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Datasets supporting the figures presented in the manuscript., The oyster experiment and field campaigns were designed and conducted in the framework of the COSELMAR project funded by the R��gion Pays de la Loire. CJR was supported later by Deutsche Forschungsgemeinschaft grant number AB 109/11-1

International audience; Seagrass meadows are monitored in the frame of several environmental programs worldwide, including the Water Framework Directive (WFD), to evaluate the ecological status of European coastal and transitional water bodies. The large size, spatial complexity, and interannual variability of seagrass ecosystems significantly challenge field monitoring. In this study, a multi-mission satellite time-series was used to estimate long-term changes in seagrass status in a macrotidal system dominated by Zostera noltei, at Bourgneuf Bay (French Atlantic coast). Metrics of seagrass extent and density were obtained from Earth Observation (EO) using validated and inter-calibrated Landsat, SPOT and Sentinel2 data from 1985 to 2020. The information provided by satellite data made it possible to compute and compare several seagrass indicators currently in use in several European countries (France, Portugal and UK) within the WFD. Both the seagrass extent and meadow-averaged density displayed increasing trends since 1985. A time-series of merged observations from various satellites revealed a high degree of interannual variability in seagrass extent, with abrupt losses (up to 50% within one year) alternating with periods of slow recovery (typically 4-6 years). The seagrass meadow which was in a moderate status (sensu the WFD) in the 1980s, achieved an overall recurrent good or high status since the mid-1990s. Altogether, the methods and results presented here demonstrated that EO is a reliable source of information for mapping and assessing the status of intertidal seagrass, complementing in situ measurements by providing long-term, spatial view and standardized observation framework. We recommend the systematic use of EO time-series in complement to traditional field measurements in seagrass monitoring programs such as the WFD.

Supplementary information

CoastObs is an EU H2020 funded project that aims at using satellite remote sensing to monitor coastal water environments and to develop a user-relevant platform that can offer validated products to users This report will present in subsequent chapters the main types of higher level products that are being developed in CoastObs. Ch 3: Phytoplankton bloom phenology CH 4: Sediment plume morphology CH 5: Coastal erosion and accretion CH 6: Water Framework Directive reporting CH 7: Integration with modelling: mussel culture potential CH 8: Integration with modelling: harmful algae bloom forecasting Each chapter will present a rationale and background, the input data for the product generation, main methods used and examples of results so far.

International audience; Aquaculture increasingly contributes to global seafood production, requiring new farm sites for continued growth. In France, oyster cultivation has conventionally taken place in the intertidal zone, where there is little or no further room for expansion. Despite interest in moving production further offshore, more information is needed regarding the biological potential for offshore oyster growth, including its spatial and temporal variability. This study shows the use of remotely-sensed chlorophyll-a and total suspended matter concentrations retrieved from the Medium Resolution Imaging Spectrometer (MERIS), and sea surface temperature from the Advanced Very High Resolution Radiometer (AVHRR), all validated using in situ matchup measurements, as input to run a Dynamic Energy Budget (DEB) Pacific oyster growth model for a study site along the French Atlantic coast (Bourgneuf Bay, France). Resulting oyster growth maps were calibrated and validated using in situ measurements of total oyster weight made throughout two growing seasons, from the intertidal zone, where cultivation currently takes place, and from experimental offshore sites, for both spat (R-2 = 0.91; RMSE = 1.60 g) and adults (R-2 = 0.95; RMSE = 4.34 g). Oyster growth time series are further digested into industry-relevant indicators, such as time to achieve market weight and quality index, elaborated in consultation with local producers and industry professionals, and which are also mapped. Offshore growth is found to be feasible and to be as much as two times faster than in the intertidal zone (p < 0.001). However, the potential for growth is also revealed to be highly variable across the investigated area. Mapping reveals a clear spatial gradient in production potential in the offshore environment, with the northeastern segment of the bay far better suited than the southwestern. Results also highlight the added value of spatiotemporal data, such as satellite image time series, to drive modeling in support of marine spatial planning. The current work demonstrates the feasibility and benefit of such a coupled remote sensing-modeling approach within a shellfish farming context, responding to real and current interests of oyster producers.

