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This article explores the impact of vateritic otoliths on hatchery-reared Coho Salmon, which are important for ecosystems, Indigenous communities, and the fishing industry. While hatcheries were once considered effective, research has shown that hatchery-reared salmon have lower survival rates in the wild compared to their wild counterparts. Vateritic otoliths, which affect hearing and balance, have been found to be common in hatchery-reared salmon. The Coho Otolith Project aims to investigate the causes and consequences of vateritic otolith development in Coho Salmon, conducting experiments to understand its influence on survival rates in both stream and marine environments. The research also aims to determine the prevalence of vateritic otoliths in hatchery-reared Coho Salmon across different facilities and stocks, providing valuable insights for hatchery managers and stakeholders to improve practices and conserve salmon stocks. [Extracted from the article]

Restoration of movement corridors is a key management action used to address threats to migratory and other mobile species. Yet, we lack restoration effectiveness studies that allow for species to reestablish naturally (i.e. without supplementation) following habitat reconnection that capture all phases (dispersal, growth, and regulation) of recovery, and that takes an ecosystems approach. We investigated the natural recovery of migratory anadromous Coho salmon following habitat reconnection across a 5‐km section of Rock Creek, a forested tributary of the Cedar River, Washington, United States, 3 km upstream of Landsburg Dam. The dam blocked upstream fish movement for 102 years until the completion of a fish ladder in 2003. We also evaluated the response of non‐migratory trout, which are closely related to Coho salmon. Juvenile Coho salmon natal to the Cedar River dispersed into Rock Creek for rearing until spawning there in 2007. After restoration, juvenile Coho salmon density (fish/m2) increased 18‐fold, approaching an asymptote (i.e. regulation phase) a decade later. Coho salmon recovery in Rock Creek was spatially variable, however, slowing with distance from the site of restoration. Trout density was also higher after restoration relative to before, likely due to several mechanisms, including increased capacity resulting from the reestablishment of marine organic matter subsidies delivered by spawning anadromous fish. Our study demonstrates that migratory species can recover naturally after the restoration of habitat connectivity and associated movement corridors. Furthermore, our results suggest that such actions can also benefit nontarget species by reestablishing key ecosystem links driven by the target species. [ABSTRACT FROM AUTHOR]

Concern over rising water temperatures for freshwater ectotherms has led to application of experimentally derived thermal thresholds to stream temperature models for estimation of streams at high risk of exceeding thermal thresholds under current and future climate conditions. We optimised an approach that links field‐relevant thermal maxima experiments to corresponding stream temperature models and identifies opportunities to reduce stream temperatures through riparian tree growth.We conducted a thermal maxima experiment on cold‐water adapted juvenile Chinook (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) that reflected natural temperatures by using incremental temperature ramping with diel fluctuations (IT‐Dmax) and refit a regionally specific stream temperature model for British Columbia, Canada to directly relate to lab‐derived thresholds. Salmon‐bearing streams across British Columbia were categorised by threshold exceedance risk (i.e., low, moderate, high, severe) based on risk tolerance scenarios for management decision making (i.e., considering a range of prediction intervals [PIs] and stream thermal sensitivities to air temperature). We linked these results directly to riparian management and restoration actions by estimating the potential for riparian tree growth to reduce threshold exceedance risk.Lab‐derived IT‐Dmax endpoints were consistently 24°C (based on the median value between the 7‐day average of the daily maximum and the mean weekly average temperature) across acclimation treatments for both species. Under current conditions, most stream reaches (99.6% using an intermediate risk tolerance scenario) were below the thermal threshold; streams with moderate to high risk of threshold exceedance were projected to increase from 0.4% to 1.5% (total linear stream length of 6,929 km) by end of century. The risk‐averse (high sensitivity, 75% PI) and risk‐tolerant (low sensitivity, 95% PI) scenarios differed by 1,107 km of streams predicted to have a moderate to severe risk of exceeding thresholds by end of century. Maximal riparian tree growth was predicted to shift 670 km of streams from moderate to low exceedance risk under end‐of‐century conditions and intermediate risk tolerance, showing the potential for mitigation from thermal impacts.Our integrative approach tackled several key considerations in identifying streams at high temperature risk for freshwater ectotherms that to date have not been addressed. Furthermore, we showcased the delineation of spatially comprehensive estimates that identify where management mitigation and a specific restoration activity may be most needed to reduce impacts of rising temperatures on rearing salmonids across an extensive region. [ABSTRACT FROM AUTHOR]

Snorkel surveys are frequently used to monitor stream-dwelling fish. Inferring local abundance from snorkel surveys is complicated by two primary factors: variable fish detection probabilities and the relative abundance of fish in habitat types below the recommended minimum depth for snorkeling. We examine these factors across three salmonid species (Oncorhynchus spp.), 4 years, and 113 location-years in Oregon coastal streams. We calibrate snorkel counts to mark-recapture estimates and develop mathematically explicit expressions that convert a new snorkel count into a probability density of abundance for streams containing mixed habitat types that were and were not snorkeled. Snorkelers detected 63%, 47%, and 39% of juvenile coho salmon (Oncorhynchus kitsutch), steelhead trout (Oncorhynchus mykiss), and cutthroat trout (Oncorhynchus clarkii clarkia) estimated by mark-recapture, respectively, but uncertainty within and among sampling units was high. Further, analytics developed here can be used to infer abundance and uncertainty for habitat types that were not snorkeled. Our quantification of uncertainty arising from using snorkel counts as a proxy for abundance will help managers balance biological risks with available resources. [ABSTRACT FROM AUTHOR]

Background: Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. Results: We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. Conclusions: Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance. [ABSTRACT FROM AUTHOR]

Simple Summary: Phyto-based foods are becoming more and more popular worldwide, and people are consuming phyto-active components for purposes other than traditional health and nutrition. The study aimed to ascertain the impact of tea polyphenols (TPs) on fish. The outcomes showed that cold-water coho salmon exhibit improved growth, feed intake, and immunity. These results are helpful in promoting the development of novel feed additives for the aquaculture industry. To evaluate the impact of nutritional tea polyphenols (TPs) on body composition, growth, biochemical markers, antioxidant capacity, and hemato-immunological levels, a ten-week feeding experiment was carried out on coho salmon (Oncorhynchus kisutch, 180.51 ± 0.15 g). The control group was fed a basal diet; the T1, T2, T3, and T4 groups were fed 0.005%, 0.01%, 0.02%, and 0.04% TPs, respectively. These results demonstrate that adding TPs significantly (p < 0.05) increased the coho salmon fish's weight gain (WG), relative growth rate (RGR), condition factor (CF), feed efficacy (FE), daily growth rate (DGR), and specific growth rate (SGR). There was no discernible difference in the body compositions of the treated TPs and the control group (p > 0.05). In addition, the T3 group showed a significant (p < 0.05) decrease in GPT, LDL, HDL, TC, and CAT. Fish given a 0.02% diet containing TPs had significantly lower levels of malondialdehyde (MDA) in their liver; yet, the TP-treated groups had higher levels of SOD and CAT than the control (p < 0.05). The data analysis shows a significant rise in lysozyme, respiratory burst activity, bactericidal activity, and blood hematological parameters in the 0.01–0.04% TP groups. According to these findings, TPs could be a useful dietary supplement for raising the antioxidant status, growth parameters, haemato-immunological response, and whole-body composition of coho salmon fish. [ABSTRACT FROM AUTHOR]

During their development, some species of salmonids may occasionally experience skeletal deformations. Several methodologies are currently being used for the diagnosis of such malformations, among which X-rays, histological techniques, diaphanization coupled either with Alizarin Red or Alcian Blue stains, as well as Scanning Electron Microscopy (SEM) can be mentioned. Each one of those methods presents inherent advantages and disadvantages. The purpose of this study was twofold: Firstly, to evaluate and compare the effectiveness of microcomputed tomography (Micro-CT) technology for anatomical analysis, three-dimensionally reconstructing the obtained images; and secondly, to contrast those images with the results obtained through the diaphanization technique. The caudal fins of five specimens of the Oncorhynchus kisutch salmon were analyzed: Two specimens were subjected to diaphanization and three were processed for Micro-CT analysis, using the BRUKER SkyScan 1272 equipment. The Micro-CT technology demonstrated superiority in the resolution of bone structures, facilitating a detailed exploration of morphological variations, as well as the distribution of mineral density. This experimental approach allowed us to identify anomalies in the morphology and growth of the last vertebrae and dorsal lepidotrichiae, as well as an increased mineral density in the malformed dorsal lepidotrichiae. The higher resolution provided by Micro-CT not only enhances our understanding of the fish ontogeny and its adaptation to diverse environments, but also opens innovative perspectives for the study of the evolution of locomotor strategies and adaptive responses to environmental changes. [ABSTRACT FROM AUTHOR]

