Experiment one revealed fishmeal (FM) replacement with soy protein concentrate (SPC) alone, and in combination with pea protein concentrate (PPC) and saponins (S) modulated the intestinal bacterial communities of D. labrax, increasing the presence of lactic acid bacteria. Intestinal histology revealed significantly reduced goblet cell’s (GC’s) in fish fed the SPC+S, epithelial microvilli densities (MD) in fish fed the SPC+PPC, SPC+PPC+S and SPC+S after two weeks feeding. Significant reductions in GC’s and intraepithelial leukocytes (IEL’s) in fish fed the SPC+S, and MD’s in fish fed the SPC+S and SPC+PPC+S after four weeks feeding, relative to fish fed the FM control. Furthermore, fish fed all plant based diets appeared to exhibit a loss of membrane integrity at the microvilli tips, most pronounced in fish fed the SPC+S diet. These results suggest a sub-acute enteritis response in the posterior intestine of D. labrax, which was deemed to be most pronounced in fish fed the SPC+S diets. Experiment two utilised the SPC+S diet as a sub-optimal basal diet to assess the potential of the probiotic Bacillus subtilis and the prebiotic Previda®, individually and in combination, in alleviating the enteritis-like effects induced by this diet, observed in the first experiment. Microbiological analyses revealed B. subtilis modulated the allochthonous bacterial communities. Fish fed the combination of B. subtilis and Previda® (synbiotic) diet exhibited a significantly increased intestinal perimeter ratio, compared to fish fed the basal. Significantly elevated GC’s in fish fed the probiotic and synbiotic treatments, and significantly elevated epithelial MD’s, and intestinal absorptive surface index in fish fed the probiotic diet was observed, relative to fed fish the basal. The loss of membrane integrity induced by the basal diet, was reduced in fish fed the probiotic, prebiotic and synbiotic diets. The intestinal gene expression of the pro-inflammatory cytokines IL-1β and TNFα was significantly up-regulated in fish fed all experimental diets, relative to fish fed the basal. The intestinal gene expression of HSP70, CASP3 and PCNA was significantly down-regulated in fish fed the probiotic, prebiotic and synbiotic relative to fish fed the basal. At the end of the experiment intestinal samples were exposed to one of four treatments [1. PBS (control), 2. B. subtilis, 3. Vibrio anguillarum and 4. B. subtilis + V. anguillarum], ex vivo, to determine if the feed additives could mitigate enteric pathogen damage. All feed additives revealed the potential to reduce the morphological damage caused by the pathogen. Experiment three assessed B. subtilis and the phytobiotic Next Enhance 150® on the growth and health of D. labrax. B. subtilis modulated the allochthonous bacterial communities and reduced the presence of some potential pathogens. The intestinal gene expression of HSP70, CASP3, PCNA and CAL was significantly down-regulation in fish fed the probiotic diet relative to fish fed the control. Significantly elevated IEL’s were observed in fish fed the probiotic and Next Enhance 150® diets relative to fish fed the control. Growth performance was remained unaffected. The present research demonstrates that dietary B. subtilis modulates the allochthonous bacterial communities, as well as, improving the intestinal morphology and localised immunity in European sea bass. Dietary Previda® and Next Enhance 150® were also observed to confer beneficial effects on the gut health of this species. No detrimental effects were observed as a consequence of any of the feed additives used in the present research.

