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Abstract Background As a major threat to the oyster industry, Pacific Oyster Mortality Syndrome (POMS) is a polymicrobial disease affecting the main oyster species farmed across the world. POMS affects oyster juveniles and became panzootic this last decade, but POMS resistance in some oyster genotypes has emerged. While we know some genetic loci associated with resistance, the underlying mechanisms remained uncharacterized. So, we developed a comparative transcriptomic approach using basal gene expression profiles between different oyster biparental families with contrasted phenotypes when confronted to POMS (resistant or susceptible). Results We showed that POMS resistant oysters show differential expression of genes involved in stress responses, protein modifications, maintenance of DNA integrity and repair, and immune and antiviral pathways. We found similarities and clear differences among different molecular pathways in the different resistant families. These results suggest that the resistance process is polygenic and partially varies according to the oyster genotype. Conclusions We found differences in basal expression levels of genes related to TLR-NFκB, JAK-STAT and STING-RLR pathways. These differences could explain the best antiviral response, as well as the robustness of resistant oysters when confronted to POMS. As some of these genes represent valuable candidates for selective breeding, we propose future studies should further examine their function.

The THAUMEX measurement campaign, carried out during the summer of 2011 in Thau, a coastal lagoon in southern France, focused on episodes of marine breezes. During the campaign, three intensive observation periods (IOPs) were conducted and a large amount of data were collected. Subsequently, standalone modelling using the FLake lake model was used, first to assess the surface temperature and the surface energy balance, and second to determine the energy budget of the water column at the measurement site. Surface fluxes were validated against in situ measurements, and it was determined that heat exchanges are dominated by evaporation. We also demonstrated that the model was sensitive to the light extinction coefficient at Thau, due to its shallowness and clarity nature. A heat balance was calculated, and the inclusion of a radiative temperature has improved it, especially by reducing the nocturnal evaporation. The FLake lake model was then evaluated in three-dimensional numerical simulations performed with the Meso-NH mesoscale model, in order to assess the changing structure of the boundary layer above the lagoon during the IOPs more accurately. We highlighted the first time ever when Meso-NH and FLake were coupled and proved the ability of the coupled system to forecast a complex phenomenon but also the importance of the use of the FLake model was pointed out. We demonstrated the impact of the lagoon and more precisely the Lido, a sandy strip of land between the lagoon and the Mediterranean Sea, on the vertical distribution of turbulent kinetic energy, evidence of the turbulence induced by the breeze. This study showed the complementarities between standalone and coupled simulations.

Although spatial studies of diseases on land have a long history, far fewer have been made on aquatic diseases. Here, we present the first large-scale, high-resolution spatial and temporal representation of a mass mortality phenomenon cause by the Ostreid herpesvirus (OsHV-1) that has affected oysters (Crassostrea gigas) every year since 2008, in relation to their energetic reserves and the quality of their food. Disease mortality was investigated in healthy oysters deployed at 106 locations in the Thau Mediterranean lagoon before the start of the epizootic in spring 2011. We found that disease mortality of oysters showed strong spatial dependence clearly reflecting the epizootic process of local transmission. Disease initiated inside oyster farms spread rapidly beyond these areas. Local differences in energetic condition of oysters, partly driven by variation in food quality, played a significant role in the spatial and temporal dynamics of disease mortality. In particular, the relative contribution of diatoms to the diet of oysters was positively correlated with their energetic reserves, which in turn decreased the risk of disease mortality.