N‐(1,3‐dimethylbutyl)‐N′‐phenyl‐p‐phenylenediamine‐quinone (6PPD‐quinone) is a widespread contaminant of emerging concern resulting from oxidation of 6PPD, which is an antidegradant substance added to tires. The recent identification of 6PPD‐quinone as the cause of acute mortality in coho salmon has quickly motivated studies on 6PPD‐quinone toxicity to other species. Subsequent findings have shown that 6PPD‐quinone toxicity is highly species specific. Closely related species can differ widely in response to 6PPD‐quinone from extremely sensitive to tolerant. Hence toxicity testing is currently the only way to establish whether a species exhibits 6PPD‐quinone toxicity. We investigated the acute toxicity of 6PPD‐quinone in pink salmon alevins (sac fry). This species has is the only Pacific salmon that so far has not been tested for 6PPD‐quinone sensitivity. Fish were exposed in static water in eight treatments with initial concentrations ranging from 0.1 to 12.8 μg/L. Fish were observed for 48 h, and changes in concentrations of 6PPD‐quinone were monitored throughout the experiment. No mortalities or substantial changes in behavior were recorded. Environ Toxicol Chem 2024;43:1332–1338. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. [ABSTRACT FROM AUTHOR]

The relationship of histopathological changes and the infection of Piscine orthoreovirus 2 (PRV‐2) was investigated in coho salmon that were suffering from the erythrocytic inclusion body syndrome (EIBS). Immunohistochemical observations revealed abundant σ1 protein of PRV‐2 in the spongy layer of the ventricle of the heart, where severe myocarditis was observed. In the spleen, the virus protein was detected in many erythrocytes, some of which were spherical‐shaped and apparently dead. The number of erythrocytes was decreased in the spleen compared to the apparently healthy fish. The virus protein was also detected in some erythrocytes in blood vessels. The viral protein was often detected in many macrophages ingesting erythrocytes or dead cell debris in the spleen or in the kidney sinusoids. Large amounts of the viral genomic segment L2 were also detected in these organs by RT‐qPCR. Many necrotic foci were found in the liver, although the virus protein was not detected in the hepatocytes. These results suggest that the primary targets of PRV‐2 are myocardial cells and erythrocytes and that clinical symptoms such as anaemia or jaundice and histopathological changes such as myocarditis in EIBS‐affected coho salmon are caused by PRV‐2 infection. [ABSTRACT FROM AUTHOR]

Cool‐water habitats provide increasingly vital refuges for cold‐water fish living on the margins of their historical ranges; consequently, efforts to enhance or create cool‐water habitat are becoming a major focus of river restoration practices. However, the effectiveness of restoration projects for providing thermal refuge and creating diverse temperature regimes at the watershed scale remains unclear. In the Klamath River in northern California, the Karuk Tribe Fisheries Program, the Mid‐Klamath Watershed Council, and the U.S. Forest Service constructed a series of off‐channel ponds that recreate floodplain habitat and support juvenile coho salmon (Oncorhynchus kisutch) and steelhead (O. mykiss) along the Klamath River and its tributaries. We instrumented these ponds and applied multivariate autoregressive time series models of fine‐scale temperature data from ponds, tributaries, and the mainstem Klamath River to assess how off‐channel ponds contributed to thermal regime diversity and thermal refuge habitat in the Klamath riverscape. Our analysis demonstrated that ponds provide diverse thermal habitats that are significantly cooler than creek or mainstem river habitats, even during severe drought. Wavelet analysis of long‐term (10 years) temperature data indicated that thermal buffering (i.e. dampening of diel variation) increased over time but was disrupted by drought conditions in 2021. Our analysis demonstrates that in certain situations, human‐made off‐channel ponds can increase thermal diversity in modified riverscapes even during drought conditions, potentially benefiting floodplain‐dependent cold‐water species. Restoration actions that create and maintain thermal regime diversity and thermal refuges will become an essential tool to conserve biodiversity in climate‐sensitive watersheds. [ABSTRACT FROM AUTHOR]

How has parasitism changed for Alaskan salmon over the past several decades? Parasitological assessments of salmon are inconsistent across time, and though parasite data are sometimes noted when processing fillets for the market, those data are not retained for more than a few years. The landscape of parasite risk is changing for salmon, and long‐term data are needed to quantify this change. Parasitic nematodes of the family Anisakidae (anisakids) use salmonid fishes as intermediate or paratenic hosts in life cycles that terminate in marine mammal definitive hosts. Alaskan marine mammals have been protected since the 1970s, and as populations recover, the density of definitive hosts in this region has increased. To assess whether the anisakid burden has changed in salmonids over time, we used a novel data source: salmon that were caught, canned, and thermally processed for human consumption in Alaska, USA. We examined canned fillets of chum (Oncorhynchus keta, n = 42), coho (Oncorhynchus kisutch, n = 22), pink (Oncorhynchus gorbuscha, n = 62), and sockeye salmon (Oncorhynchus nerka, n = 52) processed between 1979 and 2019. We dissected each fillet and quantified the number of worms per gram of salmon tissue. Anisakid burden increased over time in chum and pink salmon, but there was no change in sockeye or coho salmon. This difference may be due to differences in the prey preferences of each species, or to differences in the parasite species detected across hosts. Canned fish serve as a window into the past, providing information that would otherwise be lost, including information on changes over time in the parasite burden of commercially, culturally, and ecologically important fish species. [ABSTRACT FROM AUTHOR]

The purpose of this experiment was to investigate the effects of Bacillus pumilus (GXUN613L) on the growth performance, serum biochemical indexes, antioxidant capacity, and intestinal health of coho salmon. A total of 240 coho salmon with initial body mass of (130.2±10.1) g were randomly divided into four groups with three replicates in each group and 20 coho salmon in each replicate. Bacillus pumilus (GXUN613L) was supplemented with 0, 2x107, 4x109, and 8x1011 CFU/g in basal diet in CK group, LL group, LM group, and LH group, respectively. The trial period was six weeks. The results showed that the weight gain rate and specific growth rate of coho salmon in LL group and LM group were significantly higher than those in CK group (P<0.05), the protein efficiency ratio of coho salmon in LM group was significantly higher than that in CK group (P<0.05), and the feed conversion ratio was significantly lower than that in CK group (P<0.05). Serum total protein, albumin and total cholesterol in LL group, LM group, and LH group were significantly higher than those in CK group (P<0.05). Serum glucose content and alkaline phosphatase activity in LM group were significantly higher than those in CK group (P<0.05). The total antioxidant capacity, catalase activity, superoxide dismutase, and glutathione peroxidase activity of liver in LM group were significantly higher than those in CK group (P<0.05). The muscular layer thickness and villus height of foregut and hindgut in LM group were significantly higher than those in CK group (P<0.05), and the intestinal microbial diversity was better. The result shows that the addition of Bacillus pumilus (GXUN613 L) in feed can promote the growth, improve the serum indexes and intestinal health, and enhance the antioxidant capacity of coho salmon. The suitable addition amount of GXUN613L is 4x109 CFU/g. [ABSTRACT FROM AUTHOR]

How has parasitism changed for Alaskan salmon over the past several decades? Parasitological assessments of salmon are inconsistent across time, and though parasite data are sometimes noted when processing fillets for the market, those data are not retained for more than a few years. The landscape of parasite risk is changing for salmon, and long‐term data are needed to quantify this change. Parasitic nematodes of the family Anisakidae (anisakids) use salmonid fishes as intermediate or paratenic hosts in life cycles that terminate in marine mammal definitive hosts. Alaskan marine mammals have been protected since the 1970s, and as populations recover, the density of definitive hosts in this region has increased. To assess whether the anisakid burden has changed in salmonids over time, we used a novel data source: salmon that were caught, canned, and thermally processed for human consumption in Alaska, USA. We examined canned fillets of chum (Oncorhynchus keta, n = 42), coho (Oncorhynchus kisutch, n = 22), pink (Oncorhynchus gorbuscha, n = 62), and sockeye salmon (Oncorhynchus nerka, n = 52) processed between 1979 and 2019. We dissected each fillet and quantified the number of worms per gram of salmon tissue. Anisakid burden increased over time in chum and pink salmon, but there was no change in sockeye or coho salmon. This difference may be due to differences in the prey preferences of each species, or to differences in the parasite species detected across hosts. Canned fish serve as a window into the past, providing information that would otherwise be lost, including information on changes over time in the parasite burden of commercially, culturally, and ecologically important fish species. [ABSTRACT FROM AUTHOR]

Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate. [ABSTRACT FROM AUTHOR]

Along the northeast Pacific coast, the salmon-eating southern resident killer whale population (SRKW, Orcinus orca) have been at very low levels since the 1970s. Previous research have suggested that reduction in food availability, especially of Chinook salmon (Oncorhynchus tshawytscha), could be the main limiting factor for the SRKW population. Using the ecosystem modelling platform Ecopath with Ecosim (EwE), this study evaluated if the decline of the Pacific salmon populations between 1979 and 2020 may have been impacted by a combination of factors, including marine mammal predation, fishing activities, and climatic patterns. We found that the total mortality of most Chinook salmon populations has been relatively stable for all mature returning fish despite strong reduction in fishing mortality since the 1990s. This mortality pattern was mainly driven by pinnipeds, with increases in predation between 1979 and 2020 mortality ranging by factors of 1.8 to 8.5 across the different Chinook salmon population groups. The predation mortality on fall-run Chinook salmon smolts originating from the Salish Sea increased 4.6 times from 1979 to 2020, whereas the predation mortality on coho salmon (Oncorhynchus kisutch) smolts increased by a factor of 7.3. The model also revealed that the north Pacific gyre oscillation (NPGO) was the most important large-scale climatic index affecting the stock productivity of Chinook salmon populations from California to northern British Columbia. Overall, the model provided evidence that multiple factors may have affected Chinook salmon populations between 1979 and 2020, and suggested that predation mortality by marine mammals could be an important driver of salmon population declines during that time. [ABSTRACT FROM AUTHOR]

Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage‐based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species‐specific Genotyping‐in‐Thousands by sequencing (GT‐seq) panels. For laboratories involved in large‐scale genotyping efforts, diagnosing non‐target species and reassigning them to the appropriate monitoring program can be costly and time‐consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross‐species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species‐specific GT‐seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species‐informative amplicons (16) were newly identified from the four existing GT‐seq panels, thus demonstrating a low‐cost approach to species identification when using targeted sequencing methods. A species‐calling script was developed that is tailored for routine GT‐seq genotyping pipelines and automates the identification of non‐target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low‐frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost‐effective approach to species identification for genetic monitoring programs. [ABSTRACT FROM AUTHOR]

The value of estuaries as nursery habitat for juvenile anadromous salmon is likely variable across estuaries and species. Here, we compiled published empirical data on juvenile salmon estuarine growth and residency. We aimed to quantify the range and variability of these aspects for five species of Pacific salmon across estuaries, methodologies, and life histories. The majority of studies focused on Chinook and coho salmon, largely from their southern range. While there is some evidence of higher growth in wild-origin fish relative to hatchery-origin fish, the wide range of metrics employed made identification of trends among life histories challenging, and unification of reporting could strengthen future research. Different salmon life histories exhibited different residencies, with natural-origin subyearling coho exhibiting the longest mean residency (∼3 months) and 1+ sockeye salmon exhibiting the shortest (3.7 days). Across life histories, hatchery fish exhibited much shorter estuary residencies than wild fish. Collectively, our review highlights key patterns in salmon estuary ecology, identifies knowledge gaps, and lays the foundation for future studies to quantify the importance of estuaries for specific salmon. [ABSTRACT FROM AUTHOR]

By the 1980s, after decades of declining numbers in the mid‐1900s, Coho salmon (Oncorhynchus kisutch) were considered extirpated from the interior Columbia River. In the mid‐1990s, the Confederated Tribes of the Umatilla Indian Reservation, the Confederated Tribes and Bands of the Yakama Nation, and the Nez Perce Tribe began successful reintroduction programs of Coho salmon upstream of Bonneville Dam, but which were initially sourced from lower Columbia River hatcheries. Here we present the first Coho salmon parentage‐based tagging (PBT) baseline from seven hatchery programs located in the interior Columbia River basin, and two sites at or downstream of Bonneville Dam, composed of over 32,000 broodstock samples. Analyses of baseline collections revealed that genetic structure followed a temporal pattern based on 3‐year broodlines rather than geographic location or stocking history. Across hatchery programs, similar levels of genetic diversity was present. The PBT baseline provided multiple direct applications such as identification of origin for Coho salmon collected in a mixed stock at Priest Rapids Dam and the detection of the proportion and distribution of hatchery‐origin fish on the spawning grounds in the Methow River basin. The PBT baseline for Coho salmon is freely available for use and can be downloaded from FishGen.net. [ABSTRACT FROM AUTHOR]

Climatic warming elevates mortality for many salmonid populations during their physically challenging up-river spawning migrations, yet, the mechanisms underlying the increased mortality remain elusive. One hypothesis posits that a cardiac oxygen insufficiency impairs the heart's capacity to pump sufficient oxygen to body tissues to sustain up-river swimming, especially in warm water when oxygen availability declines and cardiac and whole-animal oxygen demand increases. We tested this hypothesis by measuring cardiac and metabolic (cardiorespiratory) performance, and assessing the upper thermal tolerance of coho salmon (Oncorhynchus kisutch) during sustained swimming and acute warming. By surgically ligating the coronary artery, which naturally accumulates arteriosclerotic lesions in migrating salmon, we partially impaired oxygen supply to the heart. Coronary ligation caused drastic cardiac impairment during swimming, even at benign temperatures, and substantially constrained cardiorespiratory performance during swimming and progressive warming compared to sham-operated control fish. Furthermore, upper thermal tolerance during swimming was markedly reduced (by 4.4 °C) following ligation. While the cardiorespiratory capacity of female salmon was generally lower at higher temperatures compared to males, upper thermal tolerance during swimming was similar between sexes within treatment groups. Cardiac oxygen supply is a crucial determinant for the migratory capacity of salmon facing climatic environmental warming. [ABSTRACT FROM AUTHOR]

An analysis of the biological value of chum salmon showed that, in terms of the balance of the amino-acid composition of the protein, chum salmon with spawning changes is not inferior to chum salmon without spawning changes (silver chum salmon). A higher content of polyunsaturated fatty acids in total lipids, including omega-3, was noted in chum salmon with spawning changes compared to silver chum salmon. The metabolic profile of chum salmon samples obtained by NMR spectroscopy showed that the levels of Asp, Glu, and glucose markedly increase during spawning migration, which is explained by the limited feeding of fish. The calculated total taste index of silver chum salmon was 4.06 ± 0.11, and that of chum salmon with spawning changes was 3.46 ± 0.09. Therefore, according to taste sensations, the silver chum salmon has a richer taste compared to the chum salmon with spawning changes. The results of the analysis of the nutritional value and metabolic profile of chum salmon with spawning changes can be used in the manufacture of minced fish for the subsequent production of specialized food products by introducing functional additives that balance the consistency and color, as well as in production of functional food additives. [ABSTRACT FROM AUTHOR]

Simple Summary: With the increasing demand for aquaculture, the resource of high-quality traditional protein (such as fishmeal) becomes limited, and plant ingredients are often used as substitutes for fishmeal because of their low price and wide availability. However, plant proteins are usually deficient in certain essential amino acids (EAAs), which adversely affects the growth performance of aquatic animals. Lysine is generally the first limiting amino acid in plant protein ingredients used to formulate the aquafeed, and it plays an important role in physiological processes including antioxidant, differentiation, growth, immunity, and reduction of nitrogen emission. In this study, the effects of dietary graded L-lysine concentrations on the growth, proximate composition, and AA (amino acid) profile of coho salmon alevins were evaluated by a feeding trial. The results showed that an adequate dietary lysine level significantly improved the specific growth rate (SGR), protein efficiency ratio (PER), body protein deposition (BPD), and feed conversion ratio (FCR). The dietary optimum L-lysine requirements for coho salmon alevins were 3.74%, 3.73%, 3.91%, and 3.77% of the diet or 6.80%, 6.78%, 7.11%, and 6.85% of dietary proteins against the SGR, PER, BPD, and FCR, respectively. The suitable dietary L-lysine concentration for coho salmon (Oncorhynchus kisutch) alevins was assessed by a dose response feeding trial. Six experimental diets were made with graded L-lysine concentrations of 2.29%, 2.81%, 3.32%, 3.80%, 4.27%, and 4.78% of the dry matter, respectively, each of which was fed to triplicate groups of 100 alevins (initial body weight: 0.30 ± 0.01 g) in 18 plastic baskets (water volume 240 L). The alevins were cultured in a flowing freshwater system and fed manually to apparent satiation four times a day for 12 weeks. The survival rate of alevins did not differ significantly among the dietary groups. The specific growth rate (SGR), protein efficiency ratio (PER), and body protein deposition (BPD) increased significantly (p < 0.05) with the increase in dietary lysine concentration up to 3.80% and then reduced as lysine level further increased. The feed conversion ratio (FCR) had an inverse trend to SGR. The whole-body crude protein content of the alevins increased significantly with increasing dietary lysine level, while crude lipid content showed the opposite trend. In comparison, the contents of morphological indices, whole-body moisture, and ash were not affected significantly (p > 0.05) by the different dietary lysine concentrations. The highest contents of lysine, arginine, and total essential amino acids (EAAs) were observed in the group with 4.27% dietary lysine concentration, which did not differ significantly from those in the 3.32%, 3.80%, and 4.78% groups but was significantly higher than those in the 2.29% and 2.81% groups. Similarly, valine had the highest content in the group with 4.78%. The variations in dietary lysine had no significant impacts on other EAA and non-EAA contents except glycine, which increased with increasing dietary lysine level. Second-order polynomial model analyses based on SGR, PER, BPD, and FCR evaluated the optimum L-lysine requirements of coho salmon alevins as 3.74%, 3.73%, 3.91%, and 3.77% of the diet or 6.80%, 6.78%, 7.11%, and 6.85% of dietary proteins, respectively. [ABSTRACT FROM AUTHOR]

