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This thesis investigated life history characteristics in anadromous brown trout (Salmo trutta L.) populations inhabiting small coastal streams in the Orkney Islands, Scotland. The main findings were as follows. 1) A total of 36 separate brown trout populations were identified with evidence of anadromy detected in 23. 2) Significant variation in freshwater growth rate occurred even between closely neighbouring populations. 3) Mature resident trout were predominantly male. Their incidence and size between populations was directly related to stream size. 4) Smolt size also varied directly with stream size although age reflected growth rates in each population. Smolts were smaller and younger on average compared to other Scottish populations. 5) Smolts represented both the fastest and slowest growing members in each population studied. Resident mature males exhibited an intermediate growth rate. 6) Some trout de-smolted one year but survived and re-smolted the next year. 7) B-growth in smolts occurred in freshwater and resulted in a significant growth increase between the end of winter and seawater entry. A strong inverse relationship was apparent between individual size at the end of winter and B-growth expression. Information was presented to rekindle the discussion on the presence of a threshold size for seaward migration among anadromous trout.

Spironucleus is an opportunistic protozoan parasite capable of causing devastating losses in the production of both ornamental and food fish. Control of infection outbreaks is problematic due to restrictions on the use of chemotherapeutics and rapid parasite transmission amongst fish. This PhD investigated the life cycle, biochemistry and chemotherapy of Spironucleus vortens. Direct transmission of S. vortens was found to be facilitated by the trophozoite form, information which may be applied in aquaculture to prevent infection outbreaks. No S. vortens cysts were observed in vitro or in vivo and trophozoites were able to survive for prolonged periods in the faeces of angelfish. This novel finding facilitated development of a non-invasive method to quantify the degree of intestinal colonization in the host, which was then applied to determine the efficacy of new and existing chemotherapeutics against S. vortens in vivo. Garlic-derived compounds were shown to be realistic alternatives to the current drug of choice, metronidazole, in the treatment of Spironucleosis in fish. Synergy between metronidazole and the garlic-derived compound, ajoene, was also observed in vitro and in vivo. The mode of action of metronidazole and garlic-derivatives involved disruption of S. vortens intracellular redox balance, a pivotal cellular process which ensures normal cellular function and survival. Further biochemical investigations into the antioxidant defence system (consisting of glutathione, thioredoxin and superoxide dismutase) as well as the carbohydrate and amino acid metabolism of S. vortens provided greater understanding of the success of this organism as a parasite. This is reflected in its ability to withstand fluctuations in O2 and nutrition during key pathogenic stages of its life cycle, including extra-intestinal systemic infection and transmission to a new host.

A checklist of parasites of freshwater fish in the UK is an important source of information concerning hosts and their distribution for all aspects of scientific research. An interactive, electronic, web-based databse, Aquatic Parasite Information has been designed, incorporating all freshwater and brackish species of fish, parasites, taxonomy, synonyms, authors and associated hosts, together with records for their distribution. One of the key features of Aquatic Parasite Information is this checklist can be updated. Interrogation of Aquatic Parastie Information has revealed that some parasites of freshwater and brackish species of fish, such as the unicellular groups or those metzoans that are difficult to identify using morphological characters, are under reported. Aquatic Parasite Information identified the monogenean family Dactylogyridae and the cestodes infecting UK freshwater fish as under-represented groups, owing to the difficulties identifying them morphologically. Both the Dactylogyridae and cestodes have implications for pathology, outbreaks of disease and morbidity in freshwater fish in the UK, therefore accurate identification is critical. Studies were undertaken using both standard morphological techniques of histology and molecular techniques to identify dactylogyrid species and tapeworms commonly found parasitizing fish in the UK. Morphological studies demonstrated that histological processes could lead to distortion of the specimins and permanent mounting may affect the orientation which may obscure vital characteristics. Moleculr techniques were successfully employed using ITS1 for the Dactylogyridae and cox1 and r28s for the cestodes, to demonstrate genetic variability for the interspecific identification of species. Histology, scanning electron microscopy and molecular techniques have also identified an Atractolytocestus sp. tapeworm, parasitizing carp in the UK, as a potentially new species. Analysis of parasite records extracted from Aquatic Parasite Information has implicated freshwater fishery management policies as impacting on the dissemination and distribution of parasites, resulting in the spread of some species and decline of others.