Les apports de l’aquaculture représentent aujourd’hui la moitié des produits aquatiques destinés à la consommation humaine. La composition de l’aliment artificiel utilisé en élevage piscicole a fortement évolué ces 30 dernières années. Les produits d’origine végétale terrestre y ont progressivement remplacé les farines et les huiles de poisson lorsque les stocks de pêche minotière utilisés pour leur production se sont rapprochés de leur limite d’exploitation. Toutefois, l’usage exclusif de ces farines et huiles végétales conduit encore à la dégradation de la croissance et de la santé des salmonidés et des poissons marins. Dans le même temps, l’amélioration génétique en pisciculture a permis, depuis 1980, des gains importants sur les caractères de croissance, de santé et de qualité et dispose aujourd’hui de méthodes pour étudier les conséquences de cette profonde transition alimentaire sur les populations actuelles et futures issues des programmes de sélection. En privilégiant la comparaison entre un aliment composé de produits d’origine marine (M) et un aliment entièrement constitué de produits d’origine végétale terrestre (PB), nous avons étudié les voies d’amélioration génétique chez deux espèces majeures du secteur français : le bar européen (Dicentrarchus labrax) et la truite arc-en-ciel (Oncorhynchus mykiss). Dans ce contexte, l’objectif était en particulier d’estimer les héritabilités des caractères d’intérêt et l’importance des interactions génotype-aliment, qui sont à l’origine de reclassement des génotypes en fonction l’aliment utilisé.Les essais réalisés ont confirmés l’effet de la substitution totale sur la croissance et la composition lipidique chez les deux espèces et sur la survie chez le bar. Les héritabilités estimées des poissons nourris avec l’aliment PB pour le poids, la croissance et les paramètres de transformation technologique (rendement carcasse, viscères, tête, filet) sont hautes chez la truite (respectivement 0,69 ; 0,65 ; 0,21-0,58) et modérées chez le bar (respectivement 0,18 et 0,11). Pour ces caractères, les interactions génotype-aliment sont modérées et les corrélations génétiques estimées entre les aliments M et PB sont élevées chez la truite (respectivement 0,90 ; 0,92 ; 0,65-0,96) et chez le bar (respectivement 0,96 ; 0,64). Les gains génétique attendus sont plus élevés avec l’aliment PB qu’avec l’aliment M chez la truite tandis qu’ils sont plus faible chez le bar. La mesure de la réponse à la sélection pour une aptitude à grandir et à survivre en utilisant l’aliment PB a confirmé des gains élevés pour le poids (+35%), la survie (+15,1%) et la biomasse produite (+54,4%) sans impact sur les paramètres de transformation technologique (carcasse, viscères, tête, filet). Les essais réalisés ont confirmé que cette meilleure aptitude était liée à des modifications de l’activité du métabolisme lipidique mais n’ont pas permis de conclure à des liens avec l’ingéré et efficacité alimentaire.Les plus fortes mortalités et le plus faible poids des lots PB durant les jours qui suivent les premières prises alimentaires ainsi que les reclassements familiaux plus importants en début de cycle de vie indiquent que les stades précoces ont une place prépondérante dans l’utilisation de l’aliment d’origine végétale aux niveaux phénotypique et génétique et devront être approfondis.A la vue des résultats obtenus, il semble donc possible d’exploiter la grande plasticité de certaines espèces de poissons pour concevoir des programmes de sélection prenant en compte l’évolution des environnements de production. La limitation mondiale des ressources alimentaire confronte les élevages à des modifications rapides de l’aliment et l’amélioration génétique des cheptels peut aider à faciliter ces transitions alimentaires. / Nowadays, aquaculture contributes to half of the aquatic products intended for human consumption. The composition of aquafeeds strongly evolved in the past 30 years. Terrestrial plant-based products gradually replace fish meal and fish oil, as fish stocks used for their production reach their exploitation limit. However, the use of diets containing vegetable oils and meals only still lead to growth and health degradation in salmonids and marine fish.Besides, breeding programmes in fish farming allowed strong genetic progress, since 1980, on growth, health and quality traits. An important issue for fish breeders is now to understand the consequences of this deep dietary change on the current and future selected populations and to adapt breeding programs accordingly.Focusing on the comparison between two experimental diets, a diet containing marine products (M) and a diet containing only plant-based products, (PB), we investigated the possible impact of the dietary changes on the organization and the objectives of breeding programs in two major species of the French sector: the European sea bass (Dicentrarchus labrax) and the rainbow trout (Oncorhynchus mykiss). A key objective was to estimate the heritabilities of the main traits of economic interest and the importance of genotype by diet interactions, which may cause genotypes rerankings according to diet used. We also sought the potential origin of the variability for ability to use the PB diet and proposed scenarii for evolution of breeding programs.The trials confirmed that substitution of marine ingredients by vegetal ones decreased growth