Pulsed subsidy events create ephemeral fluxes of hyper‐abundant resources that can shape annual patterns of consumption and growth for recipient consumers. However, environmental conditions strongly affect local resource availability for much of the year, and can heavily impact consumer foraging and growth patterns prior to pulsed subsidy events. Thus, a consumer's capacity to exploit pulse subsidy resources may be influenced by antecedent environmental conditions, but this has rarely been shown in nature and is unknown in aquatic ecosystems.Here, we sought to understand the importance of hydrologic variation and a salmon pulse subsidy on the foraging and growth patterns of two stream salmonids in a coastal southeast Alaska drainage.To do this, we sampled fish stomach contents at a high temporal frequency (daily–weekly measurements) and analyzed fish consumption rates in relation to streamflow and pulse subsidy resource availability. We then explored the influence of interannual hydrologic variation on access to pulse subsidy resources (i.e. whether fish exceeded an egg consumption gape limit) in a bioenergetic simulation.Prior to Pink Salmon spawning, Dolly Varden and Coho Salmon displayed distinct and nonlinear flow‐foraging relationships, where forage for both species consisted primarily of macroinvertebrates. During this time period, consumption maxima coincided with baseflow and the highest observed flow conditions, and consumption minima were observed at severe low‐water and intermediate flow values. After salmon spawning began, forage was not significantly related to flow and consisted primarily of salmon eggs. Further, consumption rates increased overall, and foraging patterns did not appear to be affected by flow in either species. Bioenergetic simulations revealed that patterns of interannual hydrologic variation may shift Coho Salmon growth trajectories among years.Together, our results suggest that access to marine pulse subsidy resources may depend on whether antecedent hydrologic conditions are suitable for juvenile salmonids to grow large enough to consume salmon eggs by the onset of spawning. [ABSTRACT FROM AUTHOR]

Simple Summary: Our results indicate activation of the kynurenine pathway and serotonin activity when stimulated with tryptophan and cortisol supplementation. An amount of 95% of tryptophan is degraded by the kynurenine pathway, indicating the relevance of knowing how this pathway is activated and if stress levels associated with fish culture trigger its activation. Additionally, it is essential to know the consequence of increasing KYNA levels in different species in the short and long term, and even during the fish ontogeny. Aquaculture fish are kept for long periods in sea cages or tanks. Consequently, accumulated stress causes the fish to present serious problems with critical economic losses. Fish food has been supplemented to reduce this stress, using many components as amino acids such as tryptophan. This study aims to determine the transcriptional effect of tryptophan and cortisol on primary cell cultures of salmon head and posterior kidney. Our results indicate activation of the kynurenine pathway and serotonin activity when stimulated with tryptophan and cortisol. An amount of 95% of tryptophan is degraded by the kynurenine pathway, indicating the relevance of knowing how this pathway is activated and if stress levels associated with fish culture trigger its activation. Additionally, it is essential to know the consequence of increasing kynurenic acid "KYNA" levels in the short and long term, and even during the fish ontogeny. [ABSTRACT FROM AUTHOR]

How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations,is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics. Author summary: Understanding how historical processes, such as past glaciations, may have impacted variations in population size and genetic diversity along the genome is a fundamental question in evolution. In this study, we investigated how recent postglacial demographic expansion has affected the distribution of deleterious genetic variants and the resulting deleterious mutation load in Coho salmon (Oncorhynchus kisutch), throughout its native range in North America. By sequencing the entire genome of 71 Coho salmon, we reveal that postglacial expansion has led to allele surfing, a process where alleles increase in frequency in populations that are expanding or colonizing new environments. Here, allele surfing resulted in an increased deleterious mutation load at the colonization front. Furthermore, we demonstrated that the efficacy of natural selection scales with variation in effective population size among populations. We showed that the specific genomic features of Coho salmon, namely variation in local recombination rate and variation in chromosomal inheritance, strongly impacted the segregation of deleterious mutations. [ABSTRACT FROM AUTHOR]

This experiment aims to investigate the effects of partial replacement of fish meal (FM) by soybean meal (SBM) and/or fermented soybean meal (FSBM) on the growth, serum biochemistry, digestion, antioxidation, immunity, and mTOR signaling pathway of juvenile coho salmon (Oncorhynchus kisutch). Four iso-nitrogen and iso-lipid diets were designed and fed to four groups of juvenile coho salmon (152.25 ± 2.96 g) in triplicate for 10 weeks. The four diets were the G0 diet (control group, containing 28% FM protein), the G1 diet (containing 10% SBM protein and 18% FM protein), the G2 diet (containing 5% SBM protein, 5% FSBM protein, and 18% FM protein), and the G3 diet (containing 10% FSBM protein and 18% FM protein). It was found that compared with the G0 diet (control group), the activities of catalase (CAT), superoxide dismutase (SOD), pepsin, trypsin, α-amylase, and lipase, and the expression levels of mammalian target of rapamycin (mtor), protein kinase B (akt), phosphatidylinositol 3-kinase (pi3k), plant ribosome S6K protein kinase (s6ks), and lysozyme (lyz) genes, of juvenile coho salmon fed the G3 diet increased significantly (p < 0.05), and the expression levels of tumor necrosis factor (tnf-α), interleukin-1β (il-1β), and interleukin-6 (il-6) genes of juvenile coho salmon fed the G3 diet decreased significantly (p < 0.05). However, there were no significant differences in growth, muscle composition, and serum biochemistry of juvenile coho salmon fed the G3 diet compared with the G0 diet (p > 0.05). In conclusion, replacing 10% FM protein with FSBM protein could improve the digestion, antioxidation, immunity, and mTOR signaling pathway of juvenile coho salmon. [ABSTRACT FROM AUTHOR]

Simple Summary: As an excellent but most expensive source of protein, fish meal (FM) is commonly used in 30–60% of the aquafeed for salmon fish species including coho salmon. However, the high cost and unstable supply of FM led it no longer to be considered as a sustainable protein source for aquafeeds. Accordingly, alternative protein sources with low cost and high availability have become a research hotspot in aquafeed for carnivorous species. Poultry by-product meal (PBPM), one of the rendered animal protein sources, can be used as protein substitute of FM in aquafeed due to its economical availability and high protein content and growth promotion effects in comparison to plant proteins. Until now, little information has been available on evaluating the effects of replacing FM by animal proteins including PBPM for coho salmon. In this study, the effects of PBPM instead of FM on growth, muscle composition, and tissue biochemical indexes of coho salmon were investigated. The results showed that the growth performance, feed utilization, muscle composition, serum biochemical indices, and liver antioxidant enzyme activities of coho salmon were negatively affected by high dietary inclusion level of PBPMs, and the optimum substitution level was evaluated based on the specific growth rate (SGR). The present study evaluated the effects of partially substituting fish meal (FM) with poultry by-product meal (PBPM) on the growth, muscle composition, and tissue biochemical parameters of coho salmon (Oncorhynchus kisutch) post-smolts. Five isonitrogenous (7.45% nitrogen) and isoenergetic (18.61 MJ/kg gross energy) experimental diets were made by substituting 0%, 10%, 20%, 40%, and 60% FM protein with PBPM protein, which were designated accordingly as PBPM0 (the control), PBPM10, PBPM20, PBPM40, and PBPM60, respectively. Each diet was fed to triplicates of ten post-smolts (initial individual body weight, 180.13 ± 1.32 g) in three floating cages three times daily (6:50, 11:50, and 16:50) to apparent satiation for 84 days. Both specific growth rate (SGR) and protein efficiency ratio did not differ significantly (p > 0.05) among the control, PBPM10, and PBPM20 groups, which were remarkably (p < 0.05) higher than those of the PBPM40 and PBPM60 groups. Feed conversion ratio varied inversely with SGR. The PBPM replacement had no remarkable effects on the morphological indices and proximal muscle components. The control and PBPM10 groups led to significantly higher muscle contents of leucine, lysine, and methionine than groups of higher PBPM inclusion. The groups of PBPM40 and PBPM60 obtained significantly (p < 0.05) higher serum alanine aminotransferase and aspartate aminotransferase activities than the control and low PBPM inclusion groups. The control group had significantly higher albumin and total cholesterol contents than the groups with PBPM inclusion. The control group had significantly higher triglycerides content than the PBPM60 group. The PBPM60 group had significantly lower contents of high-density lipoprotein, low-density lipoprotein, and total protein than the control and PBPM10 groups. The high PBPM replacement level up to 40% and 60% had adverse effects on hepatic malondialdehyde levels. The catalase and superoxide dismutase activities were not affected by low PBPM inclusion, but significantly decreased in high-PBPM-inclusion groups. Based on broken-line regression analysis of SGR and PER, the optimum dietary PBPM replacing level was evaluated to be 16.63–17.50% of FM protein for coho salmon post-smolts. [ABSTRACT FROM AUTHOR]

Aim: Freshwater invasions are a global conservation issue. Emerging tools for biogeographical analyses can provide critical information for their effective management and monitoring. Here, we propose a method to assess the distribution of environmental resistance of stream ecosystems to biological invasions by coupling multi‐stage habitat potential models for non‐native species. Location: Andean Patagonia (Chile and Argentina). Taxa: North American beaver (Castor canadensis), Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch). Methods: Environmental resistance to invasive species was mapped throughout a large region of Patagonia by stacking multi‐stage habitat relationships for each target species and assessing the complementation between critical habitats at multiple scales. We generated an environmental model of stream networks derived from high‐resolution topographic and climatic data representing 15,406 drainage basins (>1 km2) covering an area of 369,791 km2. We quantified the intrinsic potential of stream‐reaches (100‐m and 1000‐m) to sustain high‐quality habitats and assessed habitat complementation (i.e., abundance and proximity) at the sub‐basin scale as a proxy for environmental resistance. Results: Our model revealed high heterogeneity in the distribution of environmental resistance to invasions throughout the study region, providing case‐specific insights for the research and management of invaders. Main Conclusions: Environmental resistance modelling is a novel method to study the biogeography of riverine invasions. Our approach is compatible with additional sources of information about species and the environment and shows versatility to diverse invasion scenarios and data sources. This method can be useful in prioritising research and management of incipient and spreading invasions, especially for large and data‐poor regions. [ABSTRACT FROM AUTHOR]

Alternative life‐history tactics are predicted to affect within‐population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (Ne) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males ("jacks") to Ne in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single‐nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (Nb). Jack contribution to Nb was assessed by comparing values of Nb calculated with and without jacks and their offspring. Over a range of Nb values (108–406), the average jack contribution to Nb from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence Nb/N. The linkage disequilibrium Ne estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence Nb and Ne and can make a substantial contribution to population dynamics and conservation of threatened stocks. [ABSTRACT FROM AUTHOR]

In this study, we evaluated the effects of fermented soybean meal (FSBM) or/and unfermented SBM replacing a portion of fish meal (FM) on the growth performance, antioxidant capacity, immunity, and mechanistic target of rapamycin (mTOR) signaling pathway of juvenile coho salmon (Oncorhynchus kisutch). Four groups of juvenile coho salmon (initial weight 152.23 ± 3.21 g) in triplicate were fed for 12 weeks on four different iso-nitrogen and iso-lipid experimental diets: G0 diet (28% FM protein, control group), G1 diet (18% FM protein and 10% SBM protein), G2 diet (18% FM protein, 5% SBM protein, and 5% FSBM protein), and G3 diet (18% FM protein and 10% FSBM protein). The main results were compared with the G0 diet; the weight gain rate, specific growth rate, and condition factor of juveniles in G3 were increased significantly (p < 0.05). The content of muscle crude protein, the total protein, glucose, albumin, total cholesterol in serum, and the total antioxidant capacity in the liver of juveniles in G3 was increased significantly (p < 0.05). The activities of pepsin, trypsin, α-amylase, and lipase in the intestine, the superoxide dismutase, catalase, and alkaline phosphatase in the liver of juveniles in G3 were increased significantly (p < 0.05). The expression levels of phosphatidylinositide 3-kinases, serine/threonine kinase, mTOR, and ribosomal protein S6 kinase 1 genes in the liver of juveniles in G3 were upregulated significantly (p < 0.05). The feed coefficient ratio, viscerosomatic index, the contents of muscle moisture, and malondialdehyde in the liver of juveniles in G3 were decreased significantly (p < 0.05). The expression levels of tumor necrosis factor α, interleukin 1β, and interleukin 6 genes in the liver of juveniles in G3 were downregulated significantly (p < 0.05). However, there was no significant effect (p > 0.05) on the survival rate, food intake, and muscle crude lipid and ash of juveniles among the experimental groups. In conclusion, FSBM to replace a portion FM had a positive effect on the growth performance, protein deposition, antioxidant enzyme activity, digestive enzyme activity, protein synthesis, and immune-related genes of juvenile coho salmon. [ABSTRACT FROM AUTHOR]

Simple Summary: Protecting the welfare of animals and the 3Rs rule are very relevance, and for this reason cell culture is an important tool. In fish it has importance in several fields such as virology, toxicology, pathology and immunology. The objective was to carry out a primary culture of the head kidneys of Atlantic salmon (Salmo salar), Pacific salmon (Oncorhynchus kisutch) and rainbow trout (Oncorhynchus mykiss), and to characterize how they respond to bacterial and viral stimuli by analyzing molecules that participate in the innate and adaptive immune response. The primary cell cultures of the head kidney (HK) from the three salmonids studied were cultured and exposed to two substances that mimic molecular patterns of different pathogens, i.e., Lipopolysaccharide (LPS) and Polyinosinic: polycytidylic acid (POLY I:C). The HK primary cell cultures from the three species grown in vitro responded differently to POLY I:C and LPS. This is the first study to demonstrate and characterize the expression of immune genes in head kidney primary cell cultures isolated from three salmonid species. It also indicates their potential role in developing immune responses as defense response agents and targets of immunoregulatory factors. Fish cell culture is a common in vitro tool for studies in different fields such as virology, toxicology, pathology and immunology of fish. Fish cell cultures are a promising help to study how to diagnose and control relevant viral and intracellular bacterial infections in aquaculture. They can also be used for developing vaccines and immunostimulants, especially with the ethical demand aiming to reduce and replace the number of fish used in research. This study aimed to isolate head kidney primary cell cultures from three Chilean salmonids: Salmo salar, Oncorhynchus kisutch, and Oncorhynchus mykiss, and characterize the response to bacterial and viral stimuli by evaluating various markers of the innate and adaptive immune response. Specifically, the primary cell cultures of the head kidney from the three salmonids studied were cultured and exposed to two substances that mimic molecular patterns of different pathogens, i.e., Lipopolysaccharide (LPS) (bacterial) and Polyinosinic: polycytidylic acid (POLY I:C). Subsequently, we determined the mRNA expression profiles of the TLR-1, TLR-8, IgM, TLR-5, and MHC II genes. Head kidney primary cell cultures from the three species grown in vitro responded differently to POLY I:C and LPS. This is the first study to demonstrate and characterize the expression of immune genes in head kidney primary cell culture isolated from three salmonid species. It also indicates their potential role in developing immune responses as defense response agents and targets of immunoregulatory factors. [ABSTRACT FROM AUTHOR]

Escaped salmonids are considered among the most serious threats to the aquatic environment. One hundred and nine escape incidents were reported in Chile from 2004-2021, representing some 8.53 million escaped salmonids. Of this total, 5.73 million were Atlantic salmon Salmo salar (67.2%), 0.83 million coho salmon Oncorhynchus kisutch (9.8%), and 1.96 million were rainbow trout O. mykiss (23.0%). It is estimated that 70.1% of the escaped salmonids were recorded in the Los Lagos Region, 23% in the Aysén Region, and 4.6% in the Magallanes Region. In total, 80.5% of the escapes were recorded from seawater facilities, while freshwater units accounted for 19.5%. The highest percentage of escaped salmon recorded in seawater over 2004-2021 was 1.71% of harvested salmonids in 2013. Some 39.5% of the escapes in 2015-2021 were attributed to rupturing of net cages, mainly due to adverse climatic conditions. The additional regulations introduced in 2020 by the Chilean authority, has helped to minimize the escape of farmed salmonids. As a consequence, just one escape event was reported in 2021, corresponding to 3.85% of the total number of escapees recorded from 2004-2021. [ABSTRACT FROM AUTHOR]

This document provides a summary of three articles published in the North American Journal of Fisheries Management and the North American Journal of Aquaculture. The first article examines the factors that affect the capture of juvenile salmon in minnow traps, finding that galvanized traps are more effective than nylon coated traps. The second article investigates the population response of Brook Trout to the removal of nonnative Brown Trout in a Wisconsin stream, concluding that Brown Trout suppress Brook Trout populations and that electrofishing can be an effective removal method. The third article focuses on the economic impact of off-flavor in the U.S. catfish industry, revealing that off-flavor incidents result in significant costs for catfish farms. [Extracted from the article]

There is tremendous variation in life-history strategies among anadromous salmonids. Species that enter the ocean environment at small sizes (< 20 g) are likely under more physiological pressure from pathogens; however, little data is available on responses at these early stages. With this in mind, we performed salmon louse challenges with Coho salmon either immediately after seawater entry (SW; ca. 10 g) or after 30 days in SW (ca. 20 g). Irrespective of size or time in SW, parasites were rapidly rejected by the host, with > 90% of all parasites lost by 16 days post-infection (dpi). Rejection was concomitant with host epithelial granulomatous infiltrations that initially targeted the embedded frontal filament (4 dpi) and the entire parasite by 10 dpi. Illumina sequencing, followed by functional enrichment analysis, revealed a concerted defense response in the fin within 1 dpi that included multiple innate and adaptive immunity components. Strikingly, early indications of an allergic-type inflammatory response were associated with chitin sensing pathways orchestrated by early overexpression of the IgE-receptor, fcer1g. Additionally, there was profound overexpression of several classes of c-type lectin receptors, including dectin-2, mincle, and dc-sign at 1 dpi onward. These profiles and upregulation of cellular effector markers were corroborated by histopathological evaluation, revealing the simultaneous presence of mast cell/eosinophilic granular cells, sacciform cells, macrophages/histiocytes, and granulocytes in fin. At 10 dpi and concurrent with parasite expulsion, there was evidence of immunoregulation in addition to tissue remodelling pathways. At 16 dpi, the response was effectively abrogated. Simultaneous profiling of the parasite transcriptome revealed early induction of chitin metabolism and immunomodulation, toxin production and ECM degradation; however, after 7 dpi, these were replaced with overexpression of stress and immune defense genes. These data present the first evidence for Coho salmon demonstrating chitin- and sugar moiety-sensing as key drivers of salmon louse rejection. [ABSTRACT FROM AUTHOR]

Piscine orthoreovirus from western North America is transmissible to Atlantic salmon and Sockeye salmon but fails to cause Heart and Skeletal Muscle Inflammation. De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection. Keywords: Piscine orthoreovirus; Salmon; Respiratory performance EN Piscine orthoreovirus Salmon Respiratory performance 1 4 4 05/23/23 20230519 NES 230519 This is a reply to a correspondence from Mordecai G et al. (https://doi.org/10.1186/s12915-023-01548-8) on our research article "Innate antiviral defense demonstrates high energetic efficiency in a bony fish. [Extracted from the article]

Background: Infection with the myxozoan parasite Parvicapsula pseudobranchicola causes disease in wild and farmed salmonids in Norway. In the northeast Pacific Ocean, the parasite has been reported in Pacific salmon Oncorhynchus spp. without evidence of disease. The objectives of the present study were to confirm the identity of P. pseudobranchicola in the Pacific, document its host and geographic ranges, and describe associated pathological changes. Methods: Ocean-entry year wild pink salmon Oncorhynchus gorbuscha, chum salmon O. keta, Chinook salmon O. tshawytscha, coho salmon O. kisutch and sockeye salmon O. nerka were collected in summer and autumn surveys near Vancouver Island (VI) and from a winter survey in the Gulf of Alaska. Samples were also obtained from farmed Atlantic salmon Salmo salar and Chinook salmon near VI. Samples were analysed by qPCR and histology using conventional staining or in situ hybridisation. Parasite sequence was obtained from small subunit ribosomal RNA gene (SSU rDNA). Results: Identical 1525 base-pair SSU rDNA sequences from infected pink salmon, chum salmon and Chinook salmon shared 99.93% identity with a P. pseudobranchicola sequence from Norwegian Atlantic salmon. In autumn surveys, the prevalence was greatest in chum salmon (91.8%) and pink salmon (85.9%) and less so in Chinook salmon (68.8%) and sockeye salmon (8.3%). In farmed salmon, the prevalence was zero in Atlantic salmon (n = 967) and 41% in Chinook salmon (n = 118). Infections were preferentially sited in pseudobranch and visualised by in situ hybridisation. Heavy parasite burdens in all species of Pacific salmon were inconsistently associated with focal granulomatous pseudobranchitis. Conclusions: In the northeast Pacific, widespread occurrence of P. pseudobranchicola in Pacific salmon together with its absence or sporadic occurrence in farmed Atlantic salmon differs from its epidemiology in Norway, despite similar pathological development in the pseudobranch. Consequences of the infections to the health of wild Pacific salmon, identity of the invertebrate host and the distribution and abundance of infective actinospores are unknown and remain high priorities for research. [ABSTRACT FROM AUTHOR]

Piscine orthoreovirus genotype 1 (PRV-1) is an endemic virus to the Northeastern Pacific that infects both wild and farmed salmon. To better understand PRV-1 prevalence and transmission pathways in the region, we targeted out-migrating juvenile Pacific Salmon in the Strait of Georgia and Johnstone Strait in British Columbia, Canada, for PRV-1 molecular screening with an emphasis on Chinook (Oncorhynchus tshawytscha) and Coho (Oncorhynchus kisutch) salmon. A total of 4031 individuals were screened for PRV-1 and we identified an overall virus prevalence of 3.5% from 2011 to 2020. PRV-1 was absent in enhancement facilities and freshwater catchments and predominately found in the marine environment. The detection of PRV-1 varied greatly between species, year and stock of origin, but cumulatively identified that life history and migratory behaviors likely influenced viral prevalence. Specifically, Chinook salmon, which demonstrate long residence time in the Strait of Georgia relative to other species, had the highest PRV-1 prevalence in this study (7.4%). Varying stock composition and regional detection between year classes within the Strait of Georgia further indicated that the sources for Chinook infection were highly variable between years. These findings enhance our understanding for PRV-1 transmission in the region and more generally between/within salmon species. [ABSTRACT FROM AUTHOR]

Aim Stormwater is a major source of many contaminants of emerging concern, which can be toxic to both aquatic and terrestrial organisms. This project aimed to identify novel biodegraders of toxic tire wear particle (TWP) contaminants associated with coho salmon mortality. Methods and results This study has (i) characterized the prokaryotic communities of stormwater in both urban and rural settings; (ii) evaluated the ability of stormwater isolates to degrade two model TWP contaminants, hexa(methoxymethyl)melamine and 1,3-diphenylguanidine; and (iii) evaluated the toxicological impact of these model contaminants on the growth of six model bacteria. Rural stormwater possessed a diverse microbiome dominated by Oxalobacteraceae, Microbacteriaceae, Cellulomonadaceae, and Pseudomonadaceae taxa, while urban stormwater showed much less microbial diversity overall. Additionally, multiple stormwater isolates appeared capable of using model TWP contaminants as their sole carbon source. Each model contaminant was also found to alter growth patterns of model environmental bacteria including, with 1,3-DPG appearing more acutely toxic at high concentrations. Conclusion This study identified several stormwater isolates that have the potential to be used as a sustainable solution to stormwater quality management. [ABSTRACT FROM AUTHOR]

Anadromous fishes, such as Pacific salmon, spend portions of their life cycle in freshwater and marine systems, thus rendering them susceptible to a variety of natural and anthropogenic stressors. These stressors operate at different spatiotemporal scales, whereby freshwater conditions are more likely to impact single populations or subpopulations, while marine conditions are more likely to act on entire evolutionarily significant units (ESUs). Coherence in population parameters like survival and productivity can therefore serve as an indicator of relative influence. The goal of this study was to elucidate scale‐dependent shifts in Oregon Coast coho salmon productivity. We used a multivariate state‐space approach to analyze almost 60 years of stock‐recruitment data for the Oregon Coast ESU. Analyses were conducted separately for time periods prior to and after 1990 to account for improvements in abundance estimation methods and significant changes in conservation and management strategies. Prior to 1990, productivity declined for most Oregon Coast populations, especially through the 1980s. From 1990–onward, coherence increased, and trends tracked closely with the North Pacific Gyre Oscillation (NPGO). The latter period is associated with reductions in harvest rates and hatchery production such that the relative influence of the marine environment may have grown more apparent following the removal of these stressors. Furthermore, the link between productivity and NPGO is consistent with trends observed for several other Pacific salmon ESUs. If Oregon Coast coho salmon populations become more synchronous, managers can expect to face new challenges driven by reductions in the population portfolio effect and increasingly variable marine conditions due to climate change. [ABSTRACT FROM AUTHOR]

In this study, we have isolated four strains of Vibrio anguillarum, revealing that they share the same serotype of O1, biochemical characteristics and virulence factor genes. However, there were differences in haemolytic activity among the bacterial strains; a strain with lower pathogenicity showed γ‐haemolytic activity, whereas other virulent strains showed α‐haemolytic activity on blood agar and higher empA gene expression in RTG‐2 cell line. The most virulent strain was V. anguillarum RTBHR from diseased masu salmon (Oncorhynchus masou), which resulted in mortality of 100% and 93.3% when injected intraperitoneally at concentrations of 9 × 105 and 6.3 × 105 colony‐forming units/fish in rainbow trout (Oncorhynchus mykiss) and Coho salmon (Oncorhynchus kisutch), respectively. A formalin‐inactivated vaccine of V. anguillarum RTBHR induced a protective and specific immunity in rainbow trout as the vaccinated fish exhibited low cumulative mortality in a challenge test and a high specific antibody response in enzyme‐linked immunosorbent assay at 8 weeks post‐vaccination. The produced antibody was bound to bacterial proteins of 30–37 kDa in size. This adaptive immune response was detected as early as day 1, with quantitative polymerase chain reaction analysis revealing the upregulated expression of genes encoding for TCRα, T‐bet, mIgM and sIgM in rainbow trout. This suggested that the vaccine induced T (probably a more dominant Th1 response) and B cell responses. In conclusion, the vaccine successfully protected fish from V. anguillarum infection by eliciting cellular and humoral immune responses. [ABSTRACT FROM AUTHOR]

Background: Infection with the myxozoan parasite Parvicapsula pseudobranchicola causes disease in wild and farmed salmonids in Norway. In the northeast Pacific Ocean, the parasite has been reported in Pacific salmon Oncorhynchus spp. without evidence of disease. The objectives of the present study were to confirm the identity of P. pseudobranchicola in the Pacific, document its host and geographic ranges, and describe associated pathological changes. Methods: Ocean-entry year wild pink salmon Oncorhynchus gorbuscha, chum salmon O. keta, Chinook salmon O. tshawytscha, coho salmon O. kisutch and sockeye salmon O. nerka were collected in summer and autumn surveys near Vancouver Island (VI) and from a winter survey in the Gulf of Alaska. Samples were also obtained from farmed Atlantic salmon Salmo salar and Chinook salmon near VI. Samples were analysed by qPCR and histology using conventional staining or in situ hybridisation. Parasite sequence was obtained from small subunit ribosomal RNA gene (SSU rDNA). Results: Identical 1525 base-pair SSU rDNA sequences from infected pink salmon, chum salmon and Chinook salmon shared 99.93% identity with a P. pseudobranchicola sequence from Norwegian Atlantic salmon. In autumn surveys, the prevalence was greatest in chum salmon (91.8%) and pink salmon (85.9%) and less so in Chinook salmon (68.8%) and sockeye salmon (8.3%). In farmed salmon, the prevalence was zero in Atlantic salmon (n = 967) and 41% in Chinook salmon (n = 118). Infections were preferentially sited in pseudobranch and visualised by in situ hybridisation. Heavy parasite burdens in all species of Pacific salmon were inconsistently associated with focal granulomatous pseudobranchitis. Conclusions: In the northeast Pacific, widespread occurrence of P. pseudobranchicola in Pacific salmon together with its absence or sporadic occurrence in farmed Atlantic salmon differs from its epidemiology in Norway, despite similar pathological development in the pseudobranch. Consequences of the infections to the health of wild Pacific salmon, identity of the invertebrate host and the distribution and abundance of infective actinospores are unknown and remain high priorities for research. [ABSTRACT FROM AUTHOR]

Simple Summary: As one of the essential mineral elements, manganese (Mn) is involved in maintaining the growth and physiological function of fish species. An optimal dietary level of manganese accelerated the growth, lipid metabolism, Mn accumulation, and antioxidant capacity of coho salmon. The dietary Mn requirement for post-larvae coho salmon was 17.35 mg kg−1 and 19.75 mg kg−1 according to the SGR and FCR, respectively. An optimal dietary level of manganese had a positive effect on the antioxidant capacity by scavenging free radicals in fish bodies. In addition, dietary Mn improved lipid metabolism, and the signaling pathway of PI3K/AKT/mTOR may be involved in regulating the activity of lipid metabolism enzymes. In this study, post-larval coho salmon Oncorhynchus kisutch (initial weight 0.37 ± 0.03 g) were fed with 6 experimental diets with increasing manganese (Mn) content (2.4, 8.5, 14.8, 19.8, 24.6, and 33.7 mg kg−1) for 12 weeks. Our results indicated that the feed conversion rate (FCR), specific growth rate (SGR), condition factor (CF), crude protein, moisture, crude lipid, ash, whole-body Mn, and vertebral Mn were affected by the elevation of Mn content in the diet. The activities of hepatic GSH-PX, Mn-SOD, and CAT were enhanced with increasing Mn content in the diet and reached the highest value at 19.8 mg kg−1 Mn. However, the level of hydrogen peroxide (H2O2), superoxide anion (O2·−), and malondialdehyde (MDA) was reduced with increasing Mn content in the diet. In addition, the activity of hepatic lipase (HL) and lipoprotein lipase (LPL) was increased with the elevation of dietary Mn content and reached a peak value at 14.8 mg kg−1 Mn. The activity of fatty acid synthetase (FAS) and the content of nonesterified fatty acid (NEFA) were increased following the elevation of Mn content from 2.4 to 19.8 mg kg−1 in the diet. The results indicated that the appropriate dietary Mn supplementation improved the feeding efficiency, lipid metabolism, and antioxidant capacity of coho salmon. The dietary Mn requirement for post-larval coho salmon was 17.35 mg kg−1 and 19.75 mg kg−1 based on the SGR and FCR, respectively. An optimal dietary level of Mn enhances hepatic lipid metabolism, and the signaling pathway of PI3K/AKT/mTOR may be involved in regulating the activity of enzymes related to lipid metabolism. [ABSTRACT FROM AUTHOR]

Many aspects of natural and hatchery origin salmonid genetics, physiology, behaviour, anatomy and life histories have been compared due to the concerns about what effects domestication and hatchery rearing conditions have on fitness. Genetic and environmental stressors associated with hatchery rearing could cause greater developmental instability (DI), and therefore a higher degree of fluctuating asymmetry (FA) in various bilaterally paired characters, such as otoliths. Nonetheless, to appropriately infer the effects of DI on otolith asymmetry, otolith mineralogy must be accounted for. Vateritic otoliths differ substantially from aragonitic otoliths in terms of mass and shape and can artificially inflate any measurement of FA if not properly accounted for. In this study, measurements of otolith asymmetry between hatchery and natural origin Coho salmon Oncorhynchus kisutch from three different river systems were compared to assess the overall differences in asymmetry when the calcium carbonate polymorph accounted for 59.3% of otoliths from hatchery origin O. kisutch was vateritic compared to 11.7% of otoliths from natural origin O. kisutch. Otolith mineralogy, rather than origin, was the most significant factor influencing the differences in asymmetry for each shape metric. When only aragonitic otoliths were compared, there was no difference in absolute asymmetry between hatchery and natural origin O. kisutch. The authors recommend other researchers to assess otolith mineralogy when conducting studies regarding otolith morphometrics and otolith FA. [ABSTRACT FROM AUTHOR]

Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated a chromosome-level genome assembly. We also resequenced the genomes of 83 coho salmon across the North American range to identify nucleotide variants and understand the demographic histories of these salmon by modeling effective population size from genome-wide data. From demographic history modeling, we observed reductions in effective population sizes between 3,750 and 8,000 years ago for several northern sampling sites, which may correspond to bottleneck events during recolonization after glacial retreat. [ABSTRACT FROM AUTHOR]

Salmon hatcheries are management tools intended to stabilize declining abundance in salmon populations and sustain salmon fisheries. One key area of uncertainty is how hatchery release practices influence juvenile-to-adult survival. Data quality and quantity vary considerably among hatcheries making it difficult to assess the role of release practices. Using a Bayesian hierarchical approach, we analyzed releases and recoveries of Chinook (Oncorhynchus tshawytscha; 21 hatcheries) and coho (Oncorhynchus kisutch; 16 hatcheries) salmon in British Columbia from 1972 to 2017. Higher survival rates were associated with increasing weights-at-release, earlier releases of Chinook salmon, and later releases of coho salmon. The addition of environmental (sea surface temperature, Pacific Decadal Oscillation), and predator (harbour seals, killer whales) covariates did not improve model performance relative to models that used year effects to account for declines in survival and interannual variability in ocean conditions. Optimizing release practices could increase returns by 6%–245% for Chinook salmon and 5%–160% for coho salmon based on median posterior estimates for each hatchery. With these results, a large-scale adaptive management approach could be implemented to test our understanding of release practice–survival relationships and evaluate cost–benefit trade-offs. [ABSTRACT FROM AUTHOR]

The breakdown product of the rubber tire antioxidant N‐(1,3‐dimethylbutyl)‐N'‐phenyl‐p‐phenylenediamine‐quinone (6PPD)‐6‐PPD‐quinone has been strongly implicated in toxic injury and death in coho salmon (Oncorhynchus kisutch) in urban waterways. Whereas recent studies have reported a wide range of sensitivity to 6PPD‐quinone in several fish species, little is known about the risks to Chinook salmon (Oncorhynchus tshawytscha), the primary prey of endangered Southern Resident killer whales (Orcinus orca) and the subject of much concern. Chinook face numerous conservation threats in Canada and the United States, with many populations assessed as either endangered or threatened. We evaluated the acute toxicity of 6PPD‐quinone to newly feeding (~3 weeks post swim‐up) juvenile Chinook and coho. Juvenile Chinook and coho were exposed for 24 h under static conditions to five concentrations of 6PPD‐quinone. Juvenile coho were 3 orders of magnitude more sensitive to 6PPD‐quinone compared with juvenile Chinook, with 24‐h median lethal concentration (LC50) estimates of 41.0 and more than 67 307 ng/L, respectively. The coho LC50 was 2.3‐fold lower than what was previously reported for 1+‐year‐old coho (95 ng/L), highlighting the value of evaluating age‐related differences in sensitivity to this toxic tire‐related chemical. Both fish species exhibited typical 6PPD‐quinone symptomology (gasping, increased ventilation, loss of equilibrium, erratic swimming), with fish that were symptomatic generally exhibiting mortality. The LC50 values derived from our study for coho are below concentrations that have been measured in salmon‐bearing waterways, suggesting the potential for population‐level consequences in urban waters. The higher relative LC50 values for Chinook compared with coho merits further investigation, including for the potential for population‐relevant sublethal effects. Environ Toxicol Chem 2023;42:815–822. © 2023 His Majesty the King in Right of Canada and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Reproduced with the permission of the Minister of Fisheries and Oceans Canada. [ABSTRACT FROM AUTHOR]

Simple Summary: Fish meal has been the main aquatic feed protein source for aquaculture. However, global fish meal is lacking, and the price of fish meal continues to rise, which has been unable to meet the needs. Soybean meal is currently recognized as the best choice to replace fish meal in aquatic feed, but soybean meal contains anti-nutritional factors which can affect the health of aquatic animals. Microbial fermentation is a commonly used biological method for treating soybean meal antigens and palatability. In this study, juvenile coho salmon were fed a diet with replaced 10% fish meal protein with fermented soybean meal protein supplementation for 12 weeks. The results indicated that the diet with replaced 10% fish meal protein with fermented soybean meal protein supplementation could significantly (p < 0.05) influence the expression of superoxide dismutase, catalase, glutathione peroxidase, glutathione S-transferase, nuclear factor erythroid 2-related factor 2, tumor necrosis factor α and interleukin-6 genes, the growth performance, the serum biochemical indices, and the activity of antioxidant and immunity enzymes. This study aims to investigate the effects of partial dietary replacement of fish meal with unfermented and/or fermented soybean meal (fermented by Bacillus cereus) supplemented on the growth performance, whole-body composition, antioxidant and immunity capacity, and their related gene expression of juvenile coho salmon (Oncorhynchus kisutch). Four groups of juveniles (initial weight 159.63 ± 9.54 g) at 6 months of age in triplicate were fed for 12 weeks on four different iso-nitrogen (about 41% dietary protein) and iso-lipid (about 15% dietary lipid) experimental diets. The main results were: Compared with the control diet, the diet with replaced 10% fish meal protein with fermented soybean meal protein supplementation can significantly (p < 0.05) influence the expression of superoxide dismutase, catalase, glutathione peroxidase, glutathione S-transferase, nuclear factor erythroid 2-related factor 2, tumor necrosis factor α and interleukin-6 genes, the growth performance, the serum biochemical indices, and the activity of antioxidant and immunity enzymes. However, there was no significant effect (p > 0.05) on the survival rate (SR) and whole-body composition in the juveniles among the experimental groups. In conclusion, the diet with replaced 10% fish meal protein with fermented soybean meal protein supplementation could significantly increase the growth performance, antioxidant and immunity capacity, and their related gene expression of juveniles. [ABSTRACT FROM AUTHOR]

Female-biased mortality has been consistently reported in Pacific salmon during their adult upriver migration. We collected coho salmon (Oncorhynchus kisutch (Walbaum, 1792)) upon arrival at their spawning grounds to test whether females are more prone to cardiac oxygen limitations following exercise stress. We used a surgical approach to periodically sample arterial and venous blood over 48 h following recovery from a chase protocol to induce maximum metabolic rate. We found no significant differences in arterial or venous partial pressures of O2 between males and females. Female salmon had significantly elevated plasma cortisol levels but there were no effects of sex on either plasma lactate or K+. Our data show that female coho salmon do not suffer oxygen limitations to the spongy myocardium after a single exercise event at moderate temperatures (14 °C)—at least not when arriving to their spawning grounds. This study found no clear support for a cardiac oxygen limitation underlying elevated female mortality in Pacific salmon. Neither, however, does our study design nor specific findings allow us to rule out cardiac limitations in these fish. Future work should address whether potential oxygen limitations to the spongy myocardium at high temperatures or oxygen limitations to the compact myocardium via coronary blood flow contribute to female-biased mortality earlier on the migratory route. [ABSTRACT FROM AUTHOR]

Genetic rescue has emerged as an important tool to prevent extinction and improve fitness of declining populations. In principle, genetic rescue increases genetic variation in a population through translocation of unrelated individuals from an outside source population. Genetic rescue remains uncommon in conservation management due to concerns about the risk of outbreeding depression. Lack of data evaluating success of genetic rescue interventions has hampered willingness to use this technique to improve the genetic viability of inbred, bottlenecked populations. Here, we evaluate the success of a genetic rescue intervention within the endangered Central California Coast Coho Salmon Evolutionarily Significant Unit using ∼17 years of genetic and demographic data, including pre‐ and postoutcrossing with fish from a nearby watershed. We assessed fitness of outcrossed F1 and F2 progeny in a captive setting, and then used mark–recapture to estimate survival of juveniles released into streams. We found that outcrossing decreased relatedness among adults, and their hybrid progeny had higher fitness in both captive and stream settings relative to nonhybrids. Importantly, we did not observe evidence of outbreeding depression in either the F1 or F2 generations. This study highlights that genetic rescue can be a useful tool in the conservation of imperiled salmonids. [ABSTRACT FROM AUTHOR]

In the western US, freshwater mussels (Order Unionida) contribute valuable ecosystem functions to riverine systems, yet have declined across their range following widespread degradation of freshwater habitat and parallel declines in salmonids, host fish for larval western pearlshell mussels (Margaritifera falcata). The status of M. falcata populations is of particular conservation interest in isolated coastal watersheds given unique freshwater mussel-host fish relationships. To understand M. falcata population ecology in Oregon's coastal watersheds, we analyzed stream survey data on presence/absence of mussels collected over a recent eleven-year period, explored co-varying habitat characteristics, and summarized mussel distribution and host fish co-occurrence. We also collected M. falcata and compared condition indices among eight locations. Naïve occupancy in surveyed areas was 12.3%, about half of predicted occupancy (ψ = 0.24, CI 0.19–0.31) based on modeling repeated visits over a ten year assumed closed period. Mussel occupancy was correlated with reach-scale habitat variables, and the probability of mussel observations was positively correlated with presence of coho (Oncorhynchus kisutch) salmon. Condition varied significantly among locations. Spatial relationships between existing mussel distribution, host species, and habitat variables answer questions about coastal freshwater mussel populations, as well as serve to identify priorities for further research and population assessment. [ABSTRACT FROM AUTHOR]