Acute microcystin exposure induces reversible histopathological changes in Chinook Salmon (Oncorhynchus tshawytscha) and Atlantic Salmon (Salmo salar).

Atlantic Salmon (Salmo salar) and Chinook Salmon (Oncorhynchus tshawytscha) develop a severe liver disease called net-pen liver disease (NPLD), which is characterized by hepatic lesions that include megalocytosis and loss of gross liver structure. Based on studies where salmonids have been exposed to microcystin (MC) via intraperitoneal injection, NPLD is believed to be caused by MC exposure, a hepatotoxin produced by cyanobacteria. Despite the link between MC and NPLD, it remains uncertain if environmentally relevant MC exposure is responsible for NPLD. To determine if we could produce histopathology consistent with NPLD, we compared the response of Atlantic and Chinook Salmon sub-lethal MC exposure. Salmon were orally gavaged with saline or MC containing algal paste and sampled over 2 weeks post-exposure. Liver lesions appeared by 6 h but were resolved 2-weeks post-exposure; histopathological changes observed in other tissues were not as widespread, nor was their severity as great as those in the liver. There was no evidence for NPLD due to the absence of hepatic megalocytosis. These results indicate that the development of NPLD is not due to acute MC exposure but may be associated with higher MC concentration occurring in food, long-term exposure through drinking of contaminated seawater and/or interactions with other marine toxins.

Differential susceptibility of Yukon River and Salish Sea stocks of Chinook salmon Oncorhynchus tshawytscha to ichthyophoniasis.

Preliminary evidence suggests that Chinook salmon Oncorhynchus tshawytscha from the Yukon River may be more susceptible to Ichthyophonus sp. infections than Chinook from stocks further south. To investigate this hypothesis in a controlled environment, we experimentally challenged juvenile Chinook from the Yukon River and from the Salish Sea with Ichthyophonus sp. and evaluated mortality, infection prevalence and infection load over time. We found that juvenile Chinook salmon from a Yukon River stock were more susceptible to ichthyophoniasis than were those from a Salish Sea stock. After feeding with tissues from infected Pacific herring Clupea pallasii, Chinook salmon from both stocks became infected. The infection was persistent and progressive in Yukon River stock fish, where infections sometimes progressed to mortality, and histological examinations revealed parasite dissemination and proliferation throughout the host tissues. In Salish Sea-origin fish, however, infections were largely transient; host mortalities were rare, and parasite stages were largely cleared from most tissues after 3-4 wk. Susceptibility differences were evidenced by greater cumulative mortality, infection prevalence, parasite density, proportion of fish demonstrating a cellular response, and intensity of the cellular response among fish from the Yukon River stock. These observed differences between Chinook salmon stocks were consistent when parasite exposures occurred in both freshwater and seawater. These results support the hypothesis that a longer-standing host-pathogen relationship, resulting in decreased disease susceptibility, exists among Salish Sea Chinook salmon than among Yukon River conspecifics.

Magnetoreception in fishes: the effect of magnetic pulses on orientation of juvenile Pacific salmon.

A variety of animals sense Earth's magnetic field and use it to guide movements over a wide range of spatial scales. Little is known, however, about the mechanisms that underlie magnetic field detection. Among teleost fish, growing evidence suggests that crystals of the mineral magnetite provide the physical basis of the magnetic sense. In this study, juvenile Chinook salmon (Oncorhynchus tshawytscha) were exposed to a brief but strong magnetic pulse capable of altering the magnetic dipole moment of biogenic magnetite. Orientation behaviour of pulsed fish and untreated control fish was then compared in a magnetic coil system under two conditions: (1) the local magnetic field and (2) a magnetic field that exists near the southern boundary of the natural oceanic range of Chinook salmon. In the local field, no significant difference existed between the orientation of the control and pulsed groups. By contrast, orientation of the two groups was significantly different in the magnetic field from the distant site. These results demonstrate that a magnetic pulse can alter the magnetic orientation behaviour of a fish and are consistent with the hypothesis that salmon have magnetite-based magnetoreception.

Light exposure during embryonic and yolk-sac alevin development of Chinook salmon Oncorhynchus tshawytscha does not alter the spectral phenotype of photoreceptors.

