BackgroundDependence on marine natural resources threatens the sustainability of Atlantic salmon aquaculture. In the present study, Atlantic salmon fed for 14 weeks with an experimental diet based on animal by-products and vegetable oil (ABP) exhibited reduced growth performance compared with others fed a fish meal/fish oil based experimental diet (MAR) and a plant protein/vegetable oil-based experimental diet (VEG). To characterize the molecular changes underlying the differences in growth performance, we conducted a 44 K microarray study of the liver transcriptome of the three dietary groups.ResultsThe microarray experiment identified 122 differentially expressed features (Rank Products, PFP < 10%). Based on their associated Gene Ontology terms, 46 probes were classified as metabolic and growth-relevant genes, 25 as immune-related, and 12 as related to oxidation-reduction processes. The microarray results were validated by qPCR analysis of 29 microarray-identified transcripts. Diets significantly modulated the transcription of genes involved in carbohydrate metabolism (gck and pfkfb4), cell growth and proliferation (sgk2 and htra1), apoptosis (gadd45b), lipid metabolism (fabp3, idi1, sqs), and immunity (igd, mx, ifit5, and mhcI). Hierarchical clustering and linear correlation analyses were performed to find gene expression patterns among the qPCR-analyzed transcripts, and connections between them and muscle and liver lipid composition. Overall, our results indicate that changes in the liver transcriptome and tissue lipid composition were driven by cholesterol synthesis up-regulation by ABP and VEG diets, and the lower carbohydrate intake in the ABP group. Two of the microarray-identified genes (sgk2 and htra1) might be key to explaining glucose metabolism regulation and the dietary-modulation of the immune system in fish. To evaluate the potential of these genes as predictive biomarkers, we subjected the qPCR data to a stepwise discriminant analysis. Three sets of no more than four genes were found to be able to predict, with high accuracy (67–94%), salmon growth and fatty acid composition.ConclusionsThis study provides new findings on the impact of terrestrial animal and plant products on the nutrition and health of farmed Atlantic salmon, and a new method based on gene biomarkers for potentially predicting desired phenotypes, which could help formulate superior feeds for the Atlantic salmon aquaculture industry.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5188-6) contains supplementary material, which is available to authorized users.

Due to limited fish meal and fish oil resources and their high costs for the aquaculture industry, it is necessary to find alternative sustainable sources of protein and lipids. Therefore, seven different diets were formulated with different levels of animal by-products, vegetable proteins, fish oil and rapeseed oil, to feed farmed Atlantic salmon, and their effects on growth performance, muscle lipid class, and fatty acid composition were examined. Protein sources included anchovy, poultry, feather, blood, corn, soy and wheat. Growth performance indicated that the diet with the lowest fish meal and fish oil content resulted in the lowest weight gain and final weight, followed by the diet containing the highest level of animal by-products. The lipid class analysis showed no statistical difference in the muscle total lipid content using different diets. However, significant statistical differences were observed among the main lipid classes; triacylglycerols, phospholipids, and sterols. The diet containing 1.4% omega-3 long-chain fatty acids resulted in the highest content of triacylglycerols and phospholipids. Diets containing medium and low levels of fish oil and fish meal, respectively, led to as high a level of ω3 fatty acids in muscle as when fish were fed diets with high levels of fish meal and fish oil. The results of this study suggest that feeding a diet containing low levels of fish meal and moderate levels of fish oil does not significantly affect ω3 fatty acid composition in muscle. Fish meal could be reduced to 5% without affecting growth as long as there was a minimum of 5% fish oil, and animal by-products did not exceed 26% of the diet.

Aquaculture is the fastest growing food production sector and is expected to provide over 60% of the world's seafood by 2030. Lipids represent the major energy contribution in aquaculture nutrition, and as such, reach high inclusion levels in energy–dense aquafeeds. Lipids are a prominently studied nutrient in aquaculture, since they supply energy and essential fatty acids and because of the unique abundance of the ω3 long‐chain polyunsaturated fatty acids that are found in fish. Lipids from fish are well known to have positive impacts on human health, and as such, the transfer of lipids from the diet to fish to consumer is of great importance. Therefore, the fats and oils that are supplied for the health, growth, and development of aquaculture fish must be of good quality and sourced sustainably for the future of aquaculture production. This article describes the role of fats and oils in aquafeeds. In order to understand how the fats and oils are utilized, this article reviews the lipid and fatty acid requirements, lipid digestibility, and lipid synthesis of aquaculture fish. It also describes the most common fats and oils that are used in aquafeed formulations, as well as novel, innovative lipid sources, and new methods of formulating fatty acids in aquafeeds. The different lipid and fatty acid compositions of these fat and oil sources in the diet can directly impact the nutritional and product quality of farmed fish. The practical consideration for using high levels of dietary lipid in aquafeeds is the feed quality, particularly considering lipid oxidation.

