Tracking data of 7 grey seals were obtained from the deployment of Fastloc GPS/GSM tags developed by the Sea Mammal Research Unit (UK). Full tag description is available at: http://www.smru.st-andrews.ac.uk/Instrumentation/GPSPhoneTag/. The tags include a wet-dry sensor from which haulout events are recorded, a pressure sensor providing detailed dive data, as well as a Fastloc GPS recording irregular locations when the seal is not underwater. Data is stored onboard and transmitted via the GSM network when the seal is in the reception range. The data provided here are the individual GPS locations of the seals fitted with these tags for an average duration of 135 days.

Understanding the spatial and temporal preferences of toxic phytoplankton species is of paramount importance in managing and predicting harmful events in aquatic ecosystems. In this study we address the realised niche of the species Alexandrium minutum, Pseudo-nitzschia fraudulenta and P. australis. We used them to highlight distribution patterns at different scales and determine possible drivers. To achieve this, we have developed original procedures coupling niche theory and habitat suitability modelling using abundance data in four consecutive steps: 1) Estimate the realised niche applying kernel functions. 2) Assess differences between the species’ niche as a whole and at the local level. 3) Develop habitat and temporal suitability models using niche overlap procedures. 4) Explore species temporal and spatial distributions to highlight possible drivers. Data used are species abundance and environmental variables collected over 27 years (1988-2014) and include 139 coastal water sampling sites along the French Atlantic coast. Results show that A. minutum and P. australis niches are very different, although both species have preference for warmer months. They both respond to decadal summer NAO but in the opposite way. P. fraudulenta realised niche lies in between the two other species niches. It also prefers warmer months but does not respond to decadal summer NAO. The Brittany peninsula is now classified as an area of prevalence for the three species. The methodology used here will allow to anticipate species distribution in the event of future environmental challenges resulting from climate change scenarios.

As part of the marine water quality monitoring of the “Pertuis” and the “baie de l’Aiguillon” (France), commissioned by the OFB and carried out by setec énergie environnement, three monitoring stations were installed. Two of them were set up at the mouths of the Charente and Seudre rivers on February 6 and 27, 2019, respectively, while a third was deployed in the Bay of Aiguillon on March 24, 2021. The dataset presented here concerns the station installed in the Charente estuary. Measurements are organized into .csv files, with one file per year. Data is collected using a SAMBAT multiparameter probe, which records the following parameters: - Temperature (-5 to 35 °C) - Conductivity (0 to 10 mS/cm) - Pressure (0 to 10 m) - Turbidity (0 to 300 NTU) - Dissolved Oxygen (0 to 20 mg/L & 0 to 200 %) - Fluorescence (0 to 50 µg/l) - PH (0/14)

The SOMLIT-Antioche observation station, located at 5 nautical miles from Chef de Baie harbor (La Rochelle) is part of the French monitoring network SOMLIT (https://www.somlit.fr/), accredited by the INSU-CNRS as a national Earth Science Observatory (Service National d’Observation : SNO), which comprises 12 observation stations distributed throughout France in coastal locations. It aims to detect long-term changes  of these ecosystems under both natural and anthropogenic forcings. SOMLIT is part of the national research infrastructure for coastal ocean observation ILICO (https://www.ir-ilico.fr/?PagePrincipale&lang=en). The SOMLIT-Antioche station (46.0842 °N, 1.30833 °W) is located in the north-eastern part of the Bay of Biscay, halfway between the islands of Ré and Oléron, at the centre of what is commonly known as the Pertuis Charentais area, which correspond to a semi-enclosed shallow basin and includes four islands (Ré, Oléron, Aix and Madame) and three Pertuis (i.e., detroit) (Breton, Antioche and Maumusson). This 40m-deep site, with muddy to sandy marine bottoms, is submitted to a macro-tidal regime and is largely open to the prevailing westerly swells. It remains under a dominant oceanic/neritic influence, even though its winter/spring hydrological context is influenced by the diluted plumes of the Charente, Gironde and Loire rivers, but not by those of too small estuaries (Lay, Seudre and Sèvre Niortaise). SOMLIT-Antioche hydrological monitoring has been carried out by the LIENSs/OASU laboratory on a fortnightly basis since June 2011. Surface water samples are collected  at high-tide during intermediate tides (70 ± 10 in SHOM units) on board the research  vessel ‘L’Estran’ owned by La Rochelle University. Samples are analyzed for more than 16 core parameters: temperature, salinity, dissolved oxygen, pH, ammonia, nitrates, nitrites, phosphates, silicates, suspended matter, particulate organic carbone, particulate organic nitrogen, chlorophyll, delta15N, delta13C; pico- and nano- plankton. Measurements are carried out in accordance with the ISO/IEC 17025:2017 standard. Simultaneous monitoring of the micro-phytoplankton community (since 2013, SNO PHYTOBS: https://www.phytobs.fr/en) and monitoring of prokaryotic communities (Bacteria and Archaea) are also carried out on a monthly basis. Since 2019, seasonal observations of benthic invertebrate communities (SNO BenthObs : https://www.benthobs.fr/) have also been carried out. This monitoring is complementary to that carried out at hydrological stations in the pre-existing REPHY and DCE networks, some of which are located near marine farming areas (oyster and mussel farms).