Colour vision is mediated by the expression of different visual pigments in photoreceptors of the vertebrate retina. Each visual pigment is a complex of a protein (opsin) and a vitamin A chromophore; alterations to either component affects visual pigment absorbance and, potentially, the visual capabilities of an animal. Many species of fish undergo changes in opsin expression during retinal development. In the case of salmonid fishes the single cone photoreceptors undergo a switch in opsin expression from SWS1 (ultraviolet sensitive) to SWS2 (blue-light sensitive) starting at the yolk-sac alevin stage, around the time when they first experience light. Whether light may initiate this event or produce a plastic response in the various photoreceptors is unknown. In this study, Chinook salmon Oncorhynchus tshawytscha were exposed to light from the embryonic (5 days prior to hatching) into the yolk sac alevin (25 days post hatching) stage and the spectral phenotype of photoreceptors assessed with respect to that of unexposed controls by in situ hybridization with opsin riboprobes. Light exposure did not change the spectral phenotype of photoreceptors, their overall morphology or spatial arrangement. These results concur with those from a variety of fish species and suggest that plasticity in photoreceptor spectral phenotype via changes in opsin expression may not be a widespread occurrence among teleosts.

Integrating Genetic and Demographic Effects of Connectivity on Population Stability: The Case of Hatchery Trucking in Salmon.

Connectivity among populations can have counteracting effects on population stability. Demographically, connectivity can rescue local populations but increase the synchrony across populations. Genetically, connectivity can counteract drift locally but homogenize genotypes across populations. Population independence and diversity underlies system-level buffering against environmental variability, termed the portfolio effect. The portfolio effect has declined in California fall-run Chinook salmon, possibly in part because of the trucking of juvenile hatchery-reared fish for downstream release, which reduces juvenile mortality but increases the connectivity between rivers. We use a dynamical population model to test whether this increased connectivity can explain the loss of the portfolio effect and quantify the relative demographic and genetic contributions to portfolio effect erosion. In the model, populations experience different within-population environmental conditions and the same time-variable ocean conditions, the response to which can depend on a quantitative genetic trait. We find that increased trucking for one population's hatchery can lead to a loss of the portfolio effect, with a system-level trade-off between increased average abundance and increased variability in abundance. This trade-off is much stronger when we include the effects of genetic homogenization than when we consider demographic synchronization alone. Therefore, genetic homogenization can outweigh demographic synchrony in determining the system-level effect of connectivity.

Geomagnetic field influences upward movement of young Chinook salmon emerging from nests.

Organisms use a variety of environmental cues to orient their movements in three-dimensional space. Here, we show that the upward movement of young Chinook salmon (Oncorhynchus tshawytscha) emerging from gravel nests is influenced by the geomagnetic field. Fish in the ambient geomagnetic field travelled farther upwards through substrate than did fish tested in a field with the vertical component inverted. This suggests that the magnetic field is one of several factors that influences emergence from the gravel, possibly by serving as an orientation cue that helps fish determine which way is up. Moreover, our work indicates that the Oncorhynchus species are sensitive to the magnetic field throughout their life cycles, and that it guides their movements across a range of spatial scales and habitats.

Stress up-regulates oxidative burst in juvenile Chinook salmon leukocytes.

When fish perceive stressful scenarios, their hypothalamus-pituitary-interrenal axis is activated resulting in the release of corticotropin releasing hormone, adrenocorticotropic hormone (ACTH), and finally cortisol. The physiologic stress response of fish has most often been linked to the reduced performance of the immune system, with a few exceptions where the immune system is activated. In this report, we tested the hypothesis that oxidative burst activity levels in juvenile Chinook salmon (Oncorhynchus tshawytscha) are altered when the fish is presented with a stressor. Fish were subjected to a stressor for 3 h and then allowed to recover for 20 h following the stressor. Plasma and spleens were collected from euthanized fish before the stressor, at the end of a 3 h stressor, and 23 h after the start of the experiment. Plasma was held at -80 °C until cortisol radioimmunoassay analysis was performed to confirm stress. Spleens were held in Dulbecco's Modified Eagle Medium overnight and analyzed the day following collection. Oxidative burst activity was measured in splenic leukocytes after being stimulated with phorbol 12-myristate 13-acetate. We found a significant increase in activated oxidative burst from fish subjected to the stressor as compared to unstressed fish. Speculation is given to ACTH being the leukocyte priming agent in this experiment rather than the cortisol itself.

