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In the ocean, mesoscale or submesoscale structures and coastal processes are associated with fine scales. The simulation of such features thus requires the hydrodynamic equations to be solved at high-resolution (from a few hundred meters down to a few tens of meters). Therefore, local mesh refinement is a primary issue for regional and coastal modeling. The AGRIF (adaptive grid refinement in Fortran) library is committed to tackling such a challenge for structured grids. It has been implemented in MARS3D (Model for Application at Regional Scale), a semi-implicit, free-surface numerical model developed by Ifremer (the French Research Institute for Exploitation of the Sea) for coastal environmental research and studies. As its time scheme uses an alternating-direction implicit (ADI) algorithm, the two-way nesting implementation differs from the one in explicit models. The present paper describes the specifics of the AGRIF introduction and how the nesting preserves some essential properties (mass, momentum and tracer conservations) along with the induced constraints (bathymetric coherence between grids and increase in computation cost). The use and the performance of this new tool are detailed over two configurations that illustrate the wide range of scales and resolutions typically targeted by coastal applications. The first one is based on multiple high-resolution (500 m) grids that pave the coastal ocean over thousands of kilometers, allowing a continuum between the regional and coastal scales. The second application is more local and has a finer resolution (50 m). It targets a recurrent question for semi-enclosed bays, i.e., the renewal time indicator. Throughout these configurations, the paper intends to compare the two-way nesting method with the traditional one-way approach. It highlights how the MARS3D-AGRIF tool proves to be an efficient way to both improve the physical hydrodynamics and unravel ecological challenges.

International audience; In the ocean, mesoscale or submesoscale structures and coastal processes are associated with fine scales. The simulation of such features thus requires the hydrodynamic equations to be solved at high-resolution (from a few hundred meters down to a few tens of meters). Therefore, local mesh refinement is a primary issue for regional and coastal modeling. The AGRIF(adaptive grid refinement in Fortran) library is committed to tackling sucha challenge for structured grids. It has been implemented in MARS3D (Model for Application at Regional Scale), a semi-implicit, free-surface numerical model developed by Ifremer (the French Research Institute for Exploitation of the Sea) for coastal environmental research and studies. As its time scheme uses an alternating-direction implicit (ADI) algorithm, the two-way nesting implementation differs from the one in explicit models. The present paper describes the specifics of the AGRIF introduction and how the nesting preserves some essential properties (mass, momentum and tracer conservations) along with the induced constraints (bathymetric coherence between grids and increase in computation cost). The use and the performance of this new tool are detailed over two configurations that illustrate the wide range of scales and resolutions typically targeted by coastal applications. The first one is based on multiple high-resolution(500 m) grids that pave the coastal ocean over thousands of kilometers,allowing a continuum between the regional and coastal scales. The secondapplication is more local and has a finer resolution (50 m). It targets arecurrent question for semi-enclosed bays, i.e., the renewal time indicator. Throughout these configurations, the paper intends to compare the two-way nesting method with the traditional one-way approach. It highlights how the MARS3D-AGRIF tool proves to be an efficient way to both improve the physical hydrodynamics and unravel ecological challenges.

From 2014 to 2021 during the cyclone seasons, extensive monitoring of the hydrodynamics within a variety of lagoons of New Caledonia was conducted as a part of the PRESENCE project (PRESsures on coral Ecosystems of New CalEdonia). The PRESENCE project is aimed at building an efficient representation of the land–lagoon–ocean continuum at Grande Terre, New Caledonia's main island. Overall, coastal physical observations encompassed five different lagoons (four of which were never before monitored) and at least eight major atmospheric events ranging from tropical depressions to category 4 cyclones. The main objectives of this study were to characterize the processes controlling the hydrodynamics and hydrology of these lagoons (e.g., ocean–lagoon exchanges, circulation, level dynamics, temperature, and salinity variability), and to capture the magnitude of change during extreme events. An additional objective was to compile an adequate data set for future use in high-resolution hydrodynamic models. Autonomous oceanographic instruments were moored at strategic locations to collect time series of temperature, salinity, pressure, and Eulerian currents. Additionally, Lagrangian surface currents were observed through deploying drifter buoys, and cross-shore hydrological profile radials were carried out using CTDs (conductivity, temperature, depth). In total, five survey campaigns were conducted, beginning with the SPHYNX campaign which lasted 15 months (December 2014 to February 2016) in the Hienghène–Touho lagoon and ended with the 9 months NEMO campaign (September 2020 to April 2021) in Moindou lagoon. Between these were the 5 months NOUMEA campaign (December 2016 to April 2017) in Noumea lagoon, the 6 months ELADE campaign (February to August 2018) in the Poe lagoon, and the 5 months CADHYAK campaign (December 2019 to May 2020) in Koumac lagoon. In addition to characterizing these lagoons, the data set identifies important features and processes, such as the presence of internal waves on forereefs, wave-driven fluxes over reef barriers, and exchanges through passes. Signatures from strong events were also identified, including surges, thermal drops inside lagoons, and massive flash flood plume dispersion. Raw data sets were processed, controlled for quality, validated, and analyzed. Processed files are made publicly available in dedicated repositories on the SEANOE marine data platform in NetCDF format. Links (DOI) of individual data sets are provided herein.

