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International audience; The Thau lagoon is a Mediterranean coastal lagoon used for shellfish farming. It is periodically affected by anoxia events that trigger oyster mortality. To investigate the effects of an anoxia event focussed on nutrient dynamics and the responses of the microbial planktonic communities a 13-day in situ experiment was performed in September 2020. Transparent mesocosms (270 L) were placed at a depth of 4 m, inserted in the sediment, and kept closed throughout the experiment. The experiment comprised three treatments: i) Natural environment (N), i.e. in the natural water outside the mesocosms containing a rope of 30 oysters (Crassostrea gigas), ii) Control mesocosm (C) filled with natural water with no oysters, and iii) Oyster mesocosm (O) filled with natural water containing a rope of 30 oysters. Oyster respiration in the oyster mesocosm depleted oxygen after 54 h. All the oysters from O mesocosm were dead after nine days and decomposition of their flesh combined with releases from the water-sediment interface increased dissolved inorganic nitrogen (dominated by ammonium), phosphates, and ∑H2S up to 390, 17 and 295 μmol·L−1, respectively. Phytoplankton biomass consequently increased by 20 (11.8 μg chlal −1) and abundance by 4.5 (186 × 106 cells·L1) dominated largely by green algae \textless5 μm. During the oyster mortality period (day 6 to day 9) high abundances of heterotrophic flagellates and large ciliate specimens were observed. This shift in the community towards small phytoplankton favours the microbial loop and is detrimental to shellfish farming. In a context of global warming in which the risk of anoxia is higher, the results of the present investigation demonstrate that anoxia triggers shellfish mortality and that the change in the plankton community disrupts the normal functioning of the ecosystem, causing serious financial losses. In this context, it is crucial to predict possible hypoxia and anoxia events using high frequency measurements of dissolved oxygen, by avoiding using shallow zones for oyster production and by reducing shellfish stocks, or by mechanically lifting the oysters out of the water during the night to reduce oxygen respiration in the ecosystem.

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.

International audience; The aim of the present work was to test the influence of juvenile oyster culture on benthic-pelagic coupling in the French Mediterranean Thau Lagoon. Although the period of juvenile growth induces the introduction of millions of juvenile oysters in the lagoon over a short duration, the effects on the water-column and on the benthic ecosystem are poorly known. Using a multiple ecological approach, water column parameters, sedimentation rates, sediment characteristics and benthic fluxes were monitored on three occasions during the oyster pre-growth period, from October to December, at two sites inside the farming area and two sites outside the farming area that served as reference. In the water column, results showed a significant lower ratio between total phytoplankton biomass (chlorophyll-a) and degraded pigments (pheopigment), a significant increase in the contribution of phytoplankton containing chlorophyll-b (ie chlorophytes) to total phytoplankton biomass and a significant decrease in the contribution of phytoplankton containing chlorophyll-c (mainly diatoms) to the total phytoplankton biomass at farm sites, attributed to the grazing pressure caused by juvenile oysters on large particles, as described for adult oysters. No significant effect was observed at the benthic interface during this period, due to the dispersion of the small quantities of biodeposit produced by juveniles in the low water temperature conditions. A multivariate approach supported the effect of juvenile oysters on the water column and revealed a trend in benthic conditions with farm sites being distinct from the reference ones. The long farming history of the lagoon could have shaped sediment properties such that farming areas maintain different benthic conditions.

WOS:000540002100014; International audience; Thau lagoon is a large Mediterranean coastal lagoons and it supports traditional shellfish farming activities. It has been subject to eutrophication leading to major anoxic events associated with massive mortalities of shellfish stocks. Since the 1970s, improvements have been made to wastewater treatment systems, which have gradually led to oligotrophication of the lagoon. The aim of our study was to determine how the decrease in nutrient inputs resulted in major ecological changes in Thau lagoon, by analysing five decades of time-series (1970–2018) of observations on pelagic and benthic autotrophic communities. We were able to identify two periods during the oligotrophication process. Period 1 (1970–1992) was considered a eutrophic period, characterised by the shift from seagrass dominance to dominance of red macroalgae. Period 2 (1993–2018), characterised by improved eutrophication status, was further divided into three: a transition phase (1993–2003) during which the water column continued to recover but the benthic community lagged behind in recovery and in partial resilience; a regime shift (2003–2006), after which the water column became oligotrophic and seagrass began to recover (2007–2018). Considering anoxia crises as indicators of ecosystem resilience and resistance, we used a generalised linear model to analyse meteorological and environmental data with the aim of identifying the triggers of summer anoxia over the study period. Among the meteorological variables studied, air temperature had the strongest positive effect, followed by the period and wind intensity (both negative effects) and by rainfall in July (positive effect). The risk of triggering anoxia was lower in period 2, evidence for the increasing resistance of the ecosystem to climatic stress throughout the oligotrophication process. At the ecosystem scale and in the long term perspective, the ecological gains related to oligotrophication are especially important in the context of climate change, with more frequent and severe heat waves predicted.