Infectious disease in aquaculture is omnipresent, but traditional treatments used against the causative agents often have broad anti-parasitic properties, are not 100 % efficacious, are toxic to humans, fish and the environment, and successful application is challenging. Hence, integrated disease management that combines an understanding of parasite life history and host welfare with treatment is highly recommended. This thesis examined the life history characteristics of a ubiquitous genus of fish ectoparasites, Gyrodactylus species, and tested the efficacy of botanical treatments against gyrodactylids using the guppy (Poecilia reticulata) infected by G. turnbulli or G. bullatarudis as model, with the aim to work towards an integrated management plan for gyrodactylosis in the ornamental fish industry and the hobbyist market. The experiments conducted have shown that (1) gyrodactylids engage in sexual reproduction and on a population level show hybrid fitness and/or inter-strain competition when diverged genotypes are recombined; (2) parasite transmission is mainly driven by direct contact with potential hosts and on dead fish or after detachment gyrodactylids have a window of opportunity to re-attach of over 20 h; (3) extreme habitats provide guppies with a refuge from microbial and gyrodactylid infections in natural populations; (4) anti-parasitic treatment efficacy may be species specific using traditional methods; and (5) salt, garlic, cajuput oil and a combination treatment of the two commercially available treatments Melafix® and Pimafix® are efficacious alternatives for broad anti-parasitic aquarium treatments against gyrodactylids. Due to their efficient reproduction, gyrodactylids are unlikely to be eradicated, as just a single, pregnant worm can trigger a new disease epidemic. However, combining the knowledge on pathogen life history characteristics and host-parasite interactions with effective treatment application will reduce evolutionary pressures on the pathogen and slow its virulence evolution. Overall, this increases the time available for treatment efficacies to be maintained in a manner which corresponds with new drugs being developed as treatment resistance arises.

Fish diseases are the most important challenge that is facing the development of the aquaculture industry. Recently, there has been substantial interest to control fish diseases through the use of immunomodulators, such as β-glucans that activate a range of immune parameters. These carbohydrates are extracted from different sources and thus vary in their effectiveness. To develop a new biomaterial, with improved therapeutic and biological activities, β-glucans were modified by sulphation, which is a final chemical modification process to obtain derivatives of sulphated polysaccharide. In vitro experiments were used to establish the effect of different glucans and modified carbohydrates from animal and plant sources on the cytotoxicity and respiratory burst activity of carp pronephric cells and carp leukocytes cell lines (CLC). Dose response and administration time of glucans were examined using nitroblue tetrazolium (NBT) and MTT tetrazolium assays in CLCs. After screening 75 modified carbohydrates; only 9 were selected for their positive dose responses. The cellulose drive carbohydrate, sulphated tylose (CHO 1), induced greater respiratory burst activity in both cell types. The reproducibility of the sulphation process was established using a range of biological parameters, and analysing CHO 1 structure using FTIR and NMR analysis. Carp immune responses were determined after injection with CHO 1 alone or as an adjuvant in vaccines against Aeromonas hydrophila. The CHO1 proved to be an effective immune adjuvant in fish, enhancing and modulating a range of innate and adaptive immune response including: serum lysozyme and complement activity, leukocytes numbers and the expression of immune-related genes in carp organs e.g. cytokines (IL1β, IFNγ), complement component3 and lysozyme, as well the antibody titre against Aeromonas hydrophila was significantly improved. The potential of using CHO 1 and producing synthetic carbohydrates with identified structures maximise their role as adjuvants for vaccine or immunostimulant in anti-infective therapies has been established.

