waterfowl, we examined whether seasonally flooded rice fields could be modified to provide off-channel rearing habitat for juvenile Chinook Salmon Oncorhynchus tshawytscha. During winter and spring of 2012-2017, we conducted a series of experiments in Yolo Bypass and other regions of California’s Central Valley using hatchery Chinook Salmon as a surrogate for wild Chinook Salmon, the management target for our project. Overall, we found that seasonally flooded fields are highly productive, resulting in significantly higher levels of zooplankton and high Chinook Salmon growth rates as compared to the adjacent Sacramento River. We found similar results for multiple geographical areas in the Central Valley, and in different cover types, such as non-rice crops and fallow areas. Although field substrate type did not detectably affect fish growth and survival, connectivity with upstream and downstream areas appeared to drive fish occupancy, because rearing young salmon were generally attracted to inflow in the fields, and not all of the fish successfully emigrated off the fields without efficient drainage. In general, we faced numerous logistic and environmental challenges to complete our research. For example, periodic unmanaged floods in the Yolo Bypass made it difficult to schedule and complete experiments. During severe drought conditions, we found that managed agricultural habitats produced low and variable salmon survival results, likely because of periodically high temperatures and concentrated avian predation. In addition, our project required substantial landowner time and effort to install and maintain experimental fields. Recent and future infrastructure improvements in Yolo Bypass could substantially improve options for experimental work and broaden efforts to enhance salmon habitat.

THE BEHAVIOR OF YOUNG SALMON (SALMO SALAR L.) IN THE RIVER LIZHMA (LAKE ONEGO) IN THE SUMMER SEASON

It was found that each age group of young salmon has its own daily foraging activity pattern, mainly regulated by illumination. At the latitude of the Lizhma River (62°22ʹ40ʺ N, 34°29ʹ57ʺ E), which drains to Lake Onego, the foraging activity duration in June and July is 16 h ± 30 min. In twilight hours and in the dark (below 200 lx) it was absent in all age groups. Young-of-the-year (0+) maintained a constant level of foraging activity during the day, making about 900 darts at food. Parr aged 1+ and 2+ foraged the most actively in the morning (18,000 lx), after which the activity declined until 15 h (70,000 lx)and remained low until 19 h (21,000 lx). Then it increased slightly until dusk. The number of darts at food was about 350 per day. For 3+ parr, the activity was the lowest in the morning hours, gradually growing afterwards to reach a peak at around 15 hours, after which a gradual decline was observed. During the day they make about 300 darts at food. The foraging intensity for 0+ fish averages 63 darts per hour. Fish aged 1+ make less than 30 darts/h; 2+ make about 40 darts/h; 3+ salmon make about 25 darts/h. Foraging activity can be reduced by dense clouds and competition. Young fish aged 0+ and 1+ cannot compete with larger parr and other predators for fodder-rich sites. 2+ and 3+ parr occupy the most advantageous feeding microsites, where they perform up to 88 % of all daily darts for food in less than 50 % active time, and thus satisfy their daily nutritive demand. As a result, 2+ and 3+ parr would be more often seen inactive in “shelter” microsites compared to 0+ and 1+ individuals.

GAMETHOGENESIS OF PACIFIC SALMONS. 1. DEVELOPMENT OF GONAD IN YOUNG CHUM SALMON ONCORHYNCHUS KETA WALBAUM UNDER VARIOUS TEMPERATURE REGIMES

Early stages of gametogenesis in young chum salmon are investigated under various temperature regimes at three fish farms of Sakhalin region and in laboratory conditions. In all cases, sex differentiation started after the mass hatching, the age of differentiation varied from 65 to 213 days, but the sum of accumulated degree-days was rather stable — from 620.6 to 669.1. The period from the beginning of sex differentiation to the beginning of previtellogenesis lasted 27–144 days depending on conditions, even for fish in the same fish farm. The lower was the water temperature after the beginning of sex differentiation, the smaller sum of degree-days was accumulated by fish before the beginning of previtellogenic growth of oocytes and the shorter was the period of oocyte growth before the fish release from the farm. The period of previtellogenesis in chum salmon always began before the end of larval period, when weight of the yolk sac was from 1.8 to 18.2 % of the total body weight.

