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International audience

The Moulin des Princes control station was commissioned on the Scorff in May 1994 in order to study the dynamics of migratory fish, including Atlantic salmon. These 28 years of trapping now make it possible to have long time series, acquired at different life stages of the species concerned. This report reviews the activities of the Scorff Observatory for the year 2021., La station de contrôle du Moulin des Princes a été mise en service sur le Scorff en mai 1994 afin d’étudier la dynamique des poissons migrateurs, notamment du saumon atlantique. Ces 28 années de piégeage permettent aujourd’hui de disposer de longues séries chronologiques, acquises à différents stades de vie des espèces concernées. Ce rapport dresse un bilan des activités de l'Observatoire du Scorff pour l'année 2021.

International audience; The rise of antibiotic resistance is not only a challenge for human and animal health treatments, but is also posing the risk of spreading among bacterial populations in foodstuffs. Farmed fish-related foodstuffs, the food of animal origin most consumed worldwide, are suspected to be a reservoir of antibiotic resistance genes and resistant bacterial hazards. However, scant research has been devoted to the possible sources of diversity in fresh fillet bacterial ecosystems (farm environment including rivers and practices, and factory environment). In this study bacterial communities and the antibiotic resistance genes of fresh rainbow trout fillet were described using amplicon sequencing of the V3-V4 region of the 16S rRNA gene and high-throughput qPCR assay. The antibiotic residues were quantified using liquid chromatography/mass spectrometry methods. A total of 56 fillets (composed of muscle and skin tissue) from fish raised on two farms on the same river were collected and processed under either factory or laboratory sterile filleting conditions. We observed a core-bacterial community profile on the fresh rainbow trout fillets, but the processing conditions of the fillets has a great influence on their mean bacterial load (3.38 ± 1.01 log CFU/g vs 2.29 ± 0.72 log CFU/g) and on the inter-individual diversity of the bacterial community. The bacterial communities were dominated by Gamma- and Alpha-proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The most prevalent genera were Pseudomonas, Escherichia-Shigella, Chryseobacterium, and Carnobacterium. Of the 73 antibiotic residues searched, only oxytetracycline residues were detected in 13/56 fillets, all below the European Union maximum residue limit (6.40-40.20 μg/kg). Of the 248 antibiotic resistance genes searched, 11 were found to be present in at least 20% of the fish population (tetracycline resistance genes tetM and tetV, β-lactam resistance genes bla (DHA) and bla (ACC), macrolide resistance gene mphA, vancomycin resistance genes vanTG and vanWG and multidrug-resistance genes mdtE, mexF, vgaB and msrA) at relatively low abundances calculated proportionally to the 16S rRNA gene.

Background Glucose-6-phosphate (G6pc) is a key enzyme involved in the regulation of the glucose homeostasis. The present study aims at revisiting and clarifying the evolutionary history of g6pc genes in vertebrates. Results g6pc duplications happened by successive rounds of whole genome duplication that occurred during vertebrate evolution. g6pc duplicated before or around Osteichthyes/Chondrichthyes radiation, giving rise to g6pca and g6pcb as a consequence of the second vertebrate whole genome duplication. g6pca was lost after this duplication in Sarcopterygii whereas both g6pca and g6pcb then duplicated as a consequence of the teleost-specific whole genome duplication. One g6pca duplicate was lost after this duplication in teleosts. Similarly one g6pcb2 duplicate was lost at least in the ancestor of percomorpha. The analysis of the evolution of spatial expression patterns of g6pc genes in vertebrates showed that all g6pc were mainly expressed in intestine and liver whereas teleost-specific g6pcb2 genes were mainly and surprisingly expressed in brain and heart. g6pcb2b, one gene previously hypothesised to be involved in the glucose intolerant phenotype in trout, was unexpectedly up-regulated (as it was in liver) by carbohydrates in trout telencephalon without showing significant changes in other brain regions. This up-regulation is in striking contrast with expected glucosensing mechanisms suggesting that its positive response to glucose relates to specific unknown processes in this brain area. Conclusions Our results suggested that the fixation and the divergence of g6pc duplicated genes during vertebrates’ evolution may lead to adaptive novelty and probably to the emergence of novel phenotypes related to glucose homeostasis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3727-1) contains supplementary material, which is available to authorized users.

Deciphering mechanisms of oocyte development in female fishes still remains challenging and a comprehensive overview of this process at the level of the organ is still needed. The recent development optical tissue clearing methods have tremendously boosted the 3D imaging of large size biological samples that are naturally opaque. However, no attempt of clearing on fish ovary that accumulates extremely high concentration of lipids within oocytes has been reported to date. To face with this ovarian-specific challenge, we combined two existing clearing methods, the non-toxic solvent-based Eci method for efficient clearing and the CUBIC method to enhance lipid removal and reduce non-specific staining. The methyl green fluorescent dye was used to stain nuclei and delineate follicles. Using this procedure (named C-Eci), ovaries of both medaka and trout could be imaged in 3D and all follicles analyzed. To our knowledge this is the first procedure elaborated for clearing and imaging fish ovary in 3D. The C-Eci methods thus provides an interesting tool for getting precise quantitative data on follicular content in fish ovary and promises to be useful for further morphological studies.