Ovarian fluid impacts flagellar beating and biomechanical metrics of sperm between alternative reproductive tactics.

Alternative reproductive tactics (ARTs) are prevalent in nature, where smaller parasitic males typically have better sperm quality than larger territorial guard males. At present, it is unclear what is causing this phenomenon. Our objective was to gain insights into sperm form and function by examining flagellar beating patterns (beat frequency, wave amplitude, bend length, bend angle, wave velocity) and biomechanical sperm metrics (velocity, hydrodynamic power output, propulsive efficiency) of wild spawning Chinook salmon ARTs. Ovarian fluid and milt were collected to form a series of eight experimental blocks, each composed of ovarian fluid from a unique female and sperm from a unique pair of parasitic jack and guard hooknose males. Sperm from each ART were activated in river water and ovarian fluid. Flagellar parameters were evaluated from recordings using high-speed video microscopy and biomechanical metrics were quantified. We show that ART has an impact on flagellar beating, where jacks had a higher bend length and bend angle than hooknoses. Activation media also impacted the pattern of flagellar parameters, such that beat frequency, wave velocity and bend angle declined, while wave amplitude of flagella increased when ovarian fluid was incorporated into activation media. Furthermore, we found that sperm from jacks swam faster than those from hooknoses and required less hydrodynamic power output to propel themselves in river water and ovarian fluid. Jack sperm were also more efficient at swimming than hooknose sperm, and propulsive efficiency increased when cells were activated in ovarian fluid. The results demonstrate that sperm biomechanics may be driving divergence in competitive reproductive success between ARTs.

Effect of Ichthyophonus on blood plasma chemistry of spawning Chinook salmon and their resulting offspring in a Yukon River tributary.

Ichthyophonus is a protozoan parasite of Alaska Chinook salmon Oncorhynchus tshawytscha. In this study, we determined whether spawning Chinook salmon in the Yukon River drainage exhibited a measurable stress response (i.e. elevated plasma cortisol concentrations) and detectable changes in selected blood plasma chemistry parameters when infected with Ichthyophonus. The resulting alevin were also analyzed for any differences in blood plasma chemistry caused by parental infection with Ichthyophonus. In 2010, 2011, and 2012, spawning adult Chinook salmon were collected from the Salcha River, Alaska, USA, and the prevalence of Ichthyophonus in these fish was 7.8, 6.3, and 8.3%, respectively. Fish with no clinical signs of Ichthyophonus and Ichthyophonus-positive parents were cross-fertilized to investigate potential second-generation effects as a result of Ichthyophonus infection. We found no significant difference in cortisol concentrations in blood plasma between Ichthyophonus-positive and -negative adults or between alevin from Ichthyophonus-positive and -negative parents. There were no significant differences in blood plasma parameters (e.g. alanine aminotransferase, creatine kinase, glucose) of Ichthyophonus-negative and -positive adults, with the exception of aspartate aminotransferase, which was significantly higher in plasma of Ichthyophonus-negative adults. All clinical chemistry parameters for alevin resulting from both Ichthyophonus-negative and -positive parents were not significantly different. Based on this study, which has a limited sample size and low prevalence of Ichthyophonus, offspring of Chinook salmon appear to suffer no disadvantage as a result of Ichthyophonus infection in their parents on the Salcha River.

Setting spatial conservation priorities despite incomplete data for characterizing metapopulations.

