Fish are a major source of protein and omega-3 fatty acids. With the decline in fisheries worldwide, fish farming has increased to fill the gap and currently supplies around half of all fish consumed. Production must continue to increase in order to supply the increasing human population. The Atlantic salmon farming industry has been a major success story in Scotland, the third largest producer of Atlantic salmon globally, and is a major employer in rural areas. The sustainability of the aquaculture industry relies on good management of fish health and effective control of diseases. Within Scottish salmon farming, control of sea lice and improvement of gill health are currently the two most important health issues that the sector faces. Gill health impacts on the performance of fish at sea, and the need for expensive and often poorly efficacious therapeutic treatments. Lack of information of host (salmon) responses in gills in different disease states has been highlighted at several recent industry-led workshops in Scotland. Therefore this application proposes to address this issue by undertaking an in-depth study of the genes expressed in gills following exposure to a major gill parasite that causes amoebic gill disease (AGD), using archived samples from a past study. We will determine whether the gill, as a multifunctional organ responsible for oxygen uptake, osmoregulation, as well as defence at a major point of entry for pathogens, has a limited scope to react to pathogens in fish. We will focus on elucidating the wound healing pathways activated and the growth factors potentially released that cause tissue remodelling, since many gill diseases cause similar pathologies, in terms of lamellar fusion and epithelial cell hyperplasia. The data from this initial study will also be used to identify candidate biomarkers relevant for gill health, to be used for further study Next we will undertake qPCR analysis of the biomarkers in a variety of gill disease states. Gill samples from farmed fish will be collected during the late summer/autumn of 2017/18 by our collaborators, when gill disease is most prevalent. Initially the gill samples will be screened for pathogen presence to confirm the species causing the pathology and whether single or co-infections are involved. The biomarker analysis will reveal if common pathways are seen in different disease states, allowing the potential to alter these pathways to improve gill health against multiple diseases. Lastly, we will try to modulate the gill responses using different immunomodulators to establish if this approach can improve gill health/ disease protection. We will focus on administration of a 4 molecules that we know are potent inducers of pro-inflammatory pathways or anti-viral defences. They will include flagellin, poly I:C and two cytokines (IL-1beta and IFN-gamma, from a related salmonid the rainbow trout) that are available in our lab as recombinant protein ready for use, or can be purchased (poly I:C). Following administration we will sample gill tissue over a time course and examine the impact on the biomarkers identified earlier in the programme, as well as on known antimicrobial and anti-viral pathways. The best modulator of gill responses will be trialled on a salmon site by our industrial collaborator to assess the impact on gill health.

Fish are an important component of a healthy human diet providing high quality protein, key minerals and vitamins, and are an almost unique source of omega-3 long-chain polyunsaturated fatty acids (LC-PUFA) - EPA and DHA. Increased dietary intake by humans of these omega-3 fatty acids are associated with beneficial health effects, including reducing incidence and severity of inflammatory and pathological conditions including cardiovascular, neurological and developmental diseases. However, all marine fisheries are fully exploited and, since 2015, more than half of all fish and seafood is now supplied by aquaculture. Paradoxically, farmed fish, such as salmon, are themselves reliant on dietary supply of the LC-PUFA. However, there are finite and limited supplies of the marine resources such as fishmeal (FM) and fish oil (FO) that supply these nutrients. Alternative, more sustainable feeds have been developed over the past decade with much of the FM and FO now being replaced by plant proteins and oils. The level of replacement has now reached a critical point where it is having potentially detrimental effects on fish growth, feed efficiency and, importantly, fish health and robustness. Therefore, the key aim of the present research will be to refine our understanding of the needs for these nutrients by Atlantic salmon and thereby refine our recommendations on the need for LC-PUFA in the diets of these animals. Requirements by salmon have been estimated at ranging somewhere between 1.0% and 1.5% of diet. Given that global salmon farming presently uses about one third of global fish oil production any upward revision of those requirements may cause some significant constraint issues with supplies. Recently, studies undertaken in Norway have suggested that, under challenging environmental conditions, the requirements for LC-PUFA by Atlantic salmon are elevated to about 1.7%. However, there are various flaws with this study including a lack of statistical robustness, formulation covariates, and different nutritional backgrounds of the stock used in the study. Additionally, the use of the term "challenging environmental conditions", wasn't qualified in terms of specific environmental variables but rather a collective of various conditions. Because of that Norwegian study, there is now a perception across the industry that there is a need for higher omega-3 LC-PUFA in the diets of salmon under sea-cage conditions than previously thought, which adds considerably to production cost and undermines the sustainability of modern feeds. Therefore, the present project proposes to re-assess this link between environmental challenge and omega- 3 requirements in a more robust and structured manner, as well as assessing the implications of proto-nutrition on subsequent nutritional responses and whether this prior nutrition link can be used as a means of reducing subsequent demands by fish later in life. The studies proposed in this project include increased statistical robustness, combined with a more carefully structured experimental approach with a clear definition of the challenging environmental conditions as a decline in water oxygenation (usually the key environmental challenge in sea-cages conditions), which will be used to provide robust quantitative data on this issue. The project will also aim to separate oxygenation issues from feed intake issues, as typically fish respond to low oxygen levels by reducing appetite, which is a further confounding factor with how oxygen affects nutrition. The proposal is timely and highly relevant as it responds to an important industrial need with cutting edge research. This research will have clear deliverables to improve the utilisation of limiting marine resources in the use of modern feeds in aquaculture. In doing so it will help enhance production and feed efficiency, while maintaining the health and nutritional quality of farmed fish, delivering greater sustainability and food security.

Production of the global salmonid aquaculture industry now exceeds 2.4 megatons per annum. Major European producers expect to expand their outputs between 30-50% over the next five years. Ambitions for expansion on this scale create major concerns around fish welfare, ecological impact and the sustainability of salmon feed components. Nutrition lies at the heart of the issue. In the wild, Atlantic salmon are specialized carnivores. In aquaculture, in a move away from the unsustainable use of wild fish protein and oil, proteins of plant origin now constitute the majority (>60%) of their diet. Associated digestive abnormalities are common. In addition, plant-based diets may affect the rate at which nutrients are absorbed and the associated growth rate of salmon, which determines how quickly they grow in marine cages. Rapid marine growth is desirable since it permits more extensive fallowing of coastal aquaculture sites, which reduces the impact of farmed fish on the marine environment (pathogen transfer, nutrient pollution). Finally, while wild fish protein can be replaced by plant protein in salmon diets, oils cannot. Key omega-3 fatty acids must be sourced from the marine environment; a significant burden on wild fisheries. Ensuring the efficient assimilation of fatty acid components from salmonid diets is of paramount importance to safeguard the sustainable exploitation of marine resources. Salmon energetic phenotypes are composites of several interlinked traits: metabolic rate, body fat content, growth, energy harvest from food, energy economy in times of starvation. These traits underpin concerns around salmon nutrition. Significant energetic variation exists in both wild and farmed salmon with multiple possible drivers - both genetic and environmental. Importantly a wealth of new data indicates a role for intestinal microbiota - the bacteria that live in the guts of all vertebrates - in determining host energy metabolism. Understanding how gut bacteria influence Atlantic salmon energetics is thus fundamental to understanding their role in nutrition. This is the principal aim of this project. To achieve this we will establish the influence of gut bacteria on the energetics of salmon living in salt and freshwater, in both wild and aquaculture settings. First, in a unique experimental river system established in Burrishoole, Mayo (Marine Institute/University College Cork, ROI) we will track introduced juvenile salmon through their freshwater lifecycle, measuring both metabolic and gut microbiome variation. This 'wild' cohort will include wild and released farmed fish to establish whether differences between gut microbiota contribute to the poor performance of farmed juveniles in the wild. Secondly, we will undertake parallel freshwater experiments in simulated aquaculture conditions in the laboratory at the University of Glasgow (UoG),UK. Finally, in association with Marine Harvest, we will carry out corresponding experiments on saltwater phase pre-adult salmon in Norway. Alongside experiments with live fish, we propose to harness bioengineering expertise at the School of Engineering, UoG and biotechnological expertise via industry partner Alltech to build an artificial salmon gut system. Via the transfer and maintenance of gut bacteria from metabolically different fish from farmed and wild settings into our gut model we aim to establish how bacterial fermentation underpins differences in energy harvest from feed. Once these 'artificial' bacterial communities are established, a final exploratory phase of the project will involve their transplantation into laboratory reared juvenile salmon to evaluate their potential impact on host metabolism. Understanding how salmon gut bacteria change energetic phenotypes will open new avenues to improve fish health, nutrition and productivity. A model Atlantic salmon gut in a world class UK bio-engineering laboratory puts in place an invaluable tool for salmon aquaculture in the UK