and lipid composition in both species, as well as survival in sea bass and, to a lesser extent in rainbow trout. The estimates of heritabilities for weight, growth and processing traits (carcass viscera, head and filet yields only measured on trout) when fish were fed with the PB diet were high in rainbow trout (respectively 0.69; 0.65; 0.21-0.58) and weak in sea bass (respectively 0.18 and 0.11). In trout and sea bass, these estimates were respectively higher and lower than those obtained when fish were fed the M diet. For these traits, genotype by diet interactions were moderate and the genetic correlations between the M and PB diets were variable in trout (respectively 0.67-0.90; 0.92; 0.65-0.96) and sea bass (respectively 0.51-0.96; 0.64) but could involve important family rerankings according to the period of survey. According to heritability estimates, expected genetic gains would be higher in trout for fish fed the PB diet than for fish fed the M diet when they would be weaker in sea bass. In trout, the measurement of the response to one generation of selection for the ability to grow and survive when fed the PB diet confirmed the results, and provided high genetic gains for body weight (+35%), survival rate (+15,1%) and produced biomass (+ 54,4%) without any impact on the processing traits (carcass, viscera, head, filet). We showed that this ability was associated to modifications in the lipid metabolism activities but could not establish links with feed intake or feed efficiency from our trials. Higher mortality rate and lower body weight in the PB batches during the first days following distribution of PB diet as well as stronger family rerankings in early steps of the survey indicate than the early stages play a key role in the use of plant-based diet at both phenotypic and genetic levels. Further insights dedicated to these particular stages are strongly needed.Based on present results, it seems possible to exploit the great plasticity of some fish species to conceive breeding programs taking into account a changing dietary environment. Facing the world limitation in food resources, genetic improvement of fish livestock can be a useful lever to facilitate dietary transitions.

Aquaculture is an essential developing sector for world food production however one of the major bottlenecks for the sustainability of the aquaculture industry is the ability to control fish reproduction in captivity and to produce high quality seeds. European sea bass is a one of most commercially important species for the European fish farming industry. If broodstock management under captivity is well established, problems remain in hatcheries where survival can be low and deformity prevalence high as well as in on growing sites where fish reach puberty early especially with skewed sex ratio towards males. Sea bass displays strong seasonality in its physiology and is therefore an excellent candidate for the study of the photo-neuroendocrine control of reproduction and growth. The overall aims of this thesis were to better understand the molecular and endocrine drivers that control the Brain-Pituitary-Gonad axis in repeat spawner sea bass, and expand our knowledge of sea bass light and temperature regulation of melatonin production. First, this PhD project investigated the seasonal expression of kisspeptin, GnRH and gonadotropin genes in relation to the gonadal development throughout a reproductive cycle in male repeat spawning sea bass (Chapter 3). A partial sequence for the receptor kissr4 was isolated and described showing similarity to all other teleost species sequences available to date. QPCR molecular assays were validated to mesure the expression of a suite of genes along the BPG axis including kisspeptin related genes (Kiss1 and Kiss2 and its receptor kissr4) over a full reproductive cycle (12 months) in adult male European sea bass. Brain Kisspeptin mRNA expression levels (kiss1, 2 and kissr4) showed clear seasonal profiles and correlated well to other BPG markers (GnRHs, fshβ and lhβ), supporting a possible involvement of kisspeptin genes in the seasonal control of reproduction in repeat spawning sea bass. Moreover, clear seasonal patterns were observed for expression of the genes encoding for pituitary mRNA expression of lhβ and fshβ, with a significant correlation between expression of both subunits and GSI and steroids levels. However, no clear seasonal profiles in brain GnRHs gene expression were observed with the exception to some peaks in GnRH1 and GnRH2. The second part of this PhD project investigated the potential direct effect of the two kisspeptin core peptides (kiss1 and kiss2) on the pituitary gonadotropin gene expression (Chapter 4). The aim of this work was to better understand the mechanism by which kisspeptin acts on the BPG axis. This was done by testing the kisspeptin decapeptide core sequences on the lhβ and fshβ transcript expression in primary culture of sea bass pituitary cells using QPCR technique. The findings, as a whole, provided evidence that kisspeptin can act directly on the pituitary gonadotroph cells and modulate fshß and lhß mRNA expression in sea bass although effects were limited and not uniform. Of note, kissr4 gene expression was also detected in the sea bass pituitary. The third part of this PhD project focused on the effects of environmental signals (photoperiod and temperature) on