Poster presentation at the Joint GEO AquaWatch/GloboLakes 2018 Meeting “Water Quality Information for the Benefit of Society&rdquo

Assessing the ecological status of transitional water bodies under the WFD: study on the relevance of monitoring estuarine microphytobenthos communities as bio-indicator. Final report 2018.  Abstract In order to establish the ecological status of water bodies, the European Water Framework Directive (WFD) is based on the evaluation of a number of biological quality elements, as well as physical parameters supporting the biology. In estuaries, phytoplankton monitoring was not considered relevant because of the high turbidity characterizing the large metropolitan estuaries and the French overseas departments (Guyana). In this work, we considered the possibility of using microphytobenthos (MPB) as a biological indicator of the ecological status of estuaries. This activity report summarizes the actions undertaken in 2017 under an AFB / Université de Nantes convention, which is structured around two main axes: the first axis is based on the analysis of the composition of MPB assemblages, and involves studying changes in MPB structure along disturbance gradients to develop a bioindicator. Assemblages are collected using micro-scale cores along transects positioned in the poly-haline portion of an estuary. This report summarizes the main results obtained during the field campaigns undertaken on the Loire estuary in the spring and autumn of 2016. The MPB diversity analysis are supplemented by measurements of biotic variables (meiofauna, macrofauna) and abiotics (PAHs, heavy metals, nutrients). This first axis also includes the development of a historical database based on the collections of Tempère and Peragallo, published between 1889 and 1915, as well as on the atlas of benthic marine diatoms of the French coastlines of Peragallo & Peragallo (1897- 1908). The database was completed in 2017 with more recent data from publications, dissertations, and reports. The second axis corresponds to a macro-scale study on the analysis of spatial distribution and biomass of MPB at the scale of an entire estuary by remote sensing. The objective is to develop a metric derived from data collected at macroscale. We began to develop the method for the Loire estuary while considering the possibility of applying it to the 42 estuaries and bays identified as transitional waters in metropolitan France. For this, we estimated the potential of different multispectral sensors to map microphytobenthos for estuaries of varying size, taking into account their spatial and spectral resolution. 351 taxa have been identified and grouped into different life forms. Benthic species are the majority, but a significant contribution of freshwater phytoplankton is observed in the spring. Among the benthic forms, the diatom assemblages of the Loire estuary are dominated by epipelic life forms. They are large mobile diatoms that can move freely between sediment particles and form biofilms. Results of multivariate analyzes between diatom communities and different forms of natural and anthropogenic pressures show that communities responded to pressures. However, anthropogenic pressures had a smaller effect than natural variability, due to differences in salinity and temperature. The level of contamination at all three sites and along the transects was not as high as expected. A co-inertia analysis confirmed that the different forms of pressure appeared only behind the natural forcings that accounted for the largest percentage of model variance. The application of the indices developed for rivers such as the Index of Pollution Sensitivity Index (IPS) was tested with the OMNIDIA software. All samples were of poor ecological status. However, this ranking was mainly due to the halophilic nature of the species, which naturally withstand high salinities in the estuary, whereas for streams, species which withstand strong conductivities, are considered indicative of impacted environment. A more promising approach would be to develop a method similar to the reference species approach, where the cumulative frequency of reference condition indicator species determines the water quality of the site (Kelly, 2013). However, the pollution tolerances of estuarine and coastal diatom species are poorly known. Thus a general list of tolerant species should be compiled and we believe that the development of the historical database produced in our study, as well as the current lists of diatom species (Annexes 4 and 5) are important first steps. One of the deliverables of this work is the historical database of benthic diatoms in mainland France produced under the ACCESS software. It must be completed by a hundred modern bibliographic references currently entered on an EXCEL file. For the macro-scale approach, we have created time-series of NDVI over a period of 17 years, starting in 2000, using MODIS images. The important information is that enough data could be recovered to be able to apply the Dynamic Linear Model (DLM) time-series analysis method (Hernández-Fariñas et al., 2013). The MPB of the Loire could then be related to the variations of nitrates and phosphates, with a decrease in NDVI since 2000, as for phytoplankton. The NDVI which estimates the biomass of the MPB of a whole body of water thus responds to a form of pressure: the nutrient concentration. This is a first step towards the development of a 90-percentile DCE-compatible metric. However, the MODIS sensor does not allow small estuaries to be observed. This sensor nevertheless has important advantages: free images, integrated atmospheric corrections, archive data available since 2000. The intersensor comparison exercise has highlighted the interest of Sentinel 2 to observe the 42 METs of metropolitan France. Finally, we propose a series of recommendations to optimize the sampling and reduce the sources of variability. &nbsp