Management of spatially structured species poses unique challenges. Despite a strong theoretical foundation, practitioners rarely have sufficient empirical data to evaluate how populations interact. Rather, assumptions about connectivity and source-sink dynamics are often based on incomplete, extrapolated, or modeled data, if such interactions are even considered at all. Therefore, it has been difficult to evaluate whether spatially structured species are meeting conservation goals. We evaluated how estimated metapopulation structure responded to estimates of population sizes and dispersal probabilities and to the set of populations included. We then compared outcomes of alternative management strategies that target conservation of metapopulation processes. We illustrated these concepts for Chinook salmon (Oncorhynchus tshawytscha) in the Snake River, USA. Our description of spatial structure for this metapopulation was consistent with previous characterizations. We found substantial differences in estimated metapopulation structure when we had incomplete information about all populations and when we used different sources of data (three empirical, two modeled) to estimate dispersal, whereas responses to population size estimates were more consistent. Together, these findings suggest that monitoring efforts should target all populations occasionally and populations that play key roles frequently and that multiple types of data should be collected when feasible. When empirical data are incomplete or of uneven quality, analyses using estimates produced from an ensemble of available datasets can help conservation planners and managers weigh near-term options. Doing so, we found trade-offs in connectivity and source dominance in metapopulation-level responses to alternative management strategies that suggest which types of approaches may be inherently less risky.

Unilateral perivertebral fibrosis associated with lordosis, kyphosis and scoliosis (LKS) in farmed Chinook salmon in New Zealand.

Vertebral column lordosis, kyphosis and scoliosis (LKS) can result in downgrading of farmed Chinook salmon Oncorhynchus tshawytscha in New Zealand. No cause of LKS has been identified. Radiography and histology were used to quantify LKS and perivertebral fibrosis in 27 fish with LKS visible at harvest and 30 visually normal fish from 3 New Zealand farms. Radiographic LKS was present in all 27 fish with LKS and in 18 of 30 fish without visible LKS. Quantification of the radiographic severity revealed significantly higher radiographic severity scores in fish with visible LKS (mean ± SD = 5.89 ± 2.41) than in fish with no visible, but radiographic LKS (1.44 ± 0.86, p < 0.001). The most frequent histological finding was unilateral perivertebral fibrosis that often extended into the horizontal septum and adjacent myomeres resulting in separation or loss of myocytes. Fibrosis was visible in all fish with LKS and in 12 of 30 fish without visible LKS. Fibrosis scores were higher in fish with visible LKS (3.32 ± 1.71) than in fish without visible LKS (0.35 ± 0.57, p < 0.001). The radiographic LKS severity scores were significantly correlated to the fibrosis scores (R2 = 0.59 p < 0.001) in the fish. Histology of other tissues revealed multifocal inflammation within muscle, peripheral connective tissues and myocardium which were considered most likely incidental in these fish. In this study, LKS was consistently and significantly associated with perivertebral fibrosis, suggesting that perivertebral fibrosis is an important process in the development of LKS. Further research to determine the cause of the fibrosis is required.

Salinity effects on plasma ion levels, cortisol, and osmolality in Chinook salmon following lethal sampling.

Studies on hydromineral balance in fishes frequently employ measurements of electrolytes following euthanasia. We tested the effects of fresh- or salt-water euthanasia baths of tricaine mesylate (MS-222) on plasma magnesium (Mg(2+)) and sodium (Na(+)) ions, cortisol and osmolality in fish exposed to saltwater challenges, and the ion and steroid hormone fluctuations over time following euthanasia in juvenile spring Chinook salmon (Oncorhynchus tshawytscha). Salinity of the euthanasia bath affected plasma Mg(2+) and Na(+) concentrations as well as osmolality, with higher concentrations in fish euthanized in saltwater. Time spent in the bath positively affected plasma Mg(2+) and osmolality, negatively affected cortisol, and had no effect on Na(+) concentrations. The difference of temporal trends in plasma Mg(2+) and Na(+) suggests that Mg(2+) may be more sensitive to physiological changes and responds more rapidly than Na(+). When electrolytes and cortisol are measured as endpoints after euthanasia, care needs to be taken relative to time after death and the salinity of the euthanasia bath.

Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test.

The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution.

Interactive effects of water diversion and climate change for juvenile chinook salmon in the lemhi river basin (USA.).