The dataset dcm_dtb.txt contains bio-optical measurements and environmental parameters associated with  Deep Chlorophyll Maxima (DCM) acquired by BGC-Argo profiling floats. For each BGC-Argo profile the data files includes the World Meteorological Organization (WMO) and profile numbers, the Data Assembly Center (DAC), the geographical position (LON and LAT), the date of the profile in Julian Day (JULD) and in YYYY-MM-DD format; the region of the profile (REGION, acronyms detailed in the region.txt file), the DCM zonal attribution (ZONE, acronyms detailed in the zone.txt file), the vertical resolution of measurements of the concentration of the chlorophyll a [Chla] and of the backscattering coefficient (bbp) within the 250 first meters, the Mixed Layer Depth (MLD, m), the qualification of the vertical profile (DCM_TYPE) as Deep Biomass Maximum (3), Deep photoAcclimation Maximum (2), or presenting no DCM (1); the depth of the DCM (DCM_DEPTH); the chlorophyll a concentration (CHLA_DCM, mg chla m-3 ) the backscattering coefficient (BBP_DCM, m-1), and the Brunt-Vaisala frequency (N2_DCM) at the DCM depth; the nitracline depth (NCLINE_DEPTH, m) and steepness (NCLINE_STEEP, µmol NO3 m-3 m-1), the mean nitrate concentration within the Mixed Layer (NO3_MEAN_MLD, µmol NO3 m-3), the mean daily Photosynthetically Available Radiation in the Mixed Layer (MEAN_IPAR_MLD, E m -1 d -1), the daily Photosynthetically Available Radiation at the nitracline depth (IPAR_NCLINE, E m-2 d-1);  and the [Chla] measured by satellite (CHLA_SAT, mg chla m-3). The dataset shape_NASTG_ASEW.txt contains the seasonal median, the first and third quartiles of the [Chla] and of the bbp profiles for the North Atlantic Subtropical Gyre and Atlantic SubEquatorial Waters regions. The dataset climato_NASTG_ASEW.txt contains the monthly mean and standard deviations of the DCM depth (DCM_depth), the isolume depth of daily Photosynthetically Available Radiation of 20 E m-2 d-1 (iPAR_20), the nitracline depth, and the Mixed Layer Depth (MLD) for the profiles within the North Atlantic Subtropical Gyre and Atlantic SubEquatorial Waters regions.  The qualification and processing of the BGC-Argo profiles, as well as the DCM detection (DCM_TYPE) and the estimation of the environmental parameters, were applied as described from Cornec, M., Claustre, H., Mignot, A., Guidi, L., Lacour, L., Poteau, A., D’Ortenzio, F.,Gentili, B., Schmechtig, C., (to be updated.) Deep Chlorophyll Maxima in the global ocean: occurrences, drivers and characteristics. Global Biogeochemical Cycles, to be updated The [Chla] satellite variable was obtained by the match of each BGC-Argo profile with a L3S [Chla] product from the Ocean Colour-Climate Change Initiative v4.0 database merging observations from MERIS, MODIS, VIIRS and SeaWiFs, at a monthly and 4x4-km-pixel resolution, up to December 31, 2019 (ftp://oc-cci-data:ELaiWai8ae@oceancolour.org/occci-v4.2/).

The PHYTOBS-MARCOBOLO dataset comprises long-term time series on marine microphytoplankton, from 2003 to 2021, along the entire French metropolitan coastline. Microphytoplankton data cover microscopic taxonomic identifications and counts. The PHYTOBS-MARCOBOLO dataset corresponds to a dataset extracted from the PHYTOBS network (DOI:10.17882/85178). The PHYTOBS network provides the scientific community and stakeholders with validated and qualified data on the biomass, abundance and composition of marine microphytoplankton in coastal and lagoon waters, with the aim of supporting scientific research. PHYTOBS-MARCOBOLO is a dataset used as part of the Horizon Europe MARCO-BOLO project (https://marcobolo-project.eu/), in which we are currently working to understand and analyze multi-decadal trends in coastal and marine biodiversity on a European scale. The PHYTOBS-MARCOBOLO dataset gathers data from 18 sampling sites, selected from the PHYTOBS-Network dataset according to requirements of time series quality and geographical location of sampling sites established as part of the MARCO-COLO project. This dataset was also formatted according to a template imposed for the European project.