Fish are in contact with microbiota from the moment of hatching. Exterior organs, i.e. skin, gills and intestinal system, are colonised by commensal bacteria populations and a symbiotic relationship is formed. The fish provides a niche and nutrients for the bacteria which stimulate development of the immune response, act as an additional barrier against invading pathogens and, within the gut, aid in digestion. β-glucans are used within aquaculture as a means of improving fish health and can be applied in various forms, e.g. via diet or injection. Whilst the application of β-glucan is performed to modulate a fish’s immune system, it has also been shown to affect the gut microbiota population at concentrations above 1% w/w within the diet which is particularly important to consider when applied orally. The effect of the commercially available β-glucan MacroGard® upon the gut of common carp (Cyprinus carpio) is studied after oral application and injection. Whilst feeding with MacroGard® at 0.1% w/w within the diet does not influence the gut bacteria nor expression of bactericidal innate immune genes, injection (2mg kg-1 and 5mg kg-1) resulted in a 90% reduction in bacteria numbers in the gut after 24 hours. Injection of MacroGard® did not significantly alter the expression of CRP, iNOS, bf/C2, IL-1β, ApoA1, HAMP1, LEAP2 and Muc2 within the gut however MSS1, a synthesised β-glucan, significantly increased the gene expression of iNOS, CRP and Muc2. 0.1% MacroGard® in the diet was, however, capable of influencing bacterial species diversity when injection was also performed. This revealed a high proportion of Alphaproteobacteria, which are typically associated with plants rather than gut systems, and corresponded with a reduction in potential pathogenic bacteria. This showed combining injection and oral application of MacroGard® together is capable of influencing the gut microbiota population within a 2 week period.

The aquaculture of Atlantic salmon is a fast-growing industry that has drastically increased over the last decades. Traditionally, diets for Atlantic salmon contained wild sources fishmeal and fish oil but alternatives from plants are increasingly popular substitutes. Although fish do perform well on plant rich diets in terms of growth, carnivorous fish have not evolved to cope with many anti-nutritional factors and other plant derived chemicals. In recent years the importance of intestinal microbes to the health of humans has been established by profiling the microbiota using 16S rRNA as phylogenetic marker in highthroughput sequencing studies and more recently metagenomics profiling. To date, there is sparse information on the teleost intestinal microbiota and the relationship between the microbiota and intestinal health and function. To determine baselines of “healthy” gut microbiota, the gut microbial profiles of fish from freshwater facilities and seawater facilities were analysed. Shared core microbiota were identified, suggesting that certain microbes are actively maintained by the host to fulfil minimum functionality in the gut. Salinity of the environment was identified as important determining factor for the composition of the microbiota. Furthermore, it was found that exposure to plant-based diets including faba bean protein isolates (BPI) induced enteritis in fish fed and resulted in changes of the host transcriptomics including processes related to solute transport, metabolism, tissue integrity and inflammation. The gut microbiota of the fish fed BPI was also found significantly altered and functional analysis suggest an increased genetic potential for sporulation/germination and isoflavonoid biosynthesis. Microbes identified as uniquely present and absent in the fish showing high levels of enteritis across diets could be used as future screening targets to identify onset of enteritis in fish without external signs of sickness.

Growth and immunity are essential physiological functions that are each energetically costly. Thus, energetic allocation into these systems must be appropriately balanced throughout life. Such 'tradeoffs' require molecular-level cross talk between growth and immunity. Limited data suggests that the growth hormone (GH) – insulin-like growth factor (IGF) axis, a key pathway regulating vertebrate growth, also has a role in immune function. Here I exploit salmonid fishes to characterise the regulation of GH-IGF axis genes under multiple experimental contexts where growth and immunity were being traded-off. Specifically, I examined the transcriptional response of the GH-IGF axis to in vivo immune-stimulation at different stages of ontogeny, considering several tissue contexts (i.e. whole fish, immune tissues, and skeletal muscle) and animals with distinct growth rates driven by GH-overexpression. To better contextualise the data, I established the regulation of key gene markers for muscle growth and immune status. Further, I considered gene duplicates retained from whole-genome duplication events in salmonid evolutionary history, exploiting new genomic resources for gene characterisation (e.g. novel IGF-IR paralogues). Four major conclusions arose from my studies. First, up-regulation of IGFBP-1A1 and IGFBP-6A2 (known IGF inhibitors), following disease challenge, suggests that IGF signalling is repressed during infection, promoting energetic reallocation towards immunity. Second, the combined regulation of multiple IGF system genes in immune tissues suggests that while IGF signalling is repressed during infection, IGFBP-6A2 may directly stimulate immune tissues, likely via IGF-independent mechanisms. Third, coregulation of IGFBP-1A1 and IGFBP-6A2 with immune markers indicates direct regulation of the IGF system by conserved cytokine pathways. Finally, an altered skeletal muscle response to immune-stimulation suggests that modulation of GH-IGF axis regulation by GH-overexpression results in compromised fish health. Overall, these findings have broad implications for aquaculture, where fast growth and immunocompetence are traded-off, while improving our basic understanding of fish growth and immunity.