From 2014 to 2021, extensive monitoring of hydrodynamics was deployed within a variety of lagoons of New Caledonia during 6 tropical cyclone seasons. Globally, those coastal physical observations encompassed five different lagoons (four of which were never monitored before) and at least eight major atmospheric events ranging from tropical depression to category 4 cyclone. The main objectives were to characterize the processes at stake controlling hydrodynamics and hydrology of these lagoons (e.g ocean-lagoon exchanges, circulation, level dynamics, temperature and salinity variability) and capture their magnitude of change during extreme events. An additional objective was to build an adequate data set for assessment of high-resolution hydrodynamics models. Those field experiments took place within the PRESENCE project (PRESsures on coral Ecosystems of New CalEdonia) which aimed at building an efficient representation of the land-lagoon-ocean continuum of Grande Terre (main land) lagoons. Autonomous oceanographic instruments were moored at strategic locations to collect time-series of temperature, salinity, pressure, eulerian currents which characterize hydrodynamics at best. During field trips, whenever possible, lagrangian drifters releases and cross-shore hydrological profiles radials were additionally carried out. Surveys begun chronologically with SPHYNX campaign which lasted 15 months (December 2014 to February 2016) in the Hienghène-Touho lagoon followed with 5 months records in NOUMEA lagoon (December 2016 to April 2017). ELADE campaign in Poe lagoon encompassed 2 periods of measure (February to April 2018 and June to August 2018). In Koumac lagoon, CADHYAK survey was carried out between December 2019 until the end of May 2020 and finally, data have been recorded continuously for 9 months in Moindou lagoon (NEMO) (September 2020 to April 2021). In addition to characterize these lagoons, this data set stresses out some important features and processes, such as the presence of internal waves on reef slopes, wave-driven fluxes over reef barrier and exchanges through passes. It also contains the signatures of strong events materialized by surges, thermal drops inside lagoons or massive flash flood plumes dispersion. Raw data sets were processed, quality-controlled and validated, and processed files are publicly available in dedicated repositories on Seanoe in NetCDF format. Links (DOI) of individual data sets are provided herein.

International audience; The Pacific oyster Crassostrea gigas is established in the marine intertidal zone, experiencing rapid and highly dynamic environmental changes throughout the tidal cycle. Depending on the bathymetry, oysters face oxygen deprivation, lack of nutrients, and high changes in temperature during alternation of the cycles of emersion/ immersion. Here we showed that intertidal oysters at a bathymetry level of 3 and 5 m delayed by ten days the onset of mortality associated with Pacific Oyster Mortality Syndrome (POMS) as compared to subtidal oysters. Intertidal oysters presented a lower growth but similar energetic reserves to subtidal oysters but induced proteomic changes indicative of a boost in metabolism, inflammation, and innate immunity that may have improved their resistance during infection with the Ostreid herpes virus. Our work highlights that intertidal harsh environmental conditions modify host-pathogen interaction and improve oyster health. This study opens new perspectives on oyster farming for mitigation strategies based on tidal height.