In order to establish the ecological status of water bodies, the European Water Framework Directive (WFD) is based on the evaluation of a number of biological quality elements, as well as physical parameters supporting the biology. In estuaries, phytoplankton monitoring was not considered relevant because of the high turbidity characterizing the large metropolitan estuaries and the French overseas departments (Guyana). In this work, we considered the possibility of using microphytobenthos (MPB) as a biological indicator of the ecological status of estuaries. This activity report summarizes the actions undertaken in 2017 under an AFB / Université de Nantes convention, which is structured around two main axes: the first axis is based on the analysis of the composition of MPB assemblages, and involves studying changes in MPB structure along disturbance gradients to develop a bioindicator. Assemblages are collected using micro-scale cores along transects positioned in the poly-haline portion of an estuary. This report summarizes the main results obtained during the field campaigns undertaken on the Loire estuary in the spring and autumn of 2016. The MPB diversity analysis are supplemented by measurements of biotic variables (meiofauna, macrofauna) and abiotics (PAHs, heavy metals, nutrients). This first axis also includes the development of a historical database based on the collections of Tempère and Peragallo, published between 1889 and 1915, as well as on the atlas of benthic marine diatoms of the French coastlines of Peragallo & Peragallo (1897- 1908). The database was completed in 2017 with more recent data from publications, dissertations, and reports. The second axis corresponds to a macro-scale study on the analysis of spatial distribution and biomass of MPB at the scale of an entire estuary by remote sensing. The objective is to develop a metric derived from data collected at macroscale. We began to develop the method for the Loire estuary while considering the possibility of applying it to the 42 estuaries and bays identified as transitional waters in metropolitan France. For this, we estimated the potential of different multispectral sensors to map microphytobenthos for estuaries of varying size, taking into account their spatial and spectral resolution. 351 taxa have been identified and grouped into different life forms. Benthic species are the majority, but a significant contribution of freshwater phytoplankton is observed in the spring. Among the benthic forms, the diatom assemblages of the Loire estuary are dominated by epipelic life forms. They are large mobile diatoms that can move freely between sediment particles and form biofilms. Results of multivariate analyzes between diatom communities and different forms of natural and anthropogenic pressures show that communities responded to pressures. However, anthropogenic pressures had a smaller effect than natural variability, due to differences in salinity and temperature. The level of contamination at all three sites and along the transects was not as high as expected. A co-inertia analysis confirmed that the different forms of pressure appeared only behind the natural forcings that accounted for the largest percentage of model variance. The application of the indices developed for rivers such as the Index of Pollution Sensitivity Index (IPS) was tested with the OMNIDIA software. All samples were of poor ecological status. However, this ranking was mainly due to the halophilic nature of the species, which naturally withstand high salinities in the estuary, whereas for streams, species which withstand strong conductivities, are considered indicative of impacted environment. A more promising approach would be to develop a method similar to the reference species approach, where the cumulative frequency of reference condition indicator species determines the water quality of the site (Kelly, 2013). However, the pollution tolerances of estuarine and coastal diatom species are poorly known. Thus a general list of tolerant species should be compiled and we believe that the development of the historical database produced in our study, as well as the current lists of diatom species (Annexes 4 and 5) are important first steps. One of the deliverables of this work is the historical database of benthic diatoms in mainland France produced under the ACCESS software. It must be completed by a hundred modern bibliographic references currently entered on an EXCEL file. For the macro-scale approach, we have created time-series of NDVI over a period of 17 years, starting in 2000, using MODIS images. The important information is that enough data could be recovered to be able to apply the Dynamic Linear Model (DLM) time-series analysis method (Hernández-Fariñas et al., 2013). The MPB of the Loire could then be related to the variations of nitrates and phosphates, with a decrease in NDVI since 2000, as for phytoplankton. The NDVI which estimates the biomass of the MPB of a whole body of water thus responds to a form of pressure: the nutrient concentration. This is a first step towards the development of a 90-percentile DCE-compatible metric. However, the MODIS sensor does not allow small estuaries to be observed. This sensor nevertheless has important advantages: free images, integrated atmospheric corrections, archive data available since 2000. The inter-sensor comparison exercise has highlighted the interest of Sentinel 2 to observe the 42 METs of metropolitan France. Finally, we propose a series of recommendations to optimize the sampling and reduce the sources of variability., Afin d’établir l’état écologique des masses d’eau, la Directive Cadre Européenne sur l’Eau (DCE) s’appuie sur l’évaluation d’un certain nombre d’éléments de qualité biologique, ainsi que des paramètres physico‐chimiques soutenant la biologie. Le suivi du phytoplancton n'étant pas jugé pertinent du fait de la forte turbidité caractérisant les grands estuaires de métropole et des DOM (Guyane), il est apparu comme pertinent d’étudier la possibilité d’utiliser les peuplements du microphytobenthos (MPB) en tant qu’indicateur biologique de l’état écologique des estuaires. Ce rapport d’activité effectue la synthèse finale du projet qui s’inscrit dans le cadre d’une convention AFB/Université de Nantes. Il s’articule principalement autour de deux axes : le premier axe repose sur l’analyse de la composition spécifique du MPB, et consiste à étudier les variations de la structure des peuplements le long de gradients de perturbation, pour développer un bio-indicateur. Les peuplements sont prélevés à l’aide de carottes à micro-échelle, le long de transects positionnés dans la partie poly-haline d’un estuaire. Ce rapport synthétise les principaux résultats obtenus lors des campagnes de terrain engagées sur l’estuaire de la Loire au printemps et à l’automne de l’année 2016. Les mesures de diversité du MPB sont complétées par des mesures de variables biotiques (méïofaune, macrofaune) et abiotiques (HAP, métaux lourds, nutriments). Ce premier axe comprend également l’élaboration d’une base de données historiques reposant sur les collections de Tempère et Peragallo, publiées entre 1889 et 1915, ainsi que sur l’atlas des diatomées marines benthiques des littoraux français de Peragallo & Peragallo (1897-1908). La base de données a été complétée en 2017 par des données plus récentes issues de publications, de thèse et de rapports. Le second axe correspond à une étude à macroéchelle portant sur l’analyse de la distribution spatiale et de la biomasse de MPB à l’échelle de tout un estuaire par télédétection. L’objectif est de développer des métriques issues de données mesurées à macroéchelle. Nous avons commencé à développer la méthode pour l’estuaire de la Loire tout en considérant la possibilité de l’appliquer aux 42 estuaires et baies identifiées comme des masses d’eaux de transition en France métropolitaine. Pour cela, nous avons estimé le potentiel de différents capteurs multispectraux pour cartographier les peuplements du microphytobenthos pour des estuaires de tailles variables, en tenant compte de leur résolution spatiale et spectrale. Enfin, nous proposons une série de préconisations pour optimiser l’échantillonnage et réduire les sources de variabilité.