Intégration de caractères de résistance à cinq pathologies dans les schémas de sélection commerciale de truite, bar et daurade. 6 journées de la recherche filière

Résumé; Highlighting the role of autophagy in metabolic adaptation of trout hepatocytes to fasting. 13. International Congress on the Biology of Fish

International audience

International audience

Trout farming is the main fish production system in France. This article describes a system to classify trout farms based on environmental impacts calculated by life cycle assessment and technical and economic indicators. Since the number of surveyed farms was too small for a robust assessment, we combined principal component analysis (PCA) with a non-parametric bootstrap technique. French trout farms were surveyed to collect technical and economic indicators. The representativeness of the survey was verified by comparing it to a national inventory. Life cycle assessment was used to estimate environmental impacts of farms and the contribution of each production stage to impacts. PCA was used to evaluate both technical-economic and environmental indicators of the trout farms, which were separated into three groups based on the size of fish produced (pan-size, large and mixed-size, and very large). Non-parametric bootstrap was used to compare the groups and to test the significance of PCA results. Results validated the fish-farm classification system based on the size of fish produced and indicated that farm operations and fish feeding contributed the most to environmental impacts. The PCA method distinguished three groups via their technical indicators, with non-significant differences among the groups in environmental impacts. However, environmental indicators showed strong links with technical and economic indicators. In conclusion, bootstrapped PCA offers the ability to assess groups of trout production system when the sample size is too small and provides more conservative results by considering uncertainty. Future studies should focus on providing reliable data to reduce uncertainty.[br/]

National audience

National audience

Crédit Incitatif 2013. Champ thématique : RessourcesCrédit Incitatif 2013. Champ thématique : Ressources; Rôle de l'autophagie hépatique dans l'utilisation du glucose chez la truite. Journées d’Animation des Crédits Incitatifs du Département de Physiologie Animale et Systèmes d’Elevage (JACI Phase 2016)

Une étude a été menée sur dix plans d’eau peu profonds et eutrophes, touchés régulièrement par des efflorescences de cyanobactéries, et en particulier le genre Anabaena (A. spiroides et A flos-aquae). La recherche de composés odorants dans les truites prélevées lors des efflorescences a permis de retrouver des concentrations significatives de géosmine (jusqu’à 850 ng•kg‑1), composé odorant lipophile connu pour être produit entre autres microorganismes par Anabaena spp.. Les analyses sensorielles ont permis de retenir des descripteurs de défauts de goût de type « terreux-moisi », avec une intensité des défauts de goût notée jusqu’à 8,3/10.L’étude en microcosme de la cinétique de fixation et de libération de la géosmine dans des truites arc-en-ciel (Onchorynchus mykiss) de 250 g a permis de conclure que l’apparition de défauts de goût significatifs dans la chair apparaît après seulement quelques heures d’exposition à la géosmine. Après 30 h en présence de géosmine, la mise en eau claire dans des conditions optimales de renouvellement permet une réduction significative des défauts sensoriels au bout de quatre jours. Une corrélation significative a été retrouvée entre les densités d’Anabaena spp. et les teneurs en géosmine retrouvées dans les truites pêchées in situ (r2 = 0,74, p, A study was conducted on ten small, eutrophic water bodies affected by cyanobacteria blooms. The genus Anabaena (A. spiroides and A. flos-aquae) is often implicated in the appearance of these blooms. The consequences of these blooms on the sensory quality of fish have been studied. Anabaena spp. produce geosmin, and this earthy-musty volatile compound is found in trout flesh with significant concentrations, up to 850 ng•kg‑1. Trout are also tainted with the presence of a repulsive flavour (intensity of bad taste up to 8.3/10).A microcosm study of the kinetics of uptake and depuration of geosmin was conducted on rainbow trout (Onchorynchus mykiss). After an exposure of 6 h to geosmin, trout are significantly tainted with the appearance of significant concentrations of geosmin in the flesh and detection of repulsive flavour by taste. After an exposure of 30 h to geosmin, an open clear-water circulation system induces an elimination of the earthy-musty compound and a progressive reduction of off‑flavor intensity. The recovery of a good sensory evaluation for trout is obtained after more than four days.A significant correlation was found between Anabaena spp. density and geosmin concentrations in trout flesh (r2 = 0.74, p

Cette revue a pour objectif de faire un point sur les avancées récentes obtenues dans le domaine de la prédiction de la qualité des viandes. Elle aborde différentes démarches menées au sein des principales filières de production pour développer des équations puis des outils prédictifs basés sur différents types de marqueurs biologiques (génomiques ou phénotypiques) ou physiques (spectroscopiques). Au travers des différents exemples présentés, il apparaît que l’identification de marqueurs biologiques se confronte au déterminisme complexe des paramètres de qualité qui rend encore difficile la mise au point de tests moléculaires génériques utilisables sur le terrain. Toutefois, les avancées ont été notables ces dernières années bénéficiant des récents développements technologiques en génomique, protéomique et métabolomique. Les premières équations de prédiction de la qualité sensorielle et du potentiel technologique des viandes laissent entrevoir des possibilités d’applications dans les années à venir. Concernant la spectroscopie, les principaux résultats ont été obtenus dans le domaine de la Spectroscopie Proche Infrarouge (SPIR) avec des développements aboutis pour prédire la composition et la valeur nutritionnelle des viandes. La prédiction du potentiel technologique des viandes à l’aide de cette méthode et surtout de la qualité sensorielle est en revanche plus difficile. Enfin, l’exemple du modèle phénotypique MSA (« Meat Standards Australia ») de prévision de la qualité sensorielle de la viande bovine basée sur une combinaison de données d’amont et d’aval et dont la plus-value pour la filière a été démontrée en Australie, présente une généricité qui a déjà été éprouvée dans plusieurs pays., This review was aimed at providing an overview of recent advancements obtained in the field of meat quality prediction. The different methods used in the production sectors for the development of equations and the tools used based on different types of biological markers (genomic or phenotypic) or physical (spectroscopy) are discussed. Through the different examples that are presented, it appears that the identification of biological markers is confronted with the complex determinism of quality parameters. This makes the development of generic molecular tests to be used on the field even more difficult. However, in recent years, progress has been made, benefitting from genomics, proteomics and metabolomics technological developments. The first equations that predict the sensorial quality and the technological potential of meat hint to possible applications in the near future. Concerning spectroscopy, the main results were obtained using Near Infrared Spectroscopy (NIR) with developments obtained for the prediction of the composition and nutritional value of meats. The prediction of the technological potential of meats using this method and mainly the sensorial quality is, however, more difficult. Finally, the example of the MSA (« Meat Standards Australia ») phenotypic model which predicts the sensorial quality of bovine meat based on a combination of upstream and downstream data and whose added-value for the sector has been identified in Australia, presents a genericness that has already been proven in several countries.

Cette revue a pour objectif de faire un point sur les avancées récentes obtenues dans le domaine de la prédiction de la qualité des viandes. Elle aborde différentes démarches menées au sein des principales filières de production pour développer des équations puis des outils prédictifs basés sur différents types de marqueurs biologiques (génomiques ou phénotypiques) ou physiques (spectroscopiques). Au travers des différents exemples présentés, il apparaît que l’identification de marqueurs biologiques se confronte au déterminisme complexe des paramètres de qualité qui rend encore difficile la mise au point de tests moléculaires génériques utilisables sur le terrain. Toutefois, les avancées ont été notables ces dernières années bénéficiant des récents développements technologiques en génomique, protéomique et métabolomique. Les premières équations de prédiction de la qualité sensorielle et du potentiel technologique des viandes laissent entrevoir des possibilités d’applications dans les années à venir. Concernant la spectroscopie, les principaux résultats ont été obtenus dans le domaine de la Spectroscopie Proche Infrarouge (SPIR) avec des développements aboutis pour prédire la composition et la valeur nutritionnelle des viandes. La prédiction du potentiel technologique des viandes à l’aide de cette méthode et surtout de la qualité sensorielle est en revanche plus difficile. Enfin, l’exemple du modèle phénotypique MSA (« Meat Standards Australia ») de prévision de la qualité sensorielle de la viande bovine basée sur une combinaison de données d’amont et d’aval et dont la plus-value pour la filière a été démontrée en Australie, présente une généricité qui a déjà été éprouvée dans plusieurs pays., This review was aimed at providing an overview of recent advancements obtained in the field of meat quality prediction. The different methods used in the production sectors for the development of equations and the tools used based on different types of biological markers (genomic or phenotypic) or physical (spectroscopy) are discussed. Through the different examples that are presented, it appears that the identification of biological markers is confronted with the complex determinism of quality parameters. This makes the development of generic molecular tests to be used on the field even more difficult. However, in recent years, progress has been made, benefitting from genomics, proteomics and metabolomics technological developments. The first equations that predict the sensorial quality and the technological potential of meat hint to possible applications in the near future. Concerning spectroscopy, the main results were obtained using Near Infrared Spectroscopy (NIR) with developments obtained for the prediction of the composition and nutritional value of meats. The prediction of the technological potential of meats using this method and mainly the sensorial quality is, however, more difficult. Finally, the example of the MSA (« Meat Standards Australia ») phenotypic model which predicts the sensorial quality of bovine meat based on a combination of upstream and downstream data and whose added-value for the sector has been identified in Australia, presents a genericness that has already been proven in several countries.

A methodology for planning an optimized river water temperature monitoring network is presented. The methodology is based on sampling of the physio-climatic variability of the region to be monitored. Physio-climatic metrics are selected to describe the study region, based on principal component analysis. The sites to be monitored are then identified based on a k-means clustering in the multidimensional space defined by the selected metrics. The methodology is validated on an existing dense water temperature network in Haute-Savoie, France. Different configurations of more or less dense network scenarios are evaluated by assessing their ability to estimate water temperature indices at ungauged locations. An optimized network containing 83 sites is found to provide satisfactory estimations for seven ecologically and biologically meaningful thermal indices defined to characterize brown trout thermal habitat.

Des études microanalytiques ont été menées sur des truites Salmo trutta fario, âgées de deux ans, récoltées dans une rivière des Vosges soumise aux retombées des pluies acides et sur des truites témoins récoltées dans une rivière d'Auvergne, non soumise aux pluies acides. La rivière des Vosges est caractérisée par un pH de 5,42 et par une concentration en aluminium de 200 µg/L-1. Notre but étant de déterminer les tissus, cellules et organites cibles de bioaccumulation éventuelle de l'aluminium, nous avons analysé rein, foie, branchie et tractus digestif. Deux méthodes microanalytiques ont été utilisées pour localiser l'aluminium à l'échelle cellulaire et subcellulaire et connaître les éléments avec lesquels il peut être associé; ce sont la spectrométrie de masse par émission ionique secondaire (microscope ionique associé à un système informatisé de traitement d'images) et la spectrométrie des rayons X (microsonde électronique de Castaing associée à un microscope électronique à transmission).La microanalyse des rein, foie, branchie et tractus digestif montre l'existence de deux processus conduisant à la bioaccumulation de l'aluminium. Le premier, classiquement connu pour d'autres métaux, met en évidence une insolubilisation de l'aluminium sous forme de phosphate, dans des organites limités par une membrane : les lysosomes et les granules pigmentaires des mélanocytes. Le second, démontre la formation de volumineux dépots extra-cellulaires, atteignant 100 µm de long et entraînant la destruction du tissu. Aucune bioaccumulation significative d'aluminium n'a été observée chez des truites témoins, récoltées dans le centre de la France, où l'eau à pH 7.9 est dépourvue d'aluminium., The major harm caused by acidic precipitation is shown by a disappearance of fish. Other factors besides acidity such as aluminium levels are significantly harmful and many studies have shown that aluminium ions are toxic to fish. The only sensible course of action is to investigate the basic mechanisms by which each of the metal pollutants enters and attacks living systems. For this, one needs to be a combination of physicist, chemist, biochemist, physiologist and toxicologist. Investigations on metal bioaccumulation require very sensitive analytical instrumentation. Total analytical methods commonly used are inadequate : absorbed and adsorbed elements cannot be distinguished.Therefore, interesting information can be obtained by using physical methods of chemical microanalysis : two available microanalytical techniques are particularly suitable, X-ray spectrometry and secondary ion mass spectrometry.X-ray spectrometry, also called Electron Probe X-ray Microanalysis or Electron Microprobe (EMP) provides a means for studying the local chemical composition and structure of biological specimens. EMP can be used in association with a photon microscope or with a transmission electron microscope allowing the detection of elements at subcellular level.The Secondary Ion Mass Spectrometry (SIMS), also called Ion Microscopy, allows to visualize, analyse and photograph the microscopical distribution of the stable or radioactive isotopes of the elements present in a histological section. The sensitivity of the method is very high, ranging from 0.1 to 1 ppm. In association with SIMS, a processing of secondary ion images is used.Two years-old samples of Salmo trutta fario, from wild populations living in acidified waters of Eastern France (near Cornimont in the Vosges moutains) were studied for aluminium detection at cellular and subcellular levels. The acidified waters were characterized by a low pH (5,42) and high aluminium level reaching 200 µg/L-1. Control trouts living in non acidified waters (pH : 7.9 and aluminium free) of central France (near Clermont-Ferrand) were used for comparison. In order top determine the tissues, cells and organelles of a possible aluminium concentration, the following organs were investigated : kidney, liver, gill and digestive tractus, using both microanalytical techniques described above.In the kidney ion images showed aluminium emission from tubule lysosomes with a ring-shaped localization along the apical border of the epithetial cells; aluminium emissions from the tubule lumen and from the pigment granules of the melanocytes were also observed. Using the electron microprobe, X-ray emission spectra of aluminium associated with phosphorus were obtained from lysosomes and pigment granules. In the liver and in the gills, ion images showed a high aluminium emission from the same organelles and X-ray spectra of aluminium and phosphorus were also obtained. Moreover, in the pyloric caeca, large extracellular deposits of aluminium were detected : they measured about 100 µm in length and were located in places where tissues had been destroyed.The same structural, ultrastructural and microanalytical investigations were performed on the control trouts from which non aluminium detection was obtained.In conclusion, two processes appear to be involved in the aluminium accumulation in the brown trout. The first one corresponds to a well known insolubilisation of aluminium phosphate inside the lysosomes, due to an acidic phosphatase enzymatic activity; aluminium is also trapped inside pigment granules. Both of these mechanisms of storage inside membrane-limited organelles, prevent cells from any interior damage. The second one corresponds to the formation of large extracellular deposits which are likely to provoke injuries leading to the tissue destruction. Such data demonstrating basic mechanisms of aluminium accumulation in a fish, could not have been obtained using total analytical methods.

Environmental perturbations can affect the health, welfare, and fitness of animals. Being able to characterize and phenotype adaptive capacity is therefore of growing scientific concern in animal ecology and in animal production sciences. Terms borrowed from physics are commonly used to describe adaptive responses of animals facing an environmental perturbation, but no quantitative characterization of these responses has been made. Modeling the dynamic responses to an acute challenge was used in this study to facilitate the characterization of adaptive capacity and therefore robustness. A simple model based on a spring and damper was developed to simulate the dynamic responses of animals facing an acute challenge. The parameters characterizing the spring and the damper can be interpreted in terms of stiffness and resistance to the change of the system. The model was tested on physiological and behavioral responses of rainbow trout facing an acute confinement challenge. The model has proven to properly fit the different responses measured in this study and to quantitatively describe the different temporal patterns for each statistical individual in the study. It provides therefore a new way to explicitly describe, analyze and compare responses of individuals facing an acute perturbation. This study suggests that such physical models may be usefully applied to characterize robustness in many other biological systems.

Poster session; absent

The ability of an organism to respond to an environmental perturbation is a growing scientific concern in animal ecology and animal production sciences. Depending on animal vulnerability, these environmental perturbations can affect health, welfare, or fitness of the animal. Robustness, defined as the ability to resist to environmental change, are therefore important components of production sustainability or biodiversity. Our work aimed at better estimating and characterizing the robustness in rainbow trout by describing the degree of perturbation when facing an acute perturbation. Adaptive responses to environmental perturbations are diversified and numerous, but they can be described by temporal patterns giving indications on the resistance, the recovery ability or the environmental sensitivity of the animal. The integration of these features provides an estimation of the degree of perturbation of the animal facing the environmental change. Physiological and behavioral responses of two isogenic lines (within each line, all individuals have the same genome) of rainbow trout were followed before, during and after an acute challenge. The effects of a confinement or a hypercapnia challenge were investigated. Temporal patterns were analyzed in order to characterize within and between line variabilies in reactivity to the challenge and recovery capacities.All measures were impacted by the challenges, indicating that both lines triggered adaptive responses. The cortisol release rate was the only measure showing significant mean differences between the two lines in both studies. Multivariate analyses highlighted two independent coping strategies consisting in either favoring behavior or physiology modification. The results showed also a strong and unexpected within line variability, suggesting the importance of life history on the degree of perturbation. At last, the between-study comparison showed an inversion in physiological reactivity between the two lines, suggesting that robustness is challenge-specific or robustness implies challenge-specific reactivities.This study sets also the basis for a model able to precisely and explicitly characterize the degree of perturbation of a perturbed system. The model was validated on the data analyzed in this project but should be sufficiently generic to cope with data from other species.; La capacité des animaux à faire face à des perturbations environnementales est une préoccupation croissante en écologie et en production. En fonction de la vulnérabilité des animaux, les modifications environnementales peuvent impacter leur santé, leur bien-être ou leur capacité de reproduction. La robustesse, définie comme la capacité à conserver ses fonctions malgré les perturbations environnementales est donc une composante importante de la durabilité d’une production ou de la biodiversité. Le travail présenté ici vise à apporter des éléments de réponses quant à la robustesse chez la truite arc-en-ciel, en décrivant le degré de perturbation face à une perturbation aiguë. Le degré de perturbation de l’animal est décrit en intégrant les différentes réponses adaptatives de l’animal face à une perturbation donnée. Des réponses adaptatives physiologiques et comportementales ont été suivies chez deux lignées isogéniques (au sein de chaque lignée tous les individus présentent le même génome) de truite arc-en-ciel avant, pendant et après une perturbation aiguë. Les effets de challenges aigus de confinement ou d’hypercapnie ont été étudiés. Les cinétiques de réponses ont été analysées afin de faire ressortir la variabilité intra- et inter-lignée de réactivité au challenge et de capacité à récupérer du challenge. Chez les deux lignées, toutes les mesures effectuées montrent un effet de la perturbation indiquant la mise en place de mécanismes adaptatifs. La mesure de cortisol dans l’eau s’est avérée être la seule mesure montrant des différences moyennes inter-lignées de réponses face au challenge. Parallèlement, les analyses multivariées ont souligné la présence de deux stratégies d’adaptation indépendantes, consistant à modifier son comportement ou sa physiologie. Nous avons également observé une forte et inattendue variabilité intra-lignée, illustrant l’importance de l’histoire de vie sur le degré de perturbation de la truite arc-en-ciel. Finalement, la comparaison entre les deux expériences montre une inversion de réactivité physiologique entre les deux lignées isogéniques suggérant que la robustesse est challengespécifique ou que la robustesse nécessite des réactivités challenge-specifiques. Ce travail pose également les bases d’un modèle capable de caractériser de façon précise et explicite les degrés de perturbation à partir de cinétiques de réponses adaptativesface à une perturbation aiguë. Le modèle a été validé sur des données de truite arc-en-ciel mais devrait être suffisamment générique pour s’adapter aux réponses d’autres espèces.

National audience

National audience

Session Nutrition; absent

Stream-dwelling salmonids are territorial; from early-life stages they undergo intense competition for habitat and food. These interactions may affect mortality, migration and growth, at variable intensities in function of ontogeny and environmental factors. In Switzerland, brown trout Salmo trutta L. is the most favoured species by anglers. Most of the populations are subjected to the stocking of juveniles, released during their first summer ("summerlings"). The rearing in hatcheries of these individuals, which are the progeny of captive broodstock, can have deleterious effects on the genetic diversity as well as on the fitness of the introduced fish. In addition, these individuals are bound to affect the wild population dynamics. Some behaviours (aggression and predator avoidance) have already been studied under controlled conditions, but the consequences have rarely been measured in a natural environment. This thesis aims to evaluate the intensity of the biotic, i.e. density-dependant, mechanisms between wild and stocked trout through a series of experiments in various rivers. The biotic interactions at the juvenile stage were first described in a natural resident population. Thereafter a series of experiments were carried out in controlled and natural environments to evaluate the efficiency and limitations of two marking techniques suitable for young trout: an externally detectable fluorescent marker (calcein) and an individual marking by implantation of a PIT tag. Both techniques were used to evaluate the effects of density and size of the stocked fish on the wild juveniles, through in situ investigations in three contrasted rivers. Finally the results of the various marking-recapture experiments were used to model the apparent mortality of stocked versus wild fish, and to find which environmental factors explain the observed variability. The results show the importance of the density-dependant regulation on the apparent survival, i.e. rate of change, and the size of wild fish, as well as the interactions between fish density and environmental factors, especially water flow. In rivers subjected to stocking, survival is usually much greater for wild than for introduced fish, except in one of the rivers with low slope. Increasing the stocked density does not influence directly the survival of both stocked and wild fish, but can increase the downstream movement of individuals of both origins. By combining capture-recapture data collected from seven streams in this study, results show an increase of the initial apparent mortality (within a few days post-stocking) of stocked juveniles with increasing stocked density and stream width. The morphological characteristics of the rivers also affect the delayed over-mortality of the stocked fish. These results must be corroborated through supplementary marking-recapture experiments coupled with detailed environmental records., Les salmonidés sont des poissons territoriaux en rivière, soumis à une compétition intense pour l'habitat et la ressource trophique dès les plus jeunes stades. Ces interactions exercent une influence sur la mortalité, la migration et la croissance, avec des intensités variables en fonction de l'ontogénie et des facteurs environnementaux. En Suisse, la truite Salmo trutta L. est l'espèce la plus prisée par les pêcheurs amateurs. La majeure partie des populations fait l'objet de rempoissonnements à partir de juvéniles " estivaux " relâchés au cours de leur premier été. L'élevage en pisciculture peut avoir des effets néfastes sur la diversité génétique et la fitness des poissons introduits dans le milieu naturel. En outre, ces individus sont susceptibles d'affecter la dynamique des populations sauvages. Certains comportements (agressivité, comportement anti-prédateur) ont été étudiés en milieu contrôlé, mais les conséquences ont rarement été mesurées en milieu naturel. Ce travail de thèse vise à évaluer l'intensité des mécanismes biotiques ou densité-dépendants entre des truites sauvages et introduites sur la base d'expérimentations en rivière. Les interactions biotiques ont d'abord été décrites au stade juvénile dans une population naturelle résidente. Puis, des expérimentations ont été menées en milieu contrôlé et in situ pour évaluer l'efficacité et les limites de deux méthodes de marquages utilisables sur des jeunes stades de truites : un marquage fluorescent à détection externe utilisant la calcéine et un marquage individuel par implantation de PIT tag. Ces techniques ont été employées pour évaluer les effets de la densité et de la taille des poissons introduits sur les juvéniles sauvages, à partir d'investigations conduites in situ dans trois rivières contrastées. Enfin, les résultats des différentes expériences de marquage-recaptures ont été utilisés pour modéliser la mortalité apparente des poissons introduits comparativement aux poissons sauvages, et rechercher les facteurs environnementaux susceptibles d'expliquer la variabilité observée. Les résultats montrent l'importance de la régulation densité-dépendante sur la survie apparente (ou taux de changement) et sur la taille des poissons sauvages, ainsi que les interactions entre la densité et les facteurs environnementaux, en particulier le débit. Dans les cours d'eau soumis à repeuplement, la survie des poissons sauvages est généralement bien supérieure à celle des poissons introduits, excepté dans le cours d'eau à faible pente. L'augmentation de la densité introduite n'influence pas directement la survie des poissons introduits ni celle des poissons sauvages, mais peut augmenter la dévalaison des individus des deux origines. En agglomérant les données de marquage-recaptures collectées dans sept rivières, les résultats indiquent une augmentation de la mortalité apparente initiale (dans les premiers jours suivant l'alevinage) des juvéniles introduits en fonction de la densité repeuplée et de la largeur du cours d'eau. Les caractéristiques morphologiques des cours d'eau influencent également la surmortalité apparente des poissons introduits sur le long terme. Ces résultats doivent être confirmés sur la base d'expérimentations de marquage-recaptures couplés à des relevés environnementaux détaillés.

Spermatozoa production throughout life requires the presence of the initial germ cells, the spermatogonial stem cells (SSCs). Their self-renewal and their ability to differentiate assure to keep a reserve and to produce continuously differentiated germ cell. In mammals, several markers of the SSCs have been identified. Interestingly, some of them allow us to sort the SSCs population and further to analyze their fate in vitro and in vivo. By contrast, only scarce information has been obtained in non-mammalian vertebrates including the teleost fishes. Our model of study, the rainbow trout (Oncorynchus mykiss), presents a seasonal spermatogenesis. The growth of the immature testes, the active spermatogonial proliferation starting at puberty, and their quiescent state at the end of the cycle represent interesting stages to study the regulation on the SSCs fate. Using various testicular stages and purified testicular cell fractions we show that pou2, plzf, nanos2 and 3 and gfra1, all expressed by spermatogonial stem cells in mammals, are specifically expressed in the undifferentiated A spermatogonia population. In particular, gfra1 and nanos2 are expressed in a sub-population of these cells. Thus, we propose that the nanos2+ and/or gfra1+ cells are SSCs. Furthermore, in our study, gdnf, ligand of gfra1 regulating the SSCs fate in mouse, is highly expressed just before the end of the spermatogenetic cycle. Such expression correlates with Fsh peak of secretion. However a stimulation of gdnf expression by Fsh was not observed in our in vitro experiments, but this technique doesn’t represent reciprocal regulations nor the roles of all factors in vivo. To conclude, we discovered potent marker of SSCs in trout. In particular, gfra1 and nanos2 will allow us to investigate further the SSCs biology in teleosts. Moreover, gdnf and its receptor expression in the testis in a spermatogenetic-dependent way lead us to propose this pathway as a potent regulator of the SSCs fate in trout.; Les cellules souches spermatogoniales (SSCs) constituent la population de cellules germinales initiales support de la production des spermatozoïdes tout le long de la vie d’un individu. Ces cellules caractérisées par leur capacité d’auto-renouvellement et de différenciation maintiennent ainsi une réserve et garantissent la production continue de cellules germinales différenciées. Chez les mammifères, plusieurs marqueurs permettant de reconnaitre cette population cellulaire au sein du testicule ont été identifiés. De plus, parmi ces marqueurs, certains permettent d’isoler et de purifier les SSCs. Ils ont ainsi permis d’aborder les mécanismes de régulation du devenir des SSCs par des expériences menées in vitro et in vivo. En revanche, la biologie de ces cellules est beaucoup moins connue chez les vertébrés non mammaliens, en particulier chez les poissons téléostéens. Notre modèle d’étude, la truite arc-en-ciel (Oncorynchus mykiss) est caractérisée par une spermatogenèse cyclique et fortement saisonnée. La croissance du testicule immature, la prolifération active des spermatogonies à la puberté, et la quiescence de ces dernières en fin de cycle semblent être des étapes clés de régulation du devenir des SSCs. Grâce à l’analyse des profils d’expression au cours du cycle spermatogénétique et dans des fractions de cellules testiculaires isolées, nous montrons la conservation d’expression de gènes décrit comme marqueurs de SSCs chez les mammifères (pou2, plzf, nanos2 et 3, gfra1) dans les populations de spermatogonies A indifférenciées de truite. En particulier, gfra1 et nanos2 identifient tous deux une sous-population de cellules au sein des spermatogonies. Nous proposons donc que les cellules gfra1+ et/ou nanos2+ sont des SSCs au sein du testicule de truite. Par ailleurs, nous montrons que l’orthologue truite de gdnf, ligand de gfra1 et régulateur majeur du maintien des SSCs chez la souris, est exprimé très fortement juste avant la fin de cycle spermatogénétique. Cette expression corrélée avec un pic de sécrétion plasmatique de Fsh suggérait une régulation positive de gdnf par cette hormone. Notre étude in vitro n’a pas permis d’aboutir aux mêmes conclusions, mais cette technique ne reflète pas toutes les régulations réciproques ni le rôle des autres facteurs in vivo. En conclusion, nous avons découvert des marqueurs probables de SSCs chez la truite. En particulier, gfra1 et nanos2 qui permettront une analyse plus approfondie de la biologie des SSCs chez les téléostéens. De plus, l’expression de gdnf et de son récepteur dans le testicule, régulée en fonction du stade du cycle spermatogénétique, nous permet d’envisager cette voie comme régulateur du devenir des SSCs chez la truite.

The trunk muscle in fish is organized as longitudinal series of myomeres which are separated by sheets of connective tissue called myoseptum to which myofibers attach. In this study we show in the trout that the myoseptum separating two somites is initially acellular and composed of matricial components such as fibronectin, laminin and collagen I. However, myoseptal cells forming a continuum with skeletogenic cells surrounding axial structures are observed between adjacent myotomes after the completion of somitogenesis. The myoseptal cells do not express myogenic markers such as Pax3, Pax7 and myogenin but express several tendon-associated collagens including col1a1, col5a2 and col12a1 and angiopoietin-like 7, which is a secreted molecule involved in matrix remodelling. Using col1a1 as a marker gene, we observed in developing trout embryo an initial labelling in disseminating cells ventral to the myotome. Later, labelled cells were found more dorsally encircling the notochord or invading the intermyotomal space. This opens the possibility that the sclerotome gives rise not only to skeletogenic mesenchymal cells, as previously reported, but also to myoseptal cells. We furthermore show that myoseptal cells differ from skeletogenic cells found around the notochord by the specific expression of Scleraxis, a distinctive marker of tendon cells in amniotes. In conclusion, the location, the molecular signature and the possible sclerotomal origin of the myoseptal cells suggest that the fish myoseptal cells are homologous to the axial tenocytes in amniotes.

International audience; Aminergic metabolism was studied in discrete brain regions of the postovulated female rainbow trout using a liquid chromatography electrochemical detection method. 3 Methoxytyramine (3MT) was the major dopaminergic catabolite, suggesting that catechol-o-methyl transferase is the main dopamine (DA) catabolic enzyme. Two populations of brain regions were found: one with a high DA content and low 3MT/DA ratio (hypothalamus and telencephalon), suggesting that these regions could present a high density of DA perikarya; the other with a high 3MT/DA ratio (pituitary, preoptic area, myelencephalon and optic tectum) suggesting that these regions could present a high density of DA axonal endings. 5 Hydroxytryptamine (5HT) content differed, but an homogeneous distribution of monoamine oxidase was found in different brain regions. High 5HT content was found in the hypothalamus and telencephalon; 5HT was however not detectable in the pituitary.

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‘Trout’ are generally considered to be cool, freshwater fish species that belong phylogenetically to the rather young group of fin-rayed or Teleost fishes in the Family Salmonidae. Trout have significant economic, social and scientific importance. This book examines two ‘trout’, the rainbow trout Oncorhynchus mykiss and the brown trout Salmo trutta. This book came from the editor’s interest to bring together some of the major areas that have made ‘trout’ such an important and enduring model species. The chapters have been carefully crafted by their authors to ensure that they cover as much of the topic as possible including references that support the information. (Imprint: Nova)

Colloque organisé avec le support de l'ADEME Agence de l'Environnement et de la Maîtrise de l'Energie; absent

Il n’y a pas que le sexe dans la vie ! Et pourtant… Chez les animaux notamment, le sexe est au cœur d’une fonction essentielle à la survie des espèces : la reproduction. Dame Nature a tout de même ajouté une touche de poésie à la rencontre sexuelle animale qui s’apparente alors à une rencontre amoureuse. Cette dernière connaît plusieurs temps : la recherche d’un partenaire, puis l’attirance et la préférence… qui mènent à l’accouplement. Pour attirer un partenaire, l’odeur joue un rôle primordial : les phéromones sont une véritable arme de séduction à laquelle les insectes succombent irrésistiblement. Dans le cas des mammifères, lorsqu’elle coïncide avec la période ovulatoire d’une femelle, l’odeur peut également être source d’excitation pour le mâle. La femelle se montre parfois sélective dans le choix de son partenaire sexuel. Ses critères de préférence sont alors surprenants. Ainsi s’aventure-t-elle vers de nouveaux territoires pour s’apparier, telle la femelle chevreuil, d’ordinaire sédentaire. Dans d’autres cas, l’élu sera un partenaire capable de protéger sa progéniture. La reproduction chez l’animal fait aussi appel à l’insémination artificielle, courante en élevage. L’INRA consacre de nombreuses recherches à des méthodes innovantes en matière de reproduction, allant dans le sens de la durabilité. Dans ce dossier : des résultats inédits, des révélations étonnantes, la reproduction et les comportements sexuels animaux vus par l’Inra.

National audience; L'utilisation d'un scanner IRM pour l'analyse d'un grand nombre d'échantillons de poissons (1000) a permis d'estimer l'héritabilité du taux de lipide de la chair dans le cadre d'un projet d'évaluation généalogique assistée par empreintes génétiques pour les programmes de sélection de la filière truiticole.

In mammals, much evidence has demonstrated the important role of myostatin (MSTN) in regulating muscle mass and identified the transcription factor forkhead box O (FoxO) 1 as a key regulator of its gene expression during atrophy. However, in trout, food deprivation leads to muscle atrophy without an increase of the expression of mstn genes in the muscle. We therefore studied the relationship between FoxO1 activity and the expression of both mstn genes ( mstn1a and mstn1b) in primary culture of trout myotubes. To this aim, two complementary studies were undertaken. In the former, FoxO1 protein activity was modified with insulin-like growth factor-I (IGF-I) treatment, and the consequences on the expression of both mstn genes were monitored. In the second experiment, the expression of both studied genes was modified with growth hormone (GH) treatment, and the activation of FoxO1 protein was investigated. We found that IGF-I induced the phosphorylation of FoxO1 and FoxO4. Moreover, under IGF-I stimulation, FoxO1 was no longer localized in the nucleus, indicating that this growth factor inhibited FoxO1 activity. However, IGF-I treatment had no effect on mstn1a and mstn1b expression, suggesting that FoxO1 would not regulate the expression of mstn genes in trout myotubes. Furthermore, the treatment of myotubes with GH decreased the expression of both mstn genes but has no effect on the phosphorylation of FoxO1, FoxO3, and FoxO4 nor on the nuclear translocation of FoxO1. Altogether, our results showed that mstn1a and mstn1b expressions were not associated with FoxO activity, indicating that FoxO1 is likely not a key regulator of mstn genes in trout myotubes.

National audience

In vertebrates, the follicle-enclosed growing oocyte progressively acquires both maturational and developmental competence (ability to resume meiosis and to develop once fertilized, respectively). The aim of this work was to characterize molecular actors involved in acquisition of oocyte competence in two non-mammalian vertebrates: the rainbow trout (Oncorhynchus mykiss) and the clawed toad Xenopus (Xenopus laevis). Eight genes have been studied: star, cyp19a1, cyp17a1, hsd11b3, apoC1, cmah, tfr1 and tesc. We evidenced in both species the expression by the oocyte of a functional aromatase (cyp19a1) that had been under-estimated so far. Moreover, the identification of the oocyte expression of a transcriptional cofactor of the estradiol receptor, Rbm39, contributes to stress the significance of estradiol action in regulating the acquisition of vertebrate oocyte maturational and/or developmental competence., Chez les vertébrés, l'ovocyte acquiert progressivement lors de sa croissance une double compétence à la maturation et au développement (capacités à reprendre sa méiose et à se développer une fois fécondé). L’objectif de ce travail était de caractériser de nouveaux acteurs moléculaires impliqués dans cette acquisition de compétences chez 2 vertébrés non mammaliens : la truite arc-en-ciel (Oncorhynchus mykiss) et le xénope (Xenopus laevis). Huit gènes ont été identifiés comme différentiellement exprimés au cours de cette acquisition de compétence : star, cyp19a1, cyp17a1, hsd11b3, apoC1, cmah, tfr1 et tesc. La mise en évidence de l’expression d’une aromatase (cyp19a1) fonctionnelle par l’ovocyte des deux espèces suggère une activité œstrogénique ovocytaire. De plus, l'identification d'une expression ovocytaire régulée de Rbm39, un cofacteur transcriptionnel du récepteur aux œstrogènes, contribue à renforcer l’importance de l’œstradiol lors de l’acquisition de ces compétences par l’ovocyte chez les vertébrés.

National audience

Life Cycle Assessment(LCA) was applied to evaluate the global environmental impact of two scenarios of trout production systems based on the operational information from an operational farm using a flow through system (FFF) and an experimental pilot low head recirculating system (RSF) located on the same site. The main differences between the environmental balances of the two systems were relative to water use, eutrophication potential and energy use. Independently of the system used, feed is the key indicator in determining the environmental balance (notwithstanding eutrophication potential and water dependence) monitored by fish production, chemical products, buildings and energy consumption. Consequently, when considering the RSF with a lower feed conversion ratio (0.8 versus 1.1 for FTF), the environmental balance of the RSF is more favourable at both global and regional levels, except with regards to energy use. RSF water dependence is 93% lower than the FTF and its eutrophication potential is 26-38% lower due to reduced waste release. On the other hand, at 57,659 MJ per ton of fish produced ( 16 kWh per kg), the RSF consumes 24-40% more energy than the FTF, especially for aeration and water treatment. Nevertheless, the RSF has significant potential for energy reduction through improvements to airlift and biofilter designs which Would reduce RSF energy use to a level similar to that of the FTF (34,869-43,841 MJ per ton of fish produced, corresponding to 10 and 12 kWh respectively). LCA is therefore a powerful tool which can be used on fish farms to define and prioritise the most promising potential improvements to the system. (C) 2008 Elsevier B.V. All rights reserved.

This study examined the genetic variability and genotype × diet interactions during early growth (initial mean body weight 1.2 g) among seven heterozygous clones of rainbow trout, Oncorhynchus mykiss . The clones were hand-fed a diet containing either fishmeal or plant proteins during a 49-day trial divided into two periods (P1, 26 days, and P2, 23 days). Weight, variation of weight within clone, feed intake, feed efficiency and mortality were calculated for both periods. There was a highly significant effect of diet and of clone for all traits at both periods, except for feed efficiency and mortality at P1. Highly significant interactions between diet and clone were also recorded for all these traits, except for mortality at P1. The occurrence of genotype × diet interactions when feeding juvenile rainbow trout with an all plant-protein diet indicates that a highly performing genotype on a fishmeal diet may perform poorly when fed a plant-protein diet. Interactions were found for the two major determinants of growth, i.e. feed intake and feed efficiency, showing that the dietary response differs according to the genotype. Monitoring of the within-clone variability of weight showed that a plant-based diet is likely to enhance the overall phenotypic variance in a population, whatever its initial genetic variability.

Background Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species. Results The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map. Conclusion The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of QTL, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of MAS into rainbow trout breeding programs.

Projet EVAD : Les chercheurs dévoilent leurs conclusions