University of Tasmania
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Proteomic and phenotypic approaches to assess nutritional physiology in Atlantic salmon

posted on 2023-05-27, 11:03 authored by Nuez-Ortin, WG
Atlantic salmon aquaculture increasingly faces global sustainability and environmental challenges that influence fish growth, nutritional value of the final product and production efficiency. Proteomics has established itself as an exploratory approach to understand the impact of changes in environmental factors and to production strategies at a detailed biological level. This thesis aims to examine the use of label-free shotgun proteomics as a method to further our understanding of current and important key aspects of Atlantic salmon aquaculture production: triploidy, fish oil replacement and heat stress. Understanding diet- and environmentally-induced physiological changes in fish larvae is a major goal for the aquaculture industry. The application of proteomics to study larval fish is challenging due to the large dynamic range of protein expression in such complex biological matrix. Using sequential protein extraction to reduce sample complexity achieved proteome coverage of 40% greater than a conventional direct extraction method. Proteins and functional categories related to mitochondrial function, oxidative phosphorylation and antioxidant defense were particularly enriched, providing a platform for a better understanding of physiological changes. A considerable knowledge gap exists regarding the physiology of triploid fish. A multi-tissue (whole fish, muscle and liver) and time-series proteomics sampling-approach was combined with fatty acid analysis to explore triploid-specific physiological and phenotypic traits of freshwater Atlantic salmon under optimal growing conditions. The very high level of similarity between the triploid and diploid fish at the proteome level was paralleled by subtle differences in growth and body composition. This is the first proteome characterization of freshwater triploid Atlantic salmon and supports the idea of physiological similarity between ploidies under optimal growing conditions. The future use of novel docosahexaenoic acid (DHA)-enriched Camelina oil emerges as the most efficient and long-term strategy to reduce fish oil use in aquafeeds while improving the current nutritional value of salmon products for consumers. The formulation of an oil blend with similar fatty acid profile to DHA-enriched Camelina oil was combined with liver proteomics to understand tissue fatty acid deposition and the consequent dietary induced metabolic changes in Atlantic salmon smolt. This study demonstrated the suitability of this novel DHA-enriched oil to improve the fillet content of omega-3 long-chain (‚Äöv¢‚Ä¢C20) polyunsaturated fatty acids (n-3 LC-PUFA) obtained with a current commercial blend oil. The liver proteome reflected lipid peroxidation-induced oxidative stress and the subsequent activation of the antioxidant and detoxification response, drawing attention to the need of additional antioxidant supplementation if DHA-enriched Camelina oil is used at high inclusion rates. Heat stress causes concerns regarding negative effects on performance and health of fish. Liver proteomics was used to identify the underpinning mechanisms of adaptation to chronic elevated temperature (21¬¨‚àûC) in pre-harvest Atlantic salmon. The induction of oxidative stress was paralleled by the suppression of the protein turnover rates, with the latter and an increased dependence on amino acid catabolism as the main mechanisms to balance for the increased energy demand. This study corroborates candidate biomarkers of thermal stress and refines our understanding towards the development of salmon feeds for summer conditions. In conclusion, the studies presented in this thesis advance our understanding of some of the key factors pertinent to Atlantic salmon farming globally, that are fundamental to growth and production efficiency, nutritional value and industry sustainability. Identification of molecular mechanisms and stressors in parallel with phenotypic changes underlines the potential of proteomics to further advance animal production generally and for aquaculture specifically, and provide focus for further targeted studies towards the development of specific nutritional and husbandry strategies. This work supports the current industry standards to produce high quality triploid smolt and suggests revision of the requirements of antioxidant, amino acid and other supplements in Atlantic salmon under the present sustainability and environmental challenges.


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Copyright 2016 the author Chapter 2 appears to be the equivalent of the pre-peer reviewed version of the following article: Nuez-Ortin, W. G., Carter, C. G., Nichols, P. D., Wilson. R., 2016. Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon (Salmo salar), Proteomics, 16(14), 2043-2047, which has been published in final form at This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving Chapter 3 appears to be the equivalent of a pre-print version of the following article: Nuez-Ortin, W. G., Carter, C. G., Wilson, R., Cooke, I. R., Amoroso, G. and Cobcroft, J. M., Nichols, P. D., 2016. Triploid Atlantic salmon (Salmo salar) shows similar performance, fatty acid composition and proteome response to diploids during early freshwater rearing, Comparative biochemistry and physiology, Part D, Genomics and proteomics, 22, 67-77 Chapter 4 appears to be the equivalent of a post-print version of the following article: Nuez-Ortin, W. G., Carter, C. G., Wilson. R., Cooke, I., Nichols, P. D., 2016. Preliminary validation of a high docosahexaenoic acid (DHA) and alpha-linolenic acid (ALA) dietary oil blend: tissue fatty acid composition and liver proteome response in Atlantic salmon (Salmo salar) smolts. PLos One 11(8): e0161513.

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