Transcriptome Analysis of Atlantic Salmon (Salmo salar) Skin in Response to Sea Lice and Infectious Salmon Anemia Virus Co-Infection Under Different Experimental Functional Diets

Sea lice (Lepeophtheirus salmonis) are ectoparasitic copepods that cause significant economic loss in marine salmoniculture. In commercial salmon farms, infestation with sea lice can enhance susceptibility to other significant pathogens, such as the highly contagious infectious salmon anemia virus (ISAv). In this study, transcriptomic analysis was used to evaluate the impact of four experimental functional feeds (i.e. 0.3% EPA/DHA+high-ω6, 0.3% EPA/DHA+high-ω6+immunostimulant (IS), 1% EPA/DHA+high-ω6, and 1% EPA/DHA+high-ω3) on Atlantic salmon (Salmo salar) during a single infection with sea lice (L. salmonis) and a co-infection with sea lice and ISAv. The overall objectives were to compare the transcriptomic profiles of skin between lice infection alone with co-infection groups and assess differences in gene expression response among animals with different experimental diets. Atlantic salmon smolts were challenged with L. salmonis following a 28-day feeding trial. Fish were then challenged with ISAv at 18 days post-sea lice infection (dpi), and maintained on individual diets, to establish a co-infection model. Skin tissues sampled at 33 dpi were subjected to RNA-seq analysis. The co-infection’s overall survival rates were between 37%-50%, while no mortality was observed in the single infection with lice. With regard to the infection status, 756 and 1303 consensus differentially expressed genes (DEGs) among the four diets were identified in “lice infection vs. pre-infection” and “co-infection vs. pre-infection” groups, respectively, that were shared between the four experimental diets. The co-infection groups (co-infection vs. pre-infection) included up-regulated genes associated with glycolysis, the interferon pathway, complement cascade activity, and heat shock protein family, while the down-regulated genes were related to antigen presentation and processing, T-cell activation, collagen formation, and extracellular matrix. Pathway enrichment analysis conducted between infected groups (lice infection vs. co-infection) resulted in several immune-related significant GO terms and pathways unique to this group, such as “autophagosome”, “cytosolic DNA-sensing pathway” and “response to type I interferons”. Understanding how experimental functional feeds can impact the host response and the trajectory of co-infections will be an essential step in identifying efficacious intervention strategies that account for the complexities of disease in open cage culture.

Multispecies hierarchies and capitalist value: Insights from salmon aquaculture

Research in animal geographies is increasingly paying attention to hierarchies and inequalities within and between nonhuman animals. The way that animals are valued differently and hierarchically within this growing body of scholarship has tended to focus on a range of biopolitical differences between and within species. Collard and Dempsey’s recent contribution, in contrast, points to the importance of hierarchy and difference in the valuation of nonhuman animals under capitalism. Their framework identifies five orientations of human and nonhuman bodies in relation to capitalist value, which in turn provides a heuristic to explore how capitalist accumulation produces and depends on differentially oriented natures. Our contribution to these debates – and to the Collard and Dempsey framework – draws on our ongoing research in Eastern Canada where salmon aquaculture is a growing yet highly contested industry. We focus on two instances of multispecies hierarchy and difference in and around the salmon cage that are central to this form of ocean-based production. In focusing on multispecies relations, we build on Collard and Dempsey's framework in two main ways. First, we show how valuation and devaluation reflect competing but relational capitalist interests, which rely on and produce different natures refracted through the logic of the nature/culture divide: Atlantic salmon are valued as game fish, and as the key species for Canada's aquaculture sector. Second, we show how capital's valuation of one species, in our case farmed salmon, implicates the valuation of others, namely sea lice and lumpfish. Our case studies extend Collard and Dempsey's framework by demonstrating how capitalist differentiation produces violence through and outside of commodification in terms of multispecies difference and hierarchy; the lives and futures of wild and farmed salmon, lumpfish and sea lice are entangled, and reflect relational and changing orientations to capitalist value over time.