International audience; Beyond key ecological services, marine resources are crucial for human food security and socio-economical sustainability. Among them, shellfish aquaculture and fishing are of primary importance but become more vulnerable under anthropogenic pressure, as evidenced by reported mass mortality events linked to global changes such as ocean warming and acidification, chemical contamination, and diseases. Understanding climate-related risks is a vital objective for conservation strategies, ecosystems management and human health. We provide here a comprehensive study of the historical mortality of adult oysters related to observed climate variability along the French Atlantic coast from 1986 to 2015, and we built on this knowledge to develop hindcast and forecast assessments of the oyster mortality risk from 1900 to 2100. We show that mortality events usually occur several months after winters dominated by the occurrence of positive North Atlantic oscillation (NAO+) atmospheric regimes of circulation. We explain the lagged response by the multiseasonal long-lasting imprint of wintertime NAO+ on biological and environmental factors, which partly structure oyster mortality etiology. Very high wintertime seawater temperature anomalies at the interannual timescale, which were mostly attributable to internal climate variability through NAO+ and which led to pronounced mortality over the observed period, are then treated as 'analogs' in a large ensemble of Intergovernmental Panel on Climate Change emission scenarios and models in order to anticipate future risks. Without any adaptive process, we provide evidence that actual exceptional mortality is likely to become the norm by similar to 2035, even if global warming is limited to +2 degrees C relative to pre-industrial levels.

International audience