The combined effects of water diversion and climate change are a major conservation challenge for freshwater ecosystems. In the Lemhi Basin, Idaho (U.S.A.), water diversion causes changes in streamflow, and climate change will further affect streamflow and temperature. Shifts in streamflow and temperature regimes can affect juvenile salmon growth, movement, and survival. We examined the potential effects of water diversion and climate change on juvenile Chinook salmon (Oncorhynchus tshawytscha), a species listed as threatened under the U.S. Endangered Species Act (ESA). To examine the effects for juvenile survival, we created a model relating 19 years of juvenile survival data to streamflow and temperature and found spring streamflow and summer temperature were good predictors of juvenile survival. We used these models to project juvenile survival for 15 diversion and climate-change scenarios. Projected survival was 42-58% lower when streamflows were diverted than when streamflows were undiverted. For diverted streamflows, 2040 climate-change scenarios (ECHO-G and CGCM3.1 T47) resulted in an additional 11-39% decrease in survival. We also created models relating habitat carrying capacity to streamflow and made projections for diversion and climate-change scenarios. Habitat carrying capacity estimated for diverted streamflows was 17-58% lower than for undiverted streamflows. Climate-change scenarios resulted in additional decreases in carrying capacity for the dry (ECHO-G) climate model. Our results indicate climate change will likely pose an additional stressor that should be considered when evaluating the effects of anthropogenic actions on salmon population status. Thus, this type of analysis will be especially important for evaluating effects of specific actions on a particular species. Efectos Interactivos de la Desviación del Agua y el Cambio Climático en Individuos Juveniles de Salmón Chinook en la Cuenca del Río Lemhi (E.U.A.).

Rapid CRISPR-Cas13a genetic identification enables new opportunities for listed Chinook salmon management.

Accurate taxonomic identification is foundational for effective species monitoring and management. When visual identifications are infeasible or inaccurate, genetic approaches provide a reliable alternative. However, these approaches are sometimes less viable (e.g., need for near real-time results, remote locations, funding concerns, molecular inexperience). In these situations, CRISPR-based genetic tools can fill an unoccupied niche between real-time, inexpensive, but error-prone visual identification and more expensive or time-consuming, but accurate genetic identification for taxonomic units that are difficult or impossible to visually identify. Herein, we use genomic data to develop CRISPR-based SHERLOCK assays capable of rapidly (<1 h), accurately (94%-98% concordance between phenotypic and genotypic assignments), and sensitively (detects 1-10 DNA copies/reaction) distinguishing ESA-listed Chinook salmon runs (winter- and spring-run) from each other and from unlisted runs (fall- and late fall-run) in California's Central Valley. The assays can be field deployable with minimally invasive mucus swabbing negating the need for DNA extraction (decreasing costs and labour), minimal and inexpensive equipment needs, and minimal training to conduct following assay development. This study provides a powerful genetic approach for a species of conservation concern that benefits from near real-time management decision-making but also serves as a precedent for transforming how conservation scientists and managers view genetic identification going forward. Once developed, CRISPR-based tools can provide accurate, sensitive, and rapid results, potentially without the prohibitive need for expensive specialty equipment or extensive molecular training. Further adoption of this technology will have widespread value for the monitoring and protection of our natural resources.

An Efficient Tetraplex Surveillance Tool for Salmonid Pathogens.

Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia-like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum, and Yersinia ruckeri. The limit of detection in singleplex and tetraplex assays was reached for most targets at 10-9 ng/µl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/µl, NZ-RLO2 = 0.162 and 0.21 copies/µl, T. maritimum = 0.345 and 0.93 copies/µl, while the limit of detection for Y. ruckeri was 10-8 with 1.0 copies/µl and 0.7 copies/µl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens, respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry.

Red and White Chinook Salmon (Oncorhynchus tshawytscha): Differences in the Transcriptome Profile of Muscle, Liver, and Pylorus.

Astaxanthin (Ax), the main carotenoid responsible for the distinct red flesh color in salmonids (Oncorhynchus, Salvelinus, Salmo, and Parahucho), is added to the diet of farmed fish at a substantial cost. Despite the great economical value for the salmon industry, the key molecular mechanisms involved in the regulation of muscle coloration are poorly understood. Chinook salmon (Oncorhynchus tshawytscha) represent an ideal model to study flesh coloration because they exhibit a distinct color polymorphism responsible for two color morphs, white and red flesh pigmented fish. This study was designed to identify the molecular basis for the development of red and white coloration of fish reared under the same experimental conditions and to better understand the absorption mechanism of Ax in salmonids. Pyloric caeca, liver, and muscle of both groups (n = 6 each) were selected as the most likely critical target organs to be involved respectively in the intestinal uptake, metabolism, and retention of Ax. Difference in the transcriptome profile of each tissue using next-generation sequencing technology was conducted. Ten KEGG pathways were significantly enriched for differentially expressed genes between red and white salmon pylorus tissue, while none for the transcriptome profile in the other two tissues. Differential expressed gene (DE) analyses showed that there were relatively few differences in muscle (31 DE genes, p < 0.05) and liver (43 DE genes, p < 0.05) of white and red Chinook salmon compared approximately 1125 DE genes characterized in the pylorus tissue, with several linked to Ax binding ability, absorption, and metabolism.