Trypsin Genes Are Regulated through the miRNA Bantam and Associated with Drug Sensitivity in the Sea Louse Caligus rogercresseyi

The role of trypsin genes in pharmacological sensitivity has been described in numerous arthropod species, including the sea louse Caligus rogercresseyi. This ectoparasite species is mainly controlled by xenobiotic drugs in Atlantic salmon farming. However, the post-transcriptional regulation of trypsin genes and the molecular components involved in drug response remain unclear. In particular, the miRNA bantam family has previously been associated with drug response in arthropods and is also found in C. rogercresseyi, showing a high diversity of isomiRs. This study aimed to uncover molecular interactions among trypsin genes and bantam miRNAs in the sea louse C. rogercresseyi in response to delousing drugs. Herein, putative mRNA/miRNA sequences were identified and localized in the C. rogercresseyi genome through genome mapping and blast analyses. Expression analyses were obtained from the mRNA transcriptome and small-RNA libraries from groups with differential sensitivity to three drugs used as anti-sea lice agents: azamethiphos, deltamethrin, and cypermethrin. The validation was conducted by qPCR analyses and luciferase assay of selected bantam and trypsin genes identified from in silico transcript prediction. A total of 60 trypsin genes were identified in the C. rogercresseyi genome, and 39 bantam miRNAs were differentially expressed in response to drug exposure. Notably, expression analyses and correlation among values obtained from trypsin and bantam revealed an opposite trend and potential binding sites with significant ΔG values. The luciferase assay showed a reduction of around 50% in the expression levels of the trypsin 2-like gene, which could imply that this gene is a potential target for bantam. The role of trypsin genes and bantam miRNAs in the pharmacological sensitivity of sea lice and the use of miRNAs as potential markers in these parasites are discussed in this study.

Farmed Salmon Show No Pathological Alterations When Exposed to Acoustic Treatment for Sea Lice Infestation

The use of bioacoustic methods to address sea lice infestation in salmonid farming is a promising innovative method but implies an exposure to sound that could affect the fish. An assessment of the effects of these techniques related to the salmon’s welfare is presented here. The fish were repeatedly exposed to 350 Hz and 500 Hz tones in three- to four-hour exposure sessions, reaching received sound pressure levels of 140 to 150 dB re 1 µPa2, with the goal of reaching total sound exposure levels above 190 dB re 1 µPa2 s. Gross pathology and histopathological analysis performed on exposed salmons’ organs did not reveal any lesions that could be associated to sound exposure. The analysis of their otoliths through electron microscopy imaging confirmed that the sound dose that was used to impair the lice had no effects on the fish auditory organs.

The impact of genetic relationship between training and validation populations on genomic prediction accuracy in Atlantic salmon

The potential of genomic selection to improve production traits has been widely demonstrated in many aquaculture species. Atlantic salmon breeding programmes typically consist of sibling testing schemes, where traits that cannot be measured on the selection candidates are measured on the candidates' siblings (such as disease resistance traits). While annual testing on close relatives is effective, it is expensive due to high genotyping and phenotyping costs. Therefore, accurate prediction of breeding values in distant relatives could significantly reduce the cost of genomic selection. The aims of this study were (i) to evaluate the impact of decreasing the genomic relationship between the training and validation populations on the accuracy of genomic prediction for two key target traits; body weight and resistance to sea lice; and (ii) to assess the interaction of genetic relationship with SNP density, a major determinant of genotyping costs. Phenotype and genotype data from two year classes of a commercial breeding population of Atlantic salmon were used. The accuracy of genomic predictions obtained within a year class was similar to that obtained combining the data from the two year classes for sea lice count (0.49 - 0.48) and body weight (0.63 - 0.61), but prediction accuracy was close to zero when the prediction was performed across year groups. Systematically reducing the relatedness between the training and validation populations within a year class resulted in decreasing accuracy of genomic prediction; when the training and validation populations were set up to contain no relatives with genomic relationships >0.3, the accuracies fell from 0.48 to 0.27 for sea lice count and from 0.63 to 0.29 for body weight. Lower relatedness between training and validation populations also tended to result in highly biased predictions. No clear interaction between decreasing SNP density and relatedness between training and validation population was found. These results confirm the importance of genetic relationships between training and selection candidate populations in salmon breeding programmes, and suggests that prediction across generations using existing approaches would severely compromise the efficacy of genomic selection.