International audience; Harmonizing coastal fisheries with water-quality improvement has become an essential factor for the sustainable use of coastal ecosystem services. Here, we present the scope of our study based on an interdisciplinary approach including ecological actions, socio-economic actions and socio-psychological actions. We chose to focus on the interaction between oyster aquaculture and seagrass vegetation as a typical ecological action using the coastal ecosystem complex (CEC) concept. Coastal organisms have adapted their traits to the environment over a long period of time, so that restoration of the CEC represents reconstruction of the original process of coastal production. Subtidal seagrass vegetation with intertidal oyster reefs is the original CEC in Japan, which would be expected to enhance coastal production by improving the production efficiency without adding nutrients. A simple field experiment examining carbon and nitrogen contents and stable isotope ratios revealed that oyster spats cultivated on a tidal flat adjacent to seagrass beds had higher nitrogen contents and higher delta C-13 ratios than spats cultivated in an offshore area using only pelagic production. This result suggests that utilization of the CEC, which enables oysters to use both pelagic and benthic production, has potential to sustain a food provisioning service for humans, even in oligotrophic conditions.

International audience; In the context of increasing demand for environmental recovery, aquatic systems may face the challenge of evolving under oligotrophication. This is the case in Mediterranean lagoons, in particular the shellfish-farmed Thau lagoon in France, where we studied recruitment of the Pacific oyster Crassostrea gigas. Oyster spat and environmental parameters were monitored at several sampling sites for 3 yr (2012 to 2014) using an original method with a temporal overlap deployment of collectors to study pre- and post-settlement processes and to identify the best conditions for recruitment. Contrary to the ‘no Pacific oyster reproduction’ paradigm in Mediterranean lagoons, our study showed that recruitment of this introduced species is possible in the Thau lagoon at levels comparable to those in other traditional French breeding basins. We identified a favorable environmental window for recruitment characterized by high water temperature (>26.5°C) and high nanophytoplankton and Chaetoceros spp. abundances (>4.3 × 106 and 345 × 103 cells l-1, respectively). In these favorable conditions, we hypothesize that the ecosystem functions as an autotrophic system, in contrast to the heterotrophic system that characterizes unfavorable conditions. Under heterotrophic conditions, high abundances of mixotrophic and heterotrophic organisms (ciliates and dinoflagellates) limited the metamorphosis of C. gigas larvae, leading to poor recruitment. This study provides new knowledge on the reproduction of the Pacific oyster in a Mediterranean lagoon under warming and oligotrophication. The shellfish industry will profit from the discovery of spatfields to develop new nursery practices that are eco-friendly and limit risks of transfers with other spatfall areas.