Depuis 2008, des mortalités massives d’huîtres creuses âgées de moins d’un an sont relevées sur le littoral français dès que la température de l’eau de mer atteint le seuil de 16°C. Ces mortalités de naissains sont associées à la détection du virus OsHV-1 μVar. Depuis 2010, des travaux de qualification zoo-sanitaire ont montré qu’environ un lot de naissains de captage sur deux était infecté par le virus avant l’apparition des mortalités dans le milieu naturel. En 2014, dans le cadre de la première action QUALIF, les résultats de la qualification zoo-sanitaire des naissains du captage de l’année 2013 à l’échelle nationale ont mis en évidence le caractère infectieux des maladies développées par ces naissains porteurs latents d’OsHV-1 μVar. L’objectif 2015 du second volet QUALIF consistait à reproduire le travail de qualification zoo-sanitaire OsHV-1 μVar pour les naissains du captage de l’année 2014. Les résultats (2014 et 2015) permettront d’aborder la variation interannuelle du statut zoo-sanitaire des naissains pour chacun des sites étudiés. La méthodologie de l’épreuve de qualification zoo-sanitaire consiste en une période de 1 mois d’isolement des naissains en conditions contrôlées de laboratoire. Lors de cette épreuve, la température de l’eau de mer est maintenue constante à 21°C et la mortalité est relevée tous les 10 jours. La survie finale et les analyses qPCR permettent de qualifier le statut sanitaire en terme de portage OsHV-1 μVar de l’échantillon (infecté ou non infecté). De début janvier à fin mars 2015, 39 échantillons de naissains âgés de 5 à 7 mois ont été prélevés dans 6 sites du littoral français (étang de Thau, bassin d’Arcachon, bassin de Marennes Oléron, baie de Bourgneuf, embouchure de La Vilaine et rade de Brest) pour être testés en épreuve thermique de laboratoire (ETL) dans l’outil expérimental Ifremer à Argenton. Les résultats montrent que 25 des 39 (soit 64 %) lots de naissains de captage testés ont développé des maladies en ETL associés à des mortalités cumulées variant de 6 à 72 %. Cette valeur de 64 % de lots détectés est plus élevée que celle précédemment observée en 2014 (55 %). Les résultats de cette seconde campagne de qualification zoo-sanitaire sont favorables pour les naissains de l’étang de Thau (absence de mortalité), moins favorables pour ceux d’Arcachon, Marennes Oléron, et ceux de la baie de Bourgneuf (réponses contrastées en terme de mortalité intra-site) et très défavorables pour les naissains de La Vilaine et de la rade de Brest (mortalités observées sur tous les échantillons testés). La principale conclusion de cette seconde étude de qualification zoo-sanitaire est identique à celle de 2014, à savoir qu’il est existe dans le milieu naturel en période hivernale des lots de naissains de captage infectés par OsHV-1 μVar sans développement apparent des maladies. Ces lots de naissains porteurs latents d’OsHV-1 μVar sont détectables en ETL et la présence d’OsHV-1 μVar peut alors être confirmée par qPCR. Dans le contexte actuel d’épizooties chroniques, nos résultats confirment à nouveau qu’il est possible d’identifier précocement les lots de naissains infectés ou non par OsHV-1 μVar. Ces animaux infectés sont un réservoir du virus en période hivernale. Dès que la température de l’eau de mer franchit le seuil de 16°C, ils participeront à la réémergence des maladies en milieu naturel. Par ailleurs, cette seconde étude de qualification zoo-sanitaire confirme la possibilité d’apprécier le risque sanitaire pour chaque zone de captage en fonction de la détection précoce des lots de naissains infectés par OsHV-1 μVar.

International audience; High mortality of farmed oysters during summer leads to major economic losses. Vibrio aestuarianus is one of the pathogens associated with such recently observed severe mortality outbreaks in Pacific oysters, in France as well as in other parts of the globe. Our objective is to better understand, using a multiscale modelling framework, how this bacterium spreads in a spatially explicit metapopulation of oysters to evaluate its impact and, on a longer term, control measures to limit losses for farmers. We design a discrete time stochastic compartmental model, with farm level subpopulations connected through water neighboring relationships and anthropogenic movements of oysters between different farming sites. The model accounts for the diversity in inter-farm infection dynamics by coupling epidemiological models at intra-farm scale through a hydrodynamic particle transport model and a set of rules representing anthropogenic movements between sites based on farming practice. Farming sites are identified by land registers. The intra-farm host-pathogen dynamics is represented using three epidemiological compartments for oysters together with an infectious particle density compartment. Subpopulations exchange the pathogen particles shed by infected oysters at two scales: within a neighborhood through a local diffusion process, and on long distances using a hydrodynamic particle transport model. A mechanistic contact network is designed to simulate the anthropogenic movements of oysters between farming sites, as part of farm management practices, based on the information obtained from interviews. The model is applied on the oyster farming layout of the Baie des Veys area in Normandy, France, using observed oceano-environmental inputs for the hydrodynamic transport model, aiming to explore pathogen dynamics in a real case study. Scenarios of the initiation of pathogen outbreak are simulated to assess the respective roles of local and long distances dynamics. The next step will be to validate the model using data collected during a mortality event in summer 2014. We propose a generic modelling framework to represent pathogen spread in a metapopulation of oysters, coupling interactions at multiple scales. The specific part of the model concern the farming system practices in the area considered, which have to be adapted before using the model for different locations or types of farm management