High Prevalence of the Copepod Salmincola californiensis in Steelhead Trout in Lake Ontario Following its Recent Invasion.

Salmincola californiensis (Dana, 1853) (Subclass Copepoda: Family Lernaeopodidae) is known to parasitize salmonids of the genus Oncorhynchus including Oncorhynchus mykiss (rainbow trout), Oncorhynchus tshawytscha (chinook salmon), and Oncorhynchus kisutch (coho salmon). These 3 salmonids have been introduced to the Great Lakes intermittently since the mid-1800s. As we demonstrate here, the introduction of these salmonids to the Great Lakes was followed, at some point, by the introduction of their parasitic gill copepod, S. californiensis. Given anecdotal accounts of S. californiensis in introduced salmonids in Lake Ontario since 2012, we chose to conduct a survey to formally document the occurrence of this introduced species. Our survey took place during spring, summer, and fall of 2018 and during spring of 2019 at the south-eastern side of Lake Ontario. Prevalence of S. californiensis was 69, with a mean intensity of 2.7 in 61 rainbow trout examined in 2018. In 2019, prevalence of S. californiensis was 71, with a mean intensity of 3.6 in 59 rainbow trout examined. The prevalence of S. californiensis was 39, with a mean intensity of 1.6 in 223 chinook salmon examined in 2018. No specimens of S. californiensis were found in the 100 coho salmon examined in 2018. The prevalence of S. californiensis in rainbow trout is of great concern considering that it is double that found in rainbow trout in the native range (69 [in 2018] and 71 [in 2019] vs. 35). This is the first formal documentation of the invasion of S. californiensis in Lake Ontario. Future fisheries management decisions in Lake Ontario and its tributaries should take into account these data.

Microplastics in juvenile Chinook salmon and their nearshore environments on the east coast of Vancouver Island.

Microplastics are a significant issue in the world's oceans. These small plastic particles (<5 mm in size) are becoming globally ubiquitous in the marine environment and are ingested by various fish species. Here we investigate the incidence of microplastics in juvenile Chinook salmon and their nearshore marine environments on the east coast of Vancouver Island, British Columbia. We completed a series of beach seines, plankton tows and sediment cores in nearshore areas of importance to juvenile salmon. Microplastics were extracted from fish, water and sediment samples and concentrations were quantified. Microplastics analysis, consisting predominantly of fibrous plastics, showed juvenile Chinook salmon contained 1.2 ±â€¯1.4 (SD) microplastics per individual while water and sediment samples had 659.9 ±â€¯520.9 microplastics m-3 and 60.2 ±â€¯63.4 microplastics kg-1 dry weight, respectively. We found no differences in microplastic concentrations in juvenile Chinook and water samples among sites but observed significantly higher concentrations in sediment at the Deep Bay site compared to Nanaimo and Cowichan Bay sites. Chinook microplastic concentrations were relatively low compared to literature values and, given the size and type of microplastics we observed, are unlikely to represent an immediate threat to fish in this area. However, microplastics less than 100 µm in size were not included in the study and may represent a greater threat due to their ability to translocate through tissues.

Endangered wild salmon infected by newly discovered viruses.

The collapse of iconic, keystone populations of sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon in the Northeast Pacific is of great concern. It is thought that infectious disease may contribute to declines, but little is known about viruses endemic to Pacific salmon. Metatranscriptomic sequencing and surveillance of dead and moribund cultured Chinook salmon revealed a novel arenavirus, reovirus and nidovirus. Sequencing revealed two different arenavirus variants which each infect wild Chinook and sockeye salmon. In situ hybridisation localised arenavirus mostly to blood cells. Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture.