Atlantic Salmon Research Articles

Accuracy of genomic prediction using multiple Atlantic salmon populations

BackgroundThe accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four parallel populations often exist, thus offering the opportunity to increase the size of the reference set by combining these populations. By allowing a reduction in the number of records per population, multi-population prediction can potentially reduce cost and welfare issues related to the recording of traits, particularly for diseases. In this study, we evaluated the accuracy of multi- and across-population prediction of breeding values for resistance to amoebic gill disease (AGD) using all single nucleotide polymorphisms (SNPs) on a 55K chip or a selected subset of SNPs based on the signs of allele substitution effect estimates across populations, using both linear and nonlinear genomic prediction (GP) models in Atlantic salmon populations. In addition, we investigated genetic distance, genetic correlation estimated based on genomic relationships, and persistency of linkage disequilibrium (LD) phase across these populations.ResultsThe genetic distance between populations ranged from 0.03 to 0.07, while the genetic correlation ranged from 0.19 to 0.99. Nonetheless, compared to within-population prediction, there was limited or no impact of combining populations for multi-population prediction across the various models used or when using the selected subset of SNPs. The estimates of across-population prediction accuracy were low and to some extent proportional to the genetic correlation estimates. The persistency of LD phase between adjacent markers across populations using all SNP data ranged from 0.51 to 0.65, indicating that LD is poorly conserved across the studied populations.ConclusionsOur results show that a high genetic correlation and a high genetic relationship between populations do not guarantee a higher prediction accuracy from multi-population genomic prediction in Atlantic salmon.

Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation.

Large effects loci often contain genes with critical developmental functions with potentially broad effects across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, six6 and vgll3, is linked to age at maturity, and several physiological and behavioural traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early life survival was linked to the genotype associated with late maturation in the vgll3, but with early maturation in the six6 locus. These effects were significant in high-nutrient, but not in in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation, but by maternal genotypes in the six6 locus, and by both parents' genotypes in the vgll3 locus. Our results suggest that indirect genetic effects by large-effect loci can be significant determinants of offspring fitness. This study demonstrates an intriguing case of how large-effect loci can exhibit complex fitness associations across life stages in the wild and indicates that predicting evolutionary dynamics is difficult.

Vegetable omega-3 and omega-6 fatty acids differentially modulate the antiviral and antibacterial immune responses of Atlantic salmon

The immunomodulatory effects of omega-3 and omega-6 fatty acids are a crucial subject of investigation for sustainable fish aquaculture, as fish oil is increasingly replaced by terrestrial vegetable oils in aquafeeds. Unlike previous research focusing on fish oil replacement with vegetable alternatives, our study explored how the omega-6 to omega-3 polyunsaturated fatty acid (PUFA) ratio in low-fish oil aquafeeds influences Atlantic salmon's antiviral and antibacterial immune responses. Atlantic salmon were fed aquafeeds rich in soy oil (high in omega-6) or linseed oil (high in omega-3) for 12 weeks and then challenged with bacterial (formalin-killed Aeromonas salmonicida) or viral-like (polyriboinosinic polyribocytidylic acid) antigens. The head kidneys of salmon fed high dietary omega-3 levels exhibited a more anti-inflammatory fatty acid profile and a restrained induction of pro-inflammatory and neutrophil-related genes during the immune challenges. The high-omega-3 diet also promoted a higher expression of genes associated with the interferon-mediated signaling pathway, potentially enhancing antiviral immunity. This research highlights the capacity of vegetable oils with different omega-6 to omega-3 PUFA ratios to modulate specific components of fish immune responses, offering insights for future research on the intricate lipid nutrition-immunity interplay and the development of novel sustainable low-fish oil clinical aquaculture feeds.

Optimum eicosapentaenoic acid + docosahexaenoic acid levels for farmed Atlantic salmon: closing the gap between science and commercial practice

The shift from fish oil to vegetable oil (VO) sources has lowered eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) levels in salmon aquafeeds. VOs are high in omega-6 and low in omega-3 essential fatty acids like EPA and DHA, crucial for fish metabolism and immunity. Algal oil (AO), with high EPA + DHA and lower omega-6 levels supports fish health and growth, but transferring lab-controlled conditions to real-world commercial farming remains a challenge. This study explored the benefits of high dietary EPA + DHA levels through a commercial farm (CF) study in Chile and a Big Data (BD) study in Norway. The CF study, involving 625,000 Atlantic salmon, compared standard feed with AO-supplemented feed. The latter resulted in improved health responses and better fillet quality. The BD study analyzed real data from 232.6 million fish, revealing that EPA + DHA levels > 8% reduce mortality variability by 21%, improve economic feed conversion ratio by 11%, and increase the likelihood of superior harvests by 27%, demonstrating productivity benefits. Both studies emphasize the advantages of feeds with EPA + DHA levels above typical industry practices, enhancing growth, health, and nutritional quality. Importantly, the BD study complements the CF study, bridging the gap between science and aquafarms, and providing evidence that diets with EPA + DHA > 8% offer biological performance benefits for farmers, regardless of farming environments.

Challenges in downstream dam passage and the effect of dam removal on Atlantic salmon (Salmo salar) smolt migrations.

Migration is critical for life-cycle completion in diadromous fish species. River connectivity is vital in facilitating these large-scale movement events, but the extent of present-day river fragmentation can interfere with these migrations. Fish passage solutions (FPSs) are commonly implemented with the aim of improving river connectivity. In our study, we investigated the performance of two types of FPSs, spill regimes and complete dam removal, on Atlantic salmon (Salmo salar) smolt migrations. We used acoustic telemetry to monitor migration behavior and passage success of 120 wild smolts released in three different groups/sites: one group with two dams to pass to reach the river mouth, a second group with one dam to pass, and a control group without any barriers to pass (upstream of a recently removed hydroelectric dam). Smolt passage probabilities were similar for the two studied dams (87% and 86%) but showed variation in path choice, delay times, and loss rates. Passage success was influenced by several factors, such as body size, diel period, and water temperature, but not flow. Cumulative passage success to the river mouth was 61%, with most individuals being lost within lentic river stretches, either in the forebays of hydroelectric power stations or in naturally wide river stretches. Within the recently rehabilitated river sections (post dam removal), passage speeds were significantly faster than all other sections of the river (post-rehabilitation x¯ = 56.1 km/day) with significantly faster speeds compared to pre-rehabilitation (pre-x¯ = 28.0 km/day). Our findings provide valuable information on the benefits of dam removal and highlight the need for further rehabilitation measures in upriver reaches where barriers still affect downstream passage.

The impact of functional feed on Atlantic salmon (Salmo salar) systemic immune response to high and low levels of sea lice infection (Lepeophtheirus salmonis) and co-infection with infectious salmon anemia virus

Due to the nature of open-pen farming, salmon are exposed to numerous pathogens shared by other farms and their wild counterparts. Industry must manage these outbreaks through vaccination, oral or bath treatments, and more recently through functional feed administration. Globally, the most important pathogens of salmon are sea lice (Lepeophtheirus salmonis, and Caligus rogercresseyi) not only due to their direct impacts on the host, but indirectly by enhancing host susceptibility to co-infection. This study aims to characterize molecular responses during a co-infection of L. salmonis and a salmon orthomyxovirus (infectious salmon anemia virus; ISAv) under administration of four functional feed diets: a control feed with a low 0.3 % EPA/DHA + high-ω6 (Ctrl), an EPA/DHA enriched pro-inflammatory diet 1 % EPA/DHA + high-ω6; FA + I), an EPA/DHA enriched anti-inflammatory diet (1 % EPA/DHA+high-ω3; FA-I), and a low EPA/DHA feed (0.3 %) with an immunostimulant added (0.3 % EPA/DHA + high-ω6 + immunostimulant (IS); Ctrl + IS). Atlantic salmon (40 fish per tank; 8 tanks per feed) were acclimated to one of the four experimental diets. Sea lice copepodids were introduced to all experimental tanks and 10 fish sampled from each tank at each time point (prior to infection [−3], and 11, 33, 47 days post infection). A high virulence ISAv isolate (ISAV-HPR4) was intraperitoneally injected into donor fish 6 days prior to their transfer into the experimental tanks for cohabitation (ca. 10–15 % of tank density; 4 tanks per feed group) to achieve peak shedding rates at time of stocking. Fatty acid enriched (FA + I and FA-I) diets had a significant impact on sea lice abundance on fish infected with lice only. Gene expression profiles measured by reverse transcriptase-qPCR showed significant upregulation in several antiviral genes (irf7b and mxb) associated with the interferon system in all but the fish fed the immunostimulating diet. An increase in transcript levels (irf7b, isg15a, mmp-9, mxb) accounted for high lice and high viral loads in diets FA + I and Ctrl + IS. As feeds successful at reducing lice were the least successful in survival of co-infected fish, there appears to be a trade-off for better anti-parasitic responses, which is enhanced through dietary supplementation. This will require further research to ensure careful selection of feed combinations and expected co-infection challenges.

Potential plasma biomarkers for the onset of heart and skeletal muscle inflammation from Piscine orthoreovirus-1 infection in Atlantic salmon (Salmo salar)

Biomarkers that give quantifiable information about disease development are valuable diagnostic indicators providing opportunities to thwart adverse outcomes through timely detection and initiation of countermeasures. Whereas human medicine already relies extensively on biomarker analysis, their application in the diagnostics of fish diseases is still at a tentative beginning. However, the increased utilisation of broad-range analytical approaches such as untargeted proteomics enhances the chances to discover changes in the levels of proteins, which are connected to fish health and could serve as novel biomarkers. In the present study, proteomic analysis accompanied by biostatistical data processing was employed with the aim of identifying plasma biomarker candidates for the onset of heart and skeletal muscle inflammation (HSMI) caused by Piscine orthoreovirus (PRV)-1 infection in Atlantic salmon. HSMI is a common viral disease and threat to fish welfare and productivity in Norwegian aquaculture, so that the early detection of HSMI development would allow a timely intervention to limit the damage. In the search for biomarker candidates, salmon plasma was sampled five and eight weeks after a PRV-1 cohabitation challenge experiment and from adequate control fish, and analysed by mass spectrometry-based proteomics. The proteome dataset contained 695 proteins with >90% probability of correct identification according to the set cut-off criteria for peptide quality. Time- and condition-related differences in protein abundance levels were revealed by multivariate analysis. Comparison of the proteins identified as significant using three different biostatistical models resulted in a short list of four potential biomarkers: galectin-3-binding protein (Gal-3BP), fucolectin-6, urokinase plasminogen activator surface receptor and ryanodine receptor 3. The physiological functions described for these proteins in mammals designate them as interesting indicators of inflammatory diseases also in other species, such as PRV-1 pathogenesis in salmon. In situ-hybridisation targeting Gal-3BP and PRV-1 mRNA in heart tissue sections from the same challenge trial showed a significant upregulation of Gal-3BP mRNA in infected salmon hearts as compared to controls, supporting the findings of the proteomic analysis and suggesting a role in the onset of heart- and skeletal muscle inflammation.

Optimising seafood nutritional value and environmental sustainability in aquaculture through a novel integrated modelling tool applicable to IMTA and monoculture

Aquaculture policies that decrease the reliance on wild-caught fish and promote integrated multi-trophic aquaculture (IMTA) both aim to lessen the environmental footprint but often overlook economic-environmental trade-offs and neglect social, health, and broad-scale sustainability considerations. Here we present a new bio-physical model (FYNE) that bridges some of these gaps, by linking farm operational choices, such as feed choices and farm siting, with the nutritional value of the farm-gate seafood products and the resulting environmental eutrophication footprint at the farm level. The FYNE model operates both in conditions of monoculture or of IMTA production, and estimates feed composition effects on growth and omega-3 fatty acid content of Atlantic salmon (Salmo salar) and blue mussel (Mytilus edulis), and nitrogen and carbon concentrations, the latter being a measure of the environmental eutrophication footprint of the farm. The model here developed integrates for the first time (i) an ecosystem model of an IMTA and (ii) a fatty acid dynamics model, with new models for salmon feed digestibility and mussel ingestion. The outputs span (i) production analysis for simulation of biomass; (ii) farm mass-balance analysis on deposition analysis and environmental eutrophication footprint; and (iii) product nutritional quality, in terms of fatty acid content. An application of the model to an IMTA farm in Scotland (UK) demonstrates how fatty acid and environmental changes can be modelled in tandem and could be used to support the industry to optimize the nutritional value of cultured species and manage aquatic environmental eutrophication footprint at farm level, informing feed and siting decisions. The model effectively predicts changes in omega-3 fatty acids, particularly DHA and EPA, in response to variations in feed composition. Notably, our results confirm that salmon waste has limited influence on mussel growth due to the spatial separation within the IMTA system, which emphasizes the need for strategic siting to enhance system productivity through effective waste recycling. Additionally, results show that while increasing fishmeal in diets enhances environmental outcomes, it reduces levels of critical fatty acids like DHA and EPA, underscoring the need for balanced feed formulations. The method developed in this study described a novel integrated model (FYNE) that extend previous modelling work by incorporating the influence of farmed species feed composition on fatty acid dynamics as well as the farming environmental factors.

An aquaculture risk model to understand the causes and consequences of Atlantic Salmon mass mortality events: A review

AbstractMass mortality events (MMEs) are defined as the death of large numbers of fish over a short period of time. These events can result in catastrophic losses to the Atlantic salmon aquaculture industry and the local economy. However, they are challenging to understand because of their relative infrequency and the high number of potential factors involved. As a result, the causes and consequences of MMEs in Atlantic salmon aquaculture are not well understood. In this study, we developed a structural network of causal risk factors for MMEs for aquaculture and the communities that depend on Atlantic salmon aquaculture. Using the Interpretive Structural Modeling (ISM) technique, we analysed the causes of Atlantic salmon mass mortalities due to environmental (abiotic), biological (biotic) and nutritional risk factors. The consequences of MMEs were also assessed for the occupational health and safety of aquaculture workers and their implications for the livelihoods of local communities. This structural network deepens our understanding of MMEs and points to management actions and interventions that can help mitigate mass mortalities. MMEs are typically not the result of a single risk factor but are caused by the systematic interaction of risk factors related to the environment, fish diseases, feeding/nutrition and cage‐site management. Results also indicate that considerations of health and safety risk, through pre‐ and post‐event risk assessments, may help to minimize workplace injuries and eliminate potential risks of human fatalities. Company and government‐assisted socio‐economic measures could help mitigate post‐mass mortality impacts. Appropriate and timely management actions may help reduce MMEs at Atlantic salmon cage sites and minimize the physical and social vulnerabilities of workers and local communities.

A comparative analysis of alternative splicing patterns in Atlantic salmon (Salmo salar) in response to Moritella viscosa and sea lice (Lepeophtheirus salmonis) infection

Moritella viscosa (M. viscosa) and sea lice (Lepeophtheirus salmonis) are severe pathogens that primarily infect the skin of Atlantic salmon (Salmo salar), which cause significant economic losses in the farming industry. However, the pathogenesis and molecular mechanisms underlying the host's immune defence at the post-transcriptional level remain unclear. Alternative splicing (AS) is an evolutionarily conserved post-transcriptional mechanism that can greatly increase the richness of the transcriptome and proteome. In this study, transcriptomic data derived from skin tissues of Atlantic salmon after M. viscosa and sea lice infections were used to examine the AS profiles and their differential expression patterns. In total, we identified 33,044 AS events (involving 13,718 genes) in the control (CON) group, 35,147 AS events (involving 14,340 genes) in the M. viscosa infection (MV) group, and 30,364 AS events (involving 13,142 genes) in the sea lice infection (LC) group, respectively. Among the five types of AS identified in our study (i.e., SE, A5SS, A3SS, MXE, and RI), SE was the most prevalent type in all three groups (i.e., CON, MV, and LC groups). Decreased percent-spliced-in (PSI) levels were observed in SE events under both MV- and LC-infected conditions, suggesting that MV or LC infection elevated exon-skipping isoforms and promoted the selection of shorter transcripts in numerous DAS genes. In addition, most of the differential AS genes were found to be associated with pathways related to mRNA regulation, epithelial or muscle development, and immune response. These findings provide novel insights into the role of AS in host-pathogen interactions and represent the first comparative analysis of AS in response to bacterial and parasitic infections in fish.

A comparative study of the alternative life history of iteroparous salmonids

AbstractThe kelt phase of anadromous iteroparous salmonid life history remains mysterious, particularly aspects of their habitat use and factors influencing survival. Atlantic salmon and sea‐run brown trout were captured in the estuary during their return migration to the Vosso River, Norway, tagged with acoustic transmitters, and tracked in the watershed and estuary in three different years (2020–2023). We found a relatively narrow window of river exit timing among trout that survived overwinter, whereas salmon tended to leave during a more protracted period. Trout preferred overwintering in lakes within the river system, which provided for lower locomotor activity than fish that overwintered in pools in the river according to data from tri‐axial accelerometer transmitters. In contrast, Atlantic salmon tended to spend surprisingly little time in lakes even though the energy expenditure in this habitat is was seemingly lower for salmon that did overwinter in the lake. Our results demonstrate different use of habitat during overwintering and could suggest that measures to protect iteroparous life history strategies of salmonids will differently impact these two iteroparous salmonids.

Virus-specific antibody secreting cells reside in the peritoneal cavity and systemic immune sites of Atlantic salmon (Salmo salar) challenged intraperitoneally with salmonid alphavirus

The development and persistence of antibody secreting cells (ASC) after antigenic challenge remain inadequately understood in teleosts. In this study, intraperitoneal (ip) injection of Atlantic salmon (Salmo salar) with salmonid alphavirus (WtSAV3) increased the total ASC response, peaking 3–6 weeks post injection (wpi) locally in the peritoneal cavity (PerC) and in systemic lymphoid tissues, while at 13 wpi the response was only elevated in PerC. At the same time point a specific ASC response was induced by WtSAV3 in PerC and systemic tissues, with the highest frequency in PerC, suggesting a local role. Inactivated SAV (InSAV1) induced comparatively lower ASC responses in all sites, and specific serum antibodies were only induced by WtSAV3 and not by InSAV1. An InSAV1 boost did not increase these responses. Expression of immune marker genes implies a role for PerC adipose tissue in the PerC immune response. Overall, the study suggests the Atlantic salmon PerC as a secondary immune site and an ASC survival niche.

Sampling time for different matrices in stress assessment of farmed Atlantic salmon post-smolt

The sustainability of commercial aquaculture production depends critically on prioritizing fish welfare management. Besides monitoring welfare parameters such as fish behaviour and water quality, fish stress level can also provide a reliable measure of the welfare status of farmed fish. Cortisol and 5 of its metabolites (5β-THF, cortisone, 5β-DHE, 5β-THE, β-cortolone) were previously identified by the authors as suitable stress biomarkers of farmed Atlantic salmon. Based on this knowledge, the present study aimed to investigate the time-related dynamics of these metabolites in plasma, skin mucus, bile and faeces over a 72 h- period. The objective was to determine the optimal sampling time for each matrix and to understand the clearance pathway of these metabolites following stress. An experiment was carried out using a total of 90 Atlantic salmon with an average weight of 438 (±132) g. The average sea temperature was 6.9 °C during the experimental period. A control group of 10 fish was first collected before the remaining 80 fish were submitted to a stress of netting and subsequent relocation into two separate cages. From each of these two stress groups, 10 fish were sampled at 1h, 2h, 4h, 6h and 12h, 24h, 48h, 72h after the stress event respectively. The concentrations of cortisol and its metabolites were measured at each of the sampling timepoint. The results demonstrated that plasma cortisol metabolites reached the highest concentration 4h after stress and remained elevated despite the slight decrease for the remaining timepoints. The peak level was observed at 12h post stress in skin mucus and 24h in bile and faeces. The findings suggest that these timepoints are the optimal for sampling Atlantic salmon post-smolt following stressful events in acute stress studies. Furthermore, the results reveal that analysing cortisol and its metabolites, both in free and conjugated forms, rather than free cortisol provides greater flexibility as their concentrations are less affected by sampling procedure. This study confirms the appropriateness of skin mucus and faeces as less-invasive sample matrices for fish stress evaluation and provides a basis for further developing low invasive tools for monitoring the welfare of farmed salmonid.

Long-term substitution of fish oil with alternative sources in Atlantic salmon (Salmo salar): Performance, health, and consumer appeal

Salmon farming in Chile faces the dual challenge of maintaining growth while improving sustainability. One approach to advance sustainability involves the feeds without marine-fishery inputs. This study aimed to evaluate the effect of completely replacing fish oil (FO) on the performance of Salmo salar throghout marine grow-out. The investigation involved fish ranging from 400 g to 4000 g and explored three diets without fish meal, each which included 2.2% EPA + DHA from different sources: FO (control), transgenic canola oil (Can n-3) and Schizochytrium sp. oil (AOV) as unique type of oils. Each diet was randomly distributed in triplicate among nine tanks with a recirculation system maintained at 12 °C, with automatic feeding and a 24-h light photoperiod. Fish density was 29 fish m−3 at day 133 of the experiment and seven fish m−3 at day 319. The diets were isoproteic, isolipidic and isoenergetic. Fish were evaluated at 133 and 319 days of experiment in terms of productive performance, liver health, EPA + DHA and lipid retention efficiency, fatty acid metabolism, response to acute stress, and final product quality. The results showed similar productive performance and liver health among the three diets during both sampling periods. No differences were observed in lipid or EPA + DHA retention efficiency in the whole body or fillet. Eicosanoids and receptors for anti-inflammatory mediators derived from EPA and DHA showed similar or higher capacities in fish fed with Can n-3 and AOV than those fed FO. Responses to induced stress, measured through lactate, cortisol, sodium, potassium, chloride, glucose, and the liver profile were similar between the three diets. Similarly in fillet quality between the three diets. However, sensory analysis revealed a lower intensity of “global aroma” in Can n-3-fed fish fillets and lower evaluations in “typical salmon aroma”, “oily aroma” and “fresh flavor” in AOV-fed fish fillets when they are compared with FO. The nutritional indicators of the final product were similar between the three diets, except for PUFA/SFA, the thrombogenicity index, hypercholesterolemia/hypocholesterolemia, and the health promotion index. In these specific indicators, fish fed with Can n-3 and AOV demonstrated more favorable results for consumer health than the FO-fed fish.

Functional role of TrIL-1β in Takifugu rubripes defense against Cryptocaryon irritans infection

The Japanese puffer, Takifugu rubripes, is a commercially important fish species in China that is under serious threat from white spot disease (cyptocaryoniasis), which leads to heavy economic losses. We previously found that interleukin-1β (IL-1β), an important cytokine with a potential role in resistance against pathogens, was one of the most significantly differentially up-regulated proteins in the gills and spleen of T. rubripes infected by the protozoan parasite Cryptocaryon irritans. In this study, we assessed the potential function of T. rubripes IL-1β (TrIL-1β) in fish infected with C. irritans. Phylogenetic analysis indicated that the TrIL-1β protein sequence was most closely related to that of Atlantic salmon (Salmo salar) (67.2 %). The incubation experiments revealed that TrIL-1β may reduce trophont activity by destroying membranes. Immunofluorescence experiments showed that recombinant TrIL-1β promoted the expression of endogenous IL-1β, which penetrated and disrupted the cell membranes of trophonts. Transmission electron microscopy showed that the IL-1β group had less tissue damage compared with control groups of fish. IL-1β-small interfering RNA and IL-1β overexpression experiments were performed in head kidney primary cells, and challenge experiments were performed in vitro. Quantitative RT-PCR results showed that TrIL-1β regulated and activated MyD88/NF-κB and MyD88/MAPK/p38 signaling pathways during C. irritans infection. TrIL-1β also promoted the differential expression of IgM, showing that it was involved in humoral immunity of T. rubripes. The cumulative mortality experiment show that TrIL-1β could protect fish against C. irritans infection. These results enrich current knowledge about the molecular structure of TrIL-1β. They also suggested that recombinant TrIL-1β could be used as an adjuvant in a subunit vaccine against C. irritans infection, which is of profound importance for the prevention and control of parasitic diseases in T. rubripes.

Atlantic salmon gill epithelial cell line ASG-10, an in vitro model for studying effects of microplastics in gills

Microplastics are ubiquitous environmental pollutants frequently detected in aquatic environments. Here we used the Atlantic salmon epithelial gill cell line (ASG-10) to investigate the uptake and effects of polystyrene (PS) microplastic. The ASG-10 cell line has phagocytotic/endocytic capacities and can take up clear PS particles at 0.2 and 1.0 µm, while PS at 10 µm was not taken up. As a response to the uptake, the ASG-10 cells increased their lysosomal activity. Furthermore, no effects on the mitochondria were found, neither on the mitochondrial membrane potential nor the mitochondria morphology (branch length and diameter). Interestingly, even a very high concentration of PS (200 µg/ml) with all tested particle sizes had no effects on cell viability and cell cycle. The environmental toxin Benzo(a)pyrene (B(a)P), a known inducer of CYP1A, is highly hydrophobic and thus sticks to the PS particles. However, co-exposure of B(a)P and PS the particles did not increase the induction of CYP1A activity compared to B(a)P alone. Our study contributes to the understanding of the cellular effects of PS particles using a highly relevant Atlantic salmon gill epithelium in vitro model.

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

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

The ecohydrology of rewilding: A pressing need for evidence in the restoration of upland Atlantic salmon streams

The ecohydrology of rewilding: A pressing need for evidence in the restoration of upland Atlantic salmon streams

A comparative study of two fish farm layouts under pure current conditions

High-value finfish, such as the Atlantic Salmon (Salmo Salar), are typically raised in multi-cage fish farms. The fish farm needs to be designed with sufficient strength and water exchange. A coupling algorithm between two open-source numerical toolboxes, OpenFOAM and Code_Aster, is utilized in this work for fluid-structure interaction analysis of fish farms. The two different fish farm layouts, i.e., the 2 × 3 array layout and the Honeycomb layout, are investigated in this study under pure current conditions with different flow angles. The fluid and structure responses of the two fish farm layouts are compared, in terms of flow field in and around fish farms, tensions in anchor lines, drag force, and total cultivation volume. The present results suggest that, compared to the 2 × 3 array layout, the Honeycomb layout has a smaller covered area and reduced environmental loads, which are making this layout advantageous for fish farming.

Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex-chromosomes.

Salmon lice, Lepeophtheirus salmonis (family Caligidae), are ectoparasites that have negatively impacted the salmon aquaculture industry and vulnerable wild salmon populations. Researchers have studied salmon lice to better understand their biology to develop effective control strategies. In this study, we updated the chromosome-level reference genome assembly of the Pacific subspecies of L. salmonis using Hi-C data. The previous version placed contigs/scaffolds using an Atlantic salmon louse genetic map. By utilizing Hi-C data from Pacific salmon lice, we were able to properly assign locations to contigs/scaffolds previously unplaced or misplaced. This resulted in a more accurate genome assembly and a more comprehensive characterization of the sex-chromosome unique to females (W). We found evidence that the same ZW-ZZ mechanism is common in both Atlantic and Pacific subspecies of salmon lice using PCR assays. The W-chromosome was approximately 800 kbp in size, which is ∼30 times smaller than the Z-chromosome (24 Mbp). The W-chromosome contained 61 annotated genes, including 32 protein-coding genes, 27 long non-coding RNA (lncRNA) genes, and 2 pseudogenes. Among these 61 genes, 39 genes shared homology to genes found on other chromosomes, while 20 were unique to the W-chromosome. Two genes of interest on the W-chromosome, prohibitin-2 and kinase suppressor of ras-2, were previously identified as potential sex-linked markers in the salmon louse. However, we prioritized the 20 unique genes on the W-chromosome as sex-determining candidates. This information furthers our understanding of the biology of this ectoparasite and may help in the development of more effective management strategies.