melatonin production (Chapter 5). Environmental manipulation is routinely used in the aquaculture industry with the purpose of enhancing growth and manipulating the timing of reproduction in seasonal fish species like sea bass. Melatonin, known as the light perception and time keeping hormone, has been suggested to play key roles in the synchronisation of most physiological functions in vertebrates, although the mechanisms by which melatonin controls reproduction, growth and behaviour are still not fully understood in fish. The studies performed aimed .to determine the synergistic effects of both temperature and photoperiod on the daily phase and amplitudinal changes in melatonin production through both in vivo and in vitro trials. The results confirmed the diel melatonin rhythm in sea bass as previously reported in many teleost species with “high at night” and “low at day” melatonin profiles. Temperature showed clear effects on the amplitude of the melatonin production under both in vivo and in vitro conditions for both long day and short day photoperiods. Furthermore, no endogenous melatonin production was found under constant darkness in both in vivo and in vitro conditions. These results suggested a lack of intrapineal (or located elsewhere such as retina and/or deep brain) oscillators in sea bass, contrasting with previous reports. These results further enhance our knowledge of light perception and circadian rhythmicity in sea bass, while the circadian system remains to be characterised in sea bass and teleosts as a whole. Overall, this doctoral work broadened our understanding on the photoneuroendocrine control of reproduction in a seasonal fish species, sea bass. New knowledge gained and tools developed from this work should help to develop/optimise husbandry techniques for the sea bass farming industry with the view to increase production and profitability and thus promoting the sustainable expansion of the sea bass aquaculture in Europe. It has also the potential to help the fishery sector in the modelling of wild sea bass populations.

Dans le contexte du changement global, la diminution de la disponibilité en oxygène (hypoxie) combinée à la hausse de la température sont deux phénomènes particulièrement présents dans les eaux côtières vers lesquelles les larves de poissons peuvent dériver à la fin de leur développement. Il est admis que les régulations mises en oeuvre par les organismes pour faire face à leur environnement au cours des premières étapes de leur vie peuvent avoir des conséquences sur leur trajectoire de vie ultérieure (plasticité développementale). Ainsi, l'objectif principal de cette thèse était d’évaluer si des conditions d'oxygénation (40% et 100% de saturation) combinées à des conditions thermiques (15 et 20 °C) au stade larvaire, pouvaient avoir des impacts durables sur la physiologie des futurs juvéniles de bar (Dicentrarchus labrax). Nos résultats ont révélé que les retards de croissance associés à la plus basse température et à l’hypoxie au stade larvaire induisent une croissance compensatrice. De plus, les analyses des réserves hépatiques en glycogène et en lipides ont révélé que le métabolisme des juvéniles pourrait être affecté par les conditions environnementales au stade larvaire. Par ailleurs, nos données indiquent que la capacité d'extraction de l'oxygène a été affectée chez des juvéniles en raison de déformations operculaires causées par l’exposition précoce à l'hypoxie. Enfin, l'exposition précoce à l'hypoxie induit une sur-expression à long terme de gènes de l'hémoglobine de juvéniles replacés en situation d’hypoxie. Globalement, nos résultats contribuent à faire avancer les connaissances sur la façon dont les poissons marins font face aux changements climatiques actuels. / In the context of global change, decrease in oxygen availability (hypoxia) combined with rising water temperature are especially prevalent in coastal regions, towards which marine fish larvae may drift at the end of their development. It is well admitted that the physiological regulations implemented by organisms to cope with their environment during the early life stages of life can cause profound consequences in their subsequent life-history trajectory (developmental plasticity). Therefore, the main objective of this thesis was to investigate whether ecologically relevant conditions of oxygenation (40% and 100% air saturation) combined with thermic conditions (15 and 20 °C), occurring at the last stages of larval development of European sea bass (Dicentrarchus labrax) larvae, could have long-lasting impacts on juvenile physiology. Our data showed that growth depression resulting from low temperature and hypoxic conditions at larval stage induced a subsequent compensatory growth. Moreover, our analyses of hepatic glycogen and lipid stores revealed that metabolic features of juvenile could be affected by early exposure to oxygen and temperature conditions. Furthermore, our data revealed that oxygen extraction capacity was affected due to opercular deformities caused by early exposure to hypoxia. Finally, when seabass juveniles, that have been exposed to hypoxia at larval stage, were under chronic hypoxic condition they show a long-term up-regulation of hemoglobin genes. Overall, our findings contribute to make predictions of how the marine fish communities could be altered by current climate change.