The rising interest in environmental and ecosystem dynamics have lead coastal oceanographers to not only investigate the “traditional” physical parameters describing the ocean state and its dynamics (e.g. temperature, salinity, currents, water levels in coastal areas), but to also account for the dynamics of parameters describing its biogeochemical components. To that end, MARS3D regional and coastal modelling system has been coupled to ecosystem modules (ECO-MARS3D, ECO3M) as well as sediment dynamics modules (MARS3D-SEDIM): sediment, nutrient and primary production contents can be considered as the lower level environment and ecosystem descriptors of the “biogeochemical” ocean. Early investments into physical and biological analysis at the regional scale have led to the development of several operational configurations within PREVIMER since 2006 for physical and biological parameters, providing 3 to 5-day forecasts as well as hindcasts. The more recent introduction of sediment-related parameters into the operational chain required validating computed sediment transport at the regional scale. Such validation is mostly accessible through indirect measurements – namely turbidity measurements in the water column or derived from satellite data. This paper describes the main features of MARS3D sediment module, the sensitivity analyses and the validation procedures based on dedicated data acquisition, as well as the assessment of the operational configuration focused on the Bay of Biscay continental shelf. Comparison between in situ measurements and satellite data shows a fairly systematic overestimation of the satellite-derived SPM in Southern Brittany; this result stresses the need for further investigation regarding the correct quantitative satellite SPM determination at all times and all places. On the other hand, numerical results highlight the difficulty to simultaneously predict the correct magnitude of bottom and surface concentrations.

The dynamics of physico-chemical processes in the bay of Brest are studied to better understand the impact of local events on the coastal ocean. We are analyzing long-term in situ data (since 2000), high and low frequencies, from the COAST-HF (buoy Marel Iroise) and SOMLIT sites, located at the entrance to the bay of Brest. This study is divided into two main stages: the detection and characterization of extreme events, followed by a numerical simulation of these events to understand the underlying oceanic processes. The focus is on desalination events during the winter months (December, January, February and March), considering the season with the greatest number of extreme events. We show the relationship between local extreme events and variability at larger scales, considering climate indices such as the North Atlantic Oscillation (NAO). A comparison between the low frequency data of the SOMLIT program and the high frequency data of the Marel buoy is carried out, highlighting the interest of high frequency measurements for the detection of extreme events. A comparison between in situ data and two numerical simulations of different resolutions is also performed over salinity time series. This study also show an interannual variability of extreme events interesting in a context of climate change. We make the link between these extreme desalination and the nitrate level in the bay of Brest. To finally study the relationship between nutrients and chlorophyll in order to look at the correlation that it can exists between extreme events and biology in the coastal environment.

La conchyliculture représente une activité importante en Normandie et doit faire face à de sérieuses difficultés (mortalités, diminution de la qualité des produits). Un enjeu actuel concerne la réorganisation des zones d’élevage existantes afin d’optimiser les performances. A contrario, la pisciculture marine est très peu présente dans cette région et il existe un réel enjeu de développement économique. Dans ce contexte, les décideurs (services de l’Etat) et les professionnels ont besoin d’identifier des sites propices à la réalisation de ces activités qui soient également compatibles avec les nombreux autres usages du littoral. Au sein du projet SISQUONOR, un démonstrateur sous Système d’Information Géographique, nommé AkvaVis et développé originellement pour l’aquaculture norvégienne, a été transféré et adapté à la conchyliculture normande. L’application française SISAQUA intègre des données spatialisées variées telles que des sorties de modèles biophysiques (courants, vagues…), des données issues des satellites (température de l’eau, concentration en phytoplancton), d’autres données environnementales (bathymétrie, type de substrat…) ainsi que des informations liées au cadre réglementaire (cadastres conchylicoles, plans de protection environnementale…) nécessaires à la gestion et planification des activités conchylicoles. Des indicateurs spatiaux ont ensuite été construits afin d’identifier des sites propices à l’élevage de moules et d’huîtres. L’un de ces indicateurs est basé sur les données satellites et la simulation de la croissance des bivalves à l’aide de modèles d’écophysiologie. Des développements futurs seront conduits dans le cadre du projet H2020 AquaSpace (2015-2018) et incluront notamment la production piscicole.