Understanding the dynamics of species interactions for food (prey-predator, competition for resources) and the functioning of trophic networks (dependence on trophic pathways, food chain flows, etc.) has become a thriving ecological research field in recent decades. This empirical knowledge is then used to develop population and ecosystem modelling approaches to support ecosystem-based management. The TrophicCS data set offers spatialized trophic information on a large spatial scale (the entire Celtic Sea continental shelf and upper slope) for a wide range of species. It combines ingested prey (gut content analysis) and a more integrated indicator of food sources (stable isotope analysis). A total of 1337 samples of large epifaunal invertebrates (bivalve mollusks and decapod crustaceans), zooplankton, fish and cephalopods, corresponding to 114 species, were collected and analyzed for stable isotope analysis of their carbon and nitrogen content. Sample size varied between taxa (from 1 to 52), with an average of 11.72 individuals sampled per species, and water depths ranged from 57 to 516 m. The gut contents of 1026 fish belonging to ten commercially important species: black anglerfish (Lophius budegassa), white anglerfish (Lophius piscatorius), blue whiting (Micromesistius poutassou), cod (Gadus morhua), haddock (Melanogrammus aeglefinus), hake (Merluccius merluccius), megrim (Lepidorhombus whiffiagonis), plaice (Pleuronectes platessa), sole (Solea solea) and whiting (Merlangius merlangus) were analyzed. The stomach content data set contains the occurrence of prey in stomach, identified to the lowest taxonomic level possible. To consider potential ontogenetic diet changes, a large size range was sampled. The TrophicCS data set was used to improve understanding of trophic relationships and ecosystem functioning in the Celtic Sea. When you use the data in your publication, we request that you cite this data paper. If you use the present data set (TrophicCS) for the majority of the data analyzed in your study, you may wish to consider inviting at least one author of the core team of this data paper to become a collaborator /coauthor of your paper.

In October 2019 we chose 15 sites from the 2019 EVHOE survey for environmental DNA (eDNA) sampling. The French international EVHOE bottom trawl survey is carried out annually during autumn in the BoB to monitor demersal fish resources. At each site, we sampled seawater using Niskin bottles deployed with a circular rosette. There were nine bottles on the rosette, each of them able to hold ∼5 l of water. At each site, we first cleaned the circular rosette and bottles with freshwater, then lowered the rosette (with bottles open) to 5 m above the sea bottom, and finally closed the bottles remotely from the boat. The 45 l of sampled water was transferred to four disposable and sterilized plastic bags of 11.25 l each to perform the filtration on-board in a laboratory dedicated to the processing of eDNA samples. To speed up the filtration process, we used two identical filtration devices, each composed of an Athena® peristaltic pump (Proactive Environmental Products LLC, Bradenton, Florida, USA; nominal flow of 1.0 l min–1 ), a VigiDNA 0.20 μm filtration capsule (SPYGEN, le Bourget du Lac, France), and disposable sterile tubing. Each filtration device filtered the water contained in two plastic bags (22.5 l), which represent two replicates per sampling site. We followed a rigorous protocol to avoid contamination during fieldwork, using disposable gloves and single-use filtration equipment and plastic bags to process each water sample. At the end of each filtration, we emptied the water inside the capsule that we replaced by 80 ml of CL1 conservation buffer and stored the samples at room temperature following the specifications of the manufacturer (SPYGEN, Le Bourget du Lac, France). We processed the eDNA capsules at SPYGEN, following the protocol proposed by Polanco-Fernández et al., (2020). Half of the extracted DNA was processed by Sinsoma using newly developped ddPCR assays for European seabass (Dicentrachus labrax), European hake (Merluccius merluccius) and blackspot seabream (Pagellus bogaraveo).  The other half of the extracted DNA was analysed using metabarcoding with teleo primer. The raw metabarcoding data set is available at https://www.doi.org/10.16904/envidat.442 Bottom trawling using a GOV trawl was carried out before or after water sampling. The catch was sorted by species and catches in numbers and weight were recorded. No blackspot seabream individuals were caught.   Data content: * ddPCR/: contains the ddPCR counts and DNA concentrations for each sample and species. * SampleInfo/: contains the filter volume for each eDNA sample. * StationInfo/: contains metadata related to the data collected in the field for each filter. * Metabarcoding/: contains metabarcoding results for teleoprimer. * Trawldata/: contains catch data in numbers and weight (kg).      

Bivalves carbon and nitrogen elemental and isotopic ratios (δ13C, δ15N, C and N%, C:N) times series (1981-2021) from 33 sites in France. Bivalve species are the Pacific oyster Crassostrea gigas, and the mussels Mytilus edulis and Mytilus galloprovincialis. This extensive dataset offers a comprehensive view spanning multiple decades and ecosystems, allowing to track how coastal ecosystems and marine species record changing climate, physical-chemical environments and organic matter cycles. This dataset may also be used to study bivalve physiology. Additionally, these data are crucial for establishing isotope baselines for studying food webs. Ultimately, this data set provide valuable information for more effective ecosystem conservation and management strategies in our rapidly changing world.

This dataset gather isotopic ratios (carbon and nitrogen) and concentrations of mercury species (methyl and inorganic mercury) measured in several tissues (muscle, liver and gonad) for three commonly consumed fish species from the south Bay of Biscay (France) in 2017 and 2018.