Interactions between parasite, host and host-associated microbiota are increasingly understood as important determinants of disease progression and morbidity. Salmon lice, including the parasitic copepod Lepeophtheirus salmonis and related species, are perhaps the most important problem facing Atlantic Salmon aquaculture after feed sustainability. Salmon lice parasitize the surface of the fish, feeding off mucus, scales and underlying tissue. Secondary bacterial infections are a major source of associated morbidity. In this study we tracked the diversity and composition of Salmo salar skin surface microbiota throughout a complete L. salmonis infection cycle among 800 post-smolts as compared to healthy controls. Among infected fish we observed a significant reduction in microbial richness (Chao1, P = 0.0136), raised diversity (Shannon, P < 7.86e-06) as well as highly significant destabilisation of microbial community composition (Pairwise Unifrac, beta-diversity, P < 1.86e-05; P = 0.0132) by comparison to controls. While undetectable on an individual level, network analysis of microbial taxa on infected fish revealed the association of multiple pathogenic genera (Vibrio, Flavobacterium, Tenacibaculum, Pseudomonas) with high louse burdens. We discuss our findings in the context of ecological theory and colonisation resistance, in addition to the role microbiota in driving primary and secondary pathology in the host.

Consumption of salmon, wild or farmed, has been encouraged by many scientists and by national and international health organizations due to the potential health benefits associated with their high contents of omega-3 (n-3) highly unsaturated fatty acids (n-3 HUFAs). In 2004, there was increased public concern regarding the safety of farmed Atlantic salmon following the publication of several studies that indicated higher levels of organohalogens in their flesh relative to those noted in the flesh of wild Pacific salmon. Farmed salmon obtain most of these contaminants from the consumption of marine fish oil (MFO) present in salmon feed. In both a laboratory feeding trial and an on-farm field study, partial replacement of MFO in aquaculture feeds with economical and abundant lipids of terrestrial origin resulted in farmed Atlantic salmon with reduced flesh polychlorinated biphenyl and polychlorinated dibenzodioxin and furan concentrations. Flesh levels of n-3 HUFAs (g/(100 g serving)) were lower in farmed Atlantic salmon fed diets with alternative lipids relative to farmed salmon fed more traditional MFO-based diets. However, the former salmon were found to have higher flesh levels of n-3 HUFAs and also similar or lower flesh levels of organic contaminants than some species of market-size wild Pacific salmon. These findings showthat consumption of either farmed Atlantic salmon or wild Pacific salmon can meet recommended weekly n-3 HUFA levels with minimal concurrent intake of flesh organohalogens.

Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.

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The sea louse, Lepeophtheirus salmonis, is parasitic to salmonid species in the Northern Hemisphere and has become a widespread biological and economic problem for the salmon farming industry. A better understanding is needed of their spatial distribution and early life history to disrupt the life cycle of the sea louse. In this study, sea lice larval densities within salmon farms, between salmon farms and reference sites, and at various depths were quantified using both plankton pumps and plankton nets. Farm sites exhibited significantly higher densities than reference sites; however, these densities dropped an order of magnitude at a distance of 100 m from the cages. The majority of the larvae captured in the study were nauplii (93%), and densities ranged from 0 to 10 larvae/m . Free-swimming sea lice larvae were found to exhibit a diel cycle where nauplii larvae were in deeper waters (10-17 m) during the day and in surface waters (1-6 m) during the night. The results of this study suggest that the early life-history stages of sea lice originate from and may remain close to active salmon farms, creating a self-sustaining population.