Maternal effects and phenotypic mismatch in hatchery-reared Atlantic salmon.

Phenotypic variation was previously thought to be the result of complex interactions between an individual's genotype and the environment in which it exists. It is, however, now evident that an individual's phenotype may also be shaped by the environmental variation experienced by the mother, i.e. maternal effects. Environmental maternal effects have the potential to generate rapid phenotypic change in a population and so may be particularly important for evolution at ecological time-scales. The general aim of this thesis was to examine how maternal effects may influence offspring fitness and life history traits in Atlantic salmon (Salmo salar L.1758). For this species, the early juvenile period is the most critical due to their complex life cycle. Offspring rely on maternal provisioning during the early stages of development for growth and survival. Several studies on Atlantic salmon have emphasised the benefits of developing from larger eggs, yet it is unclear how the effects of rearing environment influence early life development. The thesis therefore investigated the effects of variation in maternal provisioning and female rearing environment on the development and physiology of embryos, the behaviour of newly emerged fry and the survival of fry released into the wild. Also assessed were the phenotypic changes among juvenile salmon released into the wild compared to those retained in the hatchery. For this maternal provisioning was manipulated by varying the length of time mothers from the same genetic background were maintained in captivity (2 months, 14 months and 26 months). The results of this thesis demonstrate that both maternal provisioning and female rearing environment alter the development and behaviour of salmon fry, opercular beat rate (a proxy for metabolic rate) and yolk sac absorption, and ultimately survival in the wild. Hatchery-reared fry were found to be maladapted to the natural environment for a number of phenotypic traits which are known to impact survival and the longer fry are retained in the hatchery prior to release the more phenotypically mismatched to the natural environment they become. However, increased egg size brought about my retaining females in captivity improved survival

Addressing the welfare needs of farmed lumpfish: knowledge gaps, challenges and solutions

Lumpfish (Cyclopterus lumpus L.) are increasingly being used as cleaner fish to control parasitic sea lice, one of the most important threats to salmon farming. However, lumpfish cannot survive feeding solely on sea lice, and their mortality in salmon net pens can be high, which has welfare, ethical and economic implications. The industry is under increasing pressure to improve the welfare of lumpfish, but little guidance exists on how this can be achieved. We undertook a knowledge gap and prioritisa tion exercise using a Delphi approach with participants from the fish farming sector, animal welfare, academia and regulators to assess consensus on the main challenges and potential solutions for improving lumpfish welfare. Consensus among participants on the utility of 5 behavioural and 12 physical welfare indicators was high (87–89%), reliable (Cronbach's alpha = 0.79, 95CI = 0.69–0.92) and independent of participant background. Participants highlighted fin erosion and body damage as the most use ful and practical operational welfare indicators, and blood parameters and behav ioural indicators as the least practical. Species profiling revealed profound differences between Atlantic salmon and lumpfish in relation to behaviour, habitat preferences, nutritional needs and response to stress, suggesting that applying a common set of welfare standards to both species cohabiting in salmon net-pens may not work well for lumpfish. Our study offers 16 practical solutions for improving the welfare of lumpfish and illustrates the merits of the Delphi approach for achieving consensus among stakeholders on welfare needs, targeting research where is most needed and generating workable solutions.info:eu-repo/semantics/publishedVersio

Addressing the welfare needs of farmed lumpfish: knowledge gaps, challenges and solutions