International audience; The recent discovery of Pacific oyster Crassostrea gigas (also known as Magallana gigas) spatfields in a Mediterranean lagoon intensely exploited for shellfish farming (Thau lagoon) revealed significant contrasts in spatial patterns of recruitment. We evaluated the processes that drive spatial patterns in oyster recruitment by comparing observed recruitment, simulated hydrodynamic connectivity and ecological variables. We hypothesized that spatial variability of recruitment depends on (1) hydrodynamic connectivity and (2) the ecology of the larval supply, settlement, metamorphosis, survival and biotic environmental parameters. We assessed recruitment at 6-8 experimental sites by larval sampling and spat collection inside and outside oyster farming areas and on an east-west gradient, from 2012-2014. Hydrodynamic connectivity was simulated using a numerical 3D transport model assessed with a Eulerian indicator. The supply of large umbo larvae did not differ significantly inside and outside oyster farming areas, whereas the supply of pediveligers to sites outside shellfish farms was structured by hydrodynamic connectivity. Inside shellfish farming zones, unfavorable conditions due to trophic competition with filter-feeders jeopardized their settlement. In this case, our results suggest loss of settlement competence by oyster larvae. This confirms our hypothesis of top-down trophic control by the oysters inside farming zones of Thau lagoon in summer that fails to meet the ecological requirements of these areas as oyster nurseries. Knowledge of oyster dispersal, connectivity and recruitment in coastal lagoons will help local development of sustainable natural spat collection. On a global scale, our method could be transposed to other basins or used for other species such as mussels, clams or scallops, to better understand the spatial patterns of bivalve recruitment. Management of the oyster industry based on natural spat collection will help develop a sustainable activity, based on locally adapted oyster strains but also by reducing the risks of transferring pathogens between basins and the global carbon footprint of this industry.

WOS:000529795300004; The decrease of microbial and nutrient inputs from the watershed has long dominated lagoon ecosystem management objectives. Phytoplankton biomass and abundance have drastically decreased for more than a decade and Zostera meadow have gradually recovered, expressing lagoon ecosystem restoration such as Thau lagoon. Do the progressive achievement of the good ecological status of the Thau lagoon possibly threatens the shellfish industry in terms of production and oyster quality, by reducing the carrying capacity? To provide answers about the right balance to be achieved between conservation and exploitation, a new numerical tool was developed to help in decision-making. We hereby propose to incorporate a Dynamic Energy Budget type shellfish production model to an existing lagoon ecosystem box-model. The influence of different scenarios of nutrient inputs (related to projections of population growth or improvement of treatment plants) and shellfish stocks were tested on oyster performances (production, oyster condition index), carrying capacity of the lagoon and ecological status indices used within the EU Water Framework Directive. Model outputs demonstrated that shellfish production was mainly controlled by nutrient inputs, which depend on hydro-meteorological variability, and specifically by phosphorus and N:P ratios of nutrient inputs. Scenarios tested, however, demonstrated smaller differences of oyster production in comparison to inter-annual variability. The overall ecological status of the lagoon remained in a "good" status with acceptable lagoon-scale phytoplankton depletion, regardless of scenarios, setting the carrying capacity of this ecosystem to be sustainable.

International audience; Reproduction and recruitment of benthic invertebrates are influenced by the climate and by the ecological structure of marine ecosystems, along with local anthropogenic pressures such as eutrophication or oligotrophication. Using the Pacific oyster Crassostrea gigas as a biological model, we tested the hypothesis that the variability in prodissoconch II (PII) size (i.e. size at metamorphosis) depends on ecological functioning. Settlement and recruitment were assessed at 5 sampling sites on the French Mediterranean shellfish farmed Thau lagoon during the main summer recruitment events in 3 consecutive years (2012-2014). Hydrobiological and planktonic analyses were conducted at 3 sampling sites. Our results showed that recruitment was extremely heterogeneous, ranging from 0 to 260 +/- 27 SE ind. dm(-2) throughout the ecosystem and was linked with variability in PII size, which ranged from 180 to 296 mu m. The annual temporal pattern of PII sizes appeared to be controlled by temperature during the settlement period, whereas the spatial pattern depended on phytoplankton biomass and on the trophic functioning of the ecosystem. Smaller PII sizes were significantly correlated with the highest phytoplankton biomass, while larger PII sizes were positively correlated with mixotrophic cryptophyte abundance. We found an inverse relationship between PII size and survival after metamorphosis, showing that recruitment success was associated with smaller PII sizes. Regional climate conditions and local trophic functioning appear to be key factors in metamorphosis and consequently contribute to recruitment heterogeneity. Further studies should be performed in other ecosystems following an oligotrophication trajectory to generalize this result.

International audience; Marine intrusion was simulated in a choked and in a restricted coastal lagoon by using a 3D-hydrodynamic model. To study the spatiotemporal progression of seawater intrusion and its mixing efficiency with lagoon waters we define Marine Mixed Volume (VMM) as a new hydrodynamic indicator. Spatial patterns in both lagoons were described by studying the time series and maps of VMM taking into account the meteorological conditions encountered during a water year. The patterns comprised well-mixed zones (WMZ) and physical barrier zones (PBZ) that act as hydrodynamic boundaries. The choked Bages-Sigean lagoon comprises four sub-basins: a PBZ at the inlet, and two WMZ's separated by another PBZ corresponding to a constriction zone. The volumes of the PBZ were 2.1 and 5.4 millions m3 with characteristic mixing timescale of 68 and 84days, respectively. The WMZ were 12.3 and 43.3 millions m3 with characteristics mixing timescale of 70 and 39days, respectively.

International audience; We present the first large-scale, high-resolution spatial and temporal pattern of disease mortality caused by Ostreid herpesvirus 1 (OsHV-1) that has affected Pacific oyster Crassostrea gigas in France every year since 2008, in relation to local farm use. Mortality was monitored in healthy oyster spat deployed at 106 locations in the Thau Mediterranean lagoon during the epizootic that occurred in spring 2011. We conducted a field survey of farming practices in the areas where the sentinel oysters were placed before the epizootic. We found that the risk of disease mortality in sentinel oysters was higher within the bivalve farming area than outside it, suggesting that the infection pressure is much higher in areas with intensive farming activity. The risk of mortality was higher in farms rearing spat, a developmental stage particularly susceptible to OsHV-1, than in farms rearing adult oysters, which are generally more resistant. Additionally, the mortality risk in farms rearing adult animals was similar to that in empty farms, which suggests that, during the study period, adult oysters did not vector the disease. Interestingly, the mortality risk for sentinel oysters deployed in mussel Mytilus galloprovincialis farms was lower than for those held in oyster farms or empty farms, suggesting that mussels reduced the infection pressure on susceptible oysters.

International audience; 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.

The Mediterranean lagoons host many anthropogenic uses including shellfish aquaculture since the beginning of the 20th century. Imported in 1970, the cupped oyster, Crassostrea gigas, has adapted perfectly and has allowed an important development of oyster’s industry until 2008, the year of occurrence of spat outbreak related to the emergence of an Ostreid Herpes-virus µvar. The scarcity of spat and the speculation on this product changed regionally cultural practices and the supply of juveniles, with in particular the wish of developing a local activity of spat collection. However the cycle of reproduction of the species and the recruitment of juveniles were poorly known in lagoon environments. In this context, the objective of this thesis is to characterize the variability of the reproduction and the recruitment of the cupped oyster in Mediterranean lagoon. The lagoon configuration offers the advantages of productivity for the broodstock and hydrodynamic connectivity for the larvae. However, it appears that the ecological functioning of the system at the base of the primary production plays an essential role on the trophic resources for the success of oyster reproduction. This work takes place in the context of the ecological restoration under oligotrophication, which first effects we describe on the oyster's reproductive cycle.; Les lagunes méditerranéennes hébergent de nombreux usages anthropiques dont la conchyliculture depuis le début du 20ème siècle. Importée en 1970, l’huître creuse, Crassostrea gigas, s’y est adaptée parfaitement et a permis un développement ostréicole important jusqu’en 2008, année d’apparition des surmortalités de naissain liées à l’émergence d’un variant du virus OsHv1. La raréfaction du naissain et la spéculation sur ce produit ont modifié régionalement les pratiques culturales et les modes d’approvisionnement en juvéniles, avec notamment la volonté de développer une activité locale de captage. Mais le cycle de reproduction de l’espèce et le recrutement de juvéniles étaient mal connus en milieu lagunaire. Dans ce contexte, l’objectif de cette thèse est de caractériser la variabilité de la reproduction et du recrutement de l’huître creuse en lagune méditerranéenne. La configuration lagunaire offre des atouts de productivité pour le cheptel de géniteurs et de connectivité hydrodynamique pour les larves. Cependant, il apparaît que le fonctionnement écologique du système à la base de la production primaire joue un rôle essentiel sur les apports trophiques pour le succès de la reproduction des huîtres. Ce travail s’inscrit, en outre, dans le contexte d’un écosystème en voie de restauration écologique entamant un processus d’oligotrophisation dont nous décrivons les premiers effets sur le cycle de reproduction de l’huître.