Macrozoobenthos in tributaries of the lower reaches of the ponoy river (Kola peninsula, Russia) in the habitats of young atlantic salmon (Salmo Salar L.) and brown trout (Salmo Trutta L.)

Macrozoobenthos in tributaries of the lower reaches of the ponoy river (Kola peninsula, Russia) in the habitats of young atlantic salmon (Salmo Salar L.) and brown trout (Salmo Trutta L.)

Effects of Extreme Hydrologic Regimes on Juvenile Chinook Salmon Prey Resources and Diet Composition in a Large River Floodplain

AbstractClimate and hydrologic variability are defining characteristics of California rivers. Recently, the region experienced an unprecedented drought, and the probability of similarly warm, dry conditions is predicted to increase. In addition to warming air and water temperatures, climate change projections predict increased flooding and sea level rise, likely aggravating the water resource issues that already challenge the western United States. Water managers balance many public interests, including the conservation of native fishes, such as the Chinook Salmon Oncorhynchus tshawytscha. Given projected changes in climate and hydrology, there is an urgent need to understand how salmon respond to these conditions. In this study, we examined how young salmon responded to extreme drought (2012–2015) versus flood (1998–1999) conditions in the Yolo Bypass, a floodplain–tidal slough complex of the Sacramento River, California. We found that the diets of juvenile Chinook Salmon were dominated by aquatic–riparian insects during flooding and were dominated by zooplankton during the drought. Although juvenile salmon that were caught during the drought seemed to have eaten a higher number of prey items on average, they also had higher metabolic costs. Therefore, it is likely that juvenile salmon must augment their foraging behavior to offset higher temperatures and prey shifts. Finally, preferentially consumed, calorically valuable prey (i.e., larger zooplankton and aquatic–riparian insects) have become rare due to habitat degradation and biological invasions, and resource managers must consider re‐establishing productive off‐channel habitats, such as riparian corridors, floodplains, and wetlands.

Estuarine and marine diets of out-migrating Chinook Salmon smolts in relation to local zooplankton populations, including harmful blooms

Changes in food availability during the early marine phase of wild Chinook Salmon (O. tshawytscha) are being investigated as a cause of their recent declines in the Salish Sea. The marine survival of hatchery smolts, in particular, has been poor. This part of the Salish Sea Marine Survival Project examined the diet of young out-migrating Chinook Salmon for four consecutive years in the Cowichan River estuary and in Cowichan Bay, British Columbia, Canada. Local zooplankton communities were monitored during the final year of the study in the Cowichan River estuary, Cowichan Bay, and eastward to the Salish Sea to better understand the bottom-up processes that may be affecting Chinook Salmon survival. Rearing environment affected body size, diet, and distribution in the study area. Clipped smolts (hatchery-reared) were larger than the unclipped smolts (primarily naturally-reared), ate larger prey, spent very little time in the estuary, and disappeared from the bay earlier, likely due to emigration or mortality. Their larger body size may be a disadvantage for hatchery smolts if it necessitates their leaving the estuary prematurely to meet energy needs; the onset of piscivory began at a forklength of approximately 74 mm, which was less than the average forklength of the clipped fish in this study. The primary zooplankton bloom occurred during the last week of April/first week of May 2013, whereas the main release of hatchery-reared Chinook Salmon smolts occurs each year in mid-May—this timing mismatch may reduce their survival. Gut fullness was correlated with zooplankton biomass; however, both the clipped and unclipped smolts were not observed in the bay until the bloom of harmful Noctiluca was finished—20 days after the maximum recorded zooplankton abundance. Jellyfish medusa flourished in nearshore areas, becoming less prevalent towards the deeper waters of the Salish Sea. The sizable presence of Noctiluca and jellyfish in the zooplankton blooms may be repelling young salmon from a critical early marine food source and reducing their survival.