Lumpfish (Cyclopterus lumpus L.) are increasingly being used as cleaner fish to control parasitic sea lice, one of most important threats to salmon farming. However, lumpfish cannot survive feeding solely on sea lice, and their mortality in salmon net-pens can be high, which has welfare, ethical and economic implications. The industry is under increasing pressure to improve the welfare of lumpfish, but little guidance exists on how this can be achieved. We undertook a knowledge gap and prioritization exercise using a Delphi approach with participants from the fish farming sector, animal welfare, academia, and regulators to assess consensus on the main challenges and potential solutions for improving lumpfish welfare. Consensus among participants on the utility of 5 behavioural and 12 physical welfare indicators was high (87-89%), reliable (Cronbach’s alpha = 0.79, 95CI = 0.69-0.92), and independent of participant background. Participants highlighted fin erosion and body damage as the most useful and practical operational welfare indicators, and blood parameters and behavioural indicators as the least practical. Species profiling revealed profound differences between Atlantic salmon and lumpfish in relation to behaviour, habitat preferences, nutritional needs and response to stress, suggesting that applying a common set of welfare standards to both species cohabiting in salmon net-pens may not work well for lumpfish. Our study offers 16 practical solutions for improving the welfare of lumpfish, and illustrates the merits of the Delphi approach for achieving consensus among stakeholders on welfare needs, targeting research where is most needed, and generating workable solutions.Additional authors: P.T.J. Deacon, B.T. Jennings, A. Deakin, A.I. Moore, D. Phillips, G. Bardera, M.F. Castanheira, M. Scolamacchia, N. Clarke, O. Parker, J. Avizienius, M. Johnstone & M. Pavlidi

Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity

The microbiome has a crucial influence on host phenotype, and is of broad interest to ecological and evolutionary research. Yet, the extent of variation that occurs in the microbiome within and between populations is unclear. We characterised the skin and gut microbiome of seven populations of juvenile Atlantic salmon (Salmo salar) inhabiting a diverse range of environments, including hatchery-reared and wild populations. We found shared skin OTUs across all populations and core gut microbiota for all wild fish, but the diversity and structure of both skin and gut microbial communities were distinct between populations. There was a marked difference between the gut microbiome of wild and captive fish. Hatchery-reared fish had lower intestinal microbial diversity, lacked core microbiota found in wild fish, and showed altered community structure and function. Captive fish skin and gut microbiomes were also less variable within populations, reflecting more uniform artificial rearing conditions. Surrounding water influenced the microbiome of the gut and, especially, the skin, but could not explain the degree of variation observed between populations. For both the gut and skin, we found that there was greater difference in microbial community structure between more genetically distinct fish populations, and also that population genetic diversity was positively correlated with microbiome diversity. However, diet is likely to be the major factor contributing to the large differences in gut microbiota between wild and captive fish. Our results highlight the scope of inter-population variation in the Atlantic salmon microbiome, and offer insights into the deterministic factors contributing to this

Data from: Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.

Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild born parrs’ gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, since the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs’ gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs’ microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery reared parrs

Comparative transcriptomics reveal conserved impacts of rearing density on immune response of two important aquaculture species

Infectious diseases represent an important barrier to sustainable aquaculture development. Rearing density can substantially impact fish productivity, health and welfare in aquaculture, including growth rates, behaviour and, crucially, immune activity. Given the current emphasis on aquaculture diversification, stress-related indicators broadly applicable across species are needed. Utilising an interspecific comparative transcriptomic (RNAseq) approach, we compared gill gene expression responses of Atlantic salmon (Salmo salar) and Nile tilapia (Oreochromis niloticus) to rearing density and Saprolegnia parasitica infection. Salmon reared at high-density showed increased expression of stress-related markers (e.g. c-fos and hsp70), and downregulation of innate immune genes. Upon pathogen challenge, only salmon reared at low density exhibited increased expression of inflammatory interleukins and lymphocyte-related genes. Tilapia immunity, in contrast, was impaired at low-density. Using overlapping gene ontology enrichment and gene ortholog analyses, we found that density-related stress similarly impacted salmon and tilapia in key immune pathways, altering the expression of genes vital to inflammatory and Th17 responses to pathogen challenge. Given the challenges posed by ectoparasites and gill diseases in fish farms, this study underscores the importance of optimal rearing densities for immunocompetence, particularly for mucosal immunity. Our comparative transcriptomics analyses identified density stress impacted immune markers common across different fish taxa, providing key molecular targets with potential for monitoring and enhancing aquaculture resilience in a wide range of farmed species