The simultaneous quantification of several transcripts via multiplex PCR can accelerate research in fish physiological responses to diet and enable the development of superior aquafeeds for farmed fish. We designed two multiplex PCR panels that included assays for 40 biomarker genes representing key aspects of fish physiology (growth, metabolism, oxidative stress, and inflammation) and 3 normalizer genes. We used both panels to assess the physiological effects of replacing fish meal and fish oil by terrestrial alternatives on Atlantic salmon smolts. In a 14-week trial, we tested three diets based on marine ingredients (MAR), animal by-products and vegetable oil (ABP), and plant protein and vegetable oil (VEG). Dietary treatments affected the expression of genes involved in hepatic glucose and lipid metabolism (e.g., srebp1, elovl2), cell redox status (e.g., txna, prdx1b), and inflammation (e.g., pgds, 5loxa). At the multivariate level, gene expression profiles were more divergent between fish fed the marine and terrestrial diets (MAR vs. ABP/VEG) than between the two terrestrial diets (ABP vs. VEG). Liver ARA was inversely related to glucose metabolism (gck)- and growth (igfbp-5b1, htra1b)-related biomarkers and hepatosomatic index. Liver DHA and EPA levels correlated negatively with elovl2, whereas ARA levels correlated positively with fadsd5. Lower hepatic EPA/ARA in ABP-fed fish correlated with the increased expression of biomarkers related to mitochondrial function (fabp3a), oxidative stress (txna, prdx1b), and inflammation (pgds, 5loxa). The analysis of hepatic biomarker gene expression via multiplex PCR revealed potential physiological impacts and nutrient-gene interactions in Atlantic salmon fed lower levels of marine-sourced nutrients.

Rivers and estuaries are important conduits and reactors for organic matter (OM). Despite the substantial export of terrestrial OM by rivers, only a small proportion of this material reaches the open ocean. One potentially important mechanism contributing to the removal of terrestrial dissolved OM (DOM) is flocculation; a process that transforms DOM into larger size fractions that can settle into sediment pools. Here we investigate the role of flocculation in adjacent boreal coastal systems over three consecutive seasons. Flocculation experiments, which include the artificial salting of freshwater DOM to mid (12 psu) and high salinity (25 psu), and a 1:1 mixture of freshwater DOM with their respective saline endmember, highlight a potentially important source of particulate carbon (PC) in boreal estuaries. Along with a 3.5% ± 1.0% removal of dissolved organic carbon (DOC) and 44% ± 16% dissolved iron (DFe), the potential for flocculation of these constituents significantly increased with increasing salinity from 12 to 25 psu. The particulate matter (PM) produced by salt‐induced flocculation was comparable to in situ PC concentrations (in situ PC = 27.5 μmol L−1 and flocculated PC = 15.0 μmol L−1) and stable carbon isotopic signatures (in situ PM = −28.8‰ and flocculated PM = −28.3‰). DFe:DOC and Sr were the only parameters that could significantly explain the degree of carbon and iron flocculation. This demonstrates the importance of DOC, DFe, and optical properties, and the predictive value of DFe:DOC for understanding DOM susceptibility to flocculation and its relevance and contribution to regional and global carbon budgets.

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Observed and predicted hydrological changes in C‐rich boreal ecosystems have the ability to change the transport trajectory of biogeochemical constituents from the land to ecologically, economically, and culturally important coastal systems. Yet, most of our current understanding of biogeochemical fluxes and cycling across salinity gradients stem from observations of large and urbanized riverine systems, which overlooks the numerically abundant smaller systems. In this study, we conducted a baseline assessment of the biogeochemical constituents across salinity gradients among two adjacent small systems in the boreal zone. Dissolved iron (DFe) and its ratio with dissolved organic carbon (DFe : DOC) were the most sensitive indicators for small catchment heterogeneity. These parameters were the best indicators of change among coastal systems across regional and seasonal scales. Our results also confirm consistencies in common optical measures (SUVA254 and S[275–295/350–400]) and DOC to nitrogen ratios that may adequately provide representation of biogeochemical composition on a regional scale. Simultaneous variation in biogeochemical parameters across particulate and dissolved pools during the summer‐to‐fall transition period indicate this as an important timeframe for targeted investigation of the linkages between biogeochemical parameters and coastal ecosystem functioning. By providing some key spatial and temporal constraints on biogeochemical fluxes among boreal river‐estuaries, our findings indicate that DFe and DFe : DOC ratios should be used to design research aimed at capturing regional and coastal ecosystem scale biogeochemical fluxes to inform Earth System Models.

(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. the diet with the lowest fish meal and fish oil content resulted in the lowest weight gain 28 and final weight, followed by the diet containing the highest level of animal by-products. 29The lipid class analysis showed no statistical difference in the muscle total lipid content 30 using different diets. However, significant statistical differences were observed among the 31 main lipid classes; triacylglycerols, phospholipids, and sterols. The diet containing 1.4% 32 omega-3 long-chain fatty acids resulted in the highest content of triacylglycerols and 33 phospholipids. Diets containing medium and low levels of fish oil and fish meal, 34 respectively, led to as high a level of ω3 fatty acids in muscle as when fish were fed diets 35 with high levels of fish meal and fish oil. The results of this study suggest that feeding a 36 diet containing low levels of fish meal and moderate levels of fish oil does not significantly 37 affect ω3 fatty acid composition in muscle. Fish meal could be reduced to 5% without 38 affecting growth as long as there was a minimum of 5% fish oil, and animal by-products 39 did not exceed 26% of the diet.