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Sequential membrane filtration of water samples is commonly used to monitor the diversity of aquatic microbial eukaryotes. This capture method is efficient to focus on specific taxonomic groups within a size fraction, but it is time‐consuming. Centrifugation, often used to collect microorganisms from pure culture, could be seen as an alternative to capture microbial eukaryotic communities from environmental samples. Here, we compared the two capture methods to assess diversity and ecological patterns of eukaryotic communities in the Thau lagoon, France. Water samples were taken twice a month over a full year and sequential filtration targeting the picoplankton (0.2–3 μm) and larger organisms (>3 μm) was used in parallel to centrifugation. The microbial eukaryotic community in the samples was described using an environmental DNA approach targeting the V4 region of the 18S rRNA gene. The most abundant divisions in the filtration fractions and the centrifugation pellet were Dinoflagellata, Metazoa, Ochrophyta, Cryptophyta. Chlorophyta were dominant in the centrifugation pellet and the picoplankton fraction but not in the larger fraction. Diversity indices and structuring patterns of the community in the two size fractions and the centrifugation pellet were comparable. Twenty amplicon sequence variants were significantly differentially abundant between the two size fractions and the centrifugation pellet, and their temporal patterns of abundance in the two fractions combined were similar to those obtained with centrifugation. Overall, centrifugation led to similar ecological conclusions as the two filtrated fractions combined, thus making it an attractive time‐efficient alternative to sequential filtration. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 (V MM ) as a new hydrodynamic indicator. Spatial patterns in both lagoons were described by studying the time series and maps of V MM 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 m 3 with characteristic mixing timescale of 68 and 84 days, respectively. The WMZ were 12.3 and 43.3 millions m 3 with characteristics mixing timescale of 70 and 39 days, respectively. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We developed a growth model for the oyster Crassostrea gigas cultured in Thau Lagoon. The oyster standing stock in the lagoon ranged between 10,000 and 15,000 tons a year. Two culture methods are presently in use in Thau Lagoon which are used in about the same proportions. At seeding, initial size of oysters is different among methods. The model was calibrated on (1) growth data accounted for both culture methods and (2) hydrobiological data (temperature, salinity, suspended particulate matter and chlorophyll a), both recorded in several sites in the lagoon between March 2000 and October 2001. The lagoon is slightly eutrophic: total chlorophyll a and total particulate matter averaged 1.2 μg l−1 and 2.2 mg l−1, respectively. Organic content accounted for ca. 40–50% of particulate matter. There was no seasonal trend in seston, whereas temperature and salinity were minimal in winter. Oyster growth varied among sites in response to spatial variations in seston. Growth was maximal in summer and minimal in winter because of temperature seasonality. For each location, we modelled growth as a function of particulate organic matter and temperature. Chlorophyll a was left out of the model because of a weaker fit with growth. Growth was modelled as G=aPOMbTcYd, where G is the growth rate in shell length (mm day−1) or in mass (g day−1), POM is particulate organic matter (mg l−1), T is temperature (°C) and Y is either shell length (mm) or mass (total individual mass or dry flesh mass in g). Allometry (Yd) allowed us to use the same model for both culture methods. The model yielded a good fit with actual size, either as measured by shell length (R2=0.96) or total individual mass (R2=0.93). [Copyright &y& Elsevier]

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 ∑H 2 S up to 390, 17 and 295 μmol·L−1, respectively. Phytoplankton biomass consequently increased by 20 (11.8 μg chl al −1) and abundance by 4.5 (186 × 106 cells·L1) dominated largely by green algae <5 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. • In presence of oysters, anoxia was reached after 54 h in the mesocosm. • A picophytoplankton bloom was observed during anoxia and oyster decomposition. • Anoxia and oyster mortalities induced a community shift towards small plankton. [ABSTRACT FROM AUTHOR]

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. • Impact of juvenile oysters on the benthic compartment was low at the time of experiment (winter). • Juvenile oysters influenced phytoplankton community through grazing. • The long farming history of Thau lagoon could have shaped sediment properties. • Multi-compartment approaches allow to better describe aquaculture-environment interactions. [ABSTRACT FROM AUTHOR]

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. Unlabelled Image • This 5-decades study explains the oligotrophication trajectory of a coastal lagoon. • The decrease in nutrient inputs resulted in ecological changes in pelagic & benthic communities. • A eutrophic period, a transition phase & a regime shift characterised recovery. • The main triggers of summer anoxia were air temperature and eutrophication status. • Oligotrophication has made the ecosystem more resistant to the threat of heat waves. [ABSTRACT FROM AUTHOR]

• The variability of oyster production is mainly controlled by the hydrometeorology. • Waste water treatment plant (WWTP) efficiency affect oyster production, without significantly improving the ecological status of the Thau lagoon. • Scenario of oyster stocking density to its authorized maximum triggered an increase of oyster productions at the expenses of thinner oysters with a lower condition index. • The Thau lagoon remains an exceptional site for oyster farming associated with "good" ecological status condition and where the carrying capacity was not limiting. • Oyster production might be threatened by drastic measures to be undertaken on WWPT, particularly on phosphorus that seems to control primary production in the Thau ecosystem. 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. [ABSTRACT FROM AUTHOR]