The SOMLIT-SOGIR time-series data characterize the hydrology of the Gironde Estuary ecosystem, located in the South-western France and flowing into the Bay of Biscay. Monthly-like measurements have been undertaken since 1997 by the OASU and EPOC teams (Univ. Bordeaux/CNRS). The SOMLIT-SOGIR time series is a part of the French monitoring network SOMLIT (https://www.somlit.fr/), labelled by the CNRS as a national Earth Science Observatory (Service National d’Observation : SNO). It aims to detect the long-term evolution of monitored ecosystems including both natural and anthropogenic forcings. Implemented at three sites (PK 30: 45.06833°N, 0.63833°W; PK 52: 45.24667°N, 0.725°W; PK 86:  45.5167°N, 0.95°W), the SOMLIT-SOGIR time series is among the oldest long-term coastal observation time series of the French Research Infrastructure dedicated to coastal ocean observations (RI ILICO, https://www.ir-ilico.fr). SOMLIT-SOGIR samples are collected at 1m below the water surface and 1m above the floor, at high and low tide, during slack water. Samples collected are analysed for 15 core parameters: water temperature and salinity, dissolved oxygen, pH, ammonia, nitrate, nitrite, phosphate, silicic acid, suspended particulate matter, particulate organic carbone, particulate nitrogen, chlorophyll a, delta15N and delta13C. CTD-PAR-profile is also performed at site PK86 during high tide. The SOMLIT network quality management system is in line with the ISO/IEC 17025:2017 standard: “General requirements for the competence of testing and calibration laboratories”. Further information on standard operating procedures for sample collection and data acquisition are available at: https://www.somlit.fr/parametres-et-protocoles. For more information on the quality flagging scheme: https://www.somlit.fr/codes-qualite/.

The BenthOBS dataset includes long-term time series on marine benthic macrofauna, since 1967, along the whole French metropolitan coast. It includes 20 sampling location. BenthOBS aims to establish a national network for the observation of macrozoobenthos. In a context of global change, It is essential to have time series capable of highlighting and understanding ongoing changes in the specific diversity within communities and their consequences on the functioning of marine ecosystems. The BenthOBS network provides the scientific community and stackers with validated data on the following parameters: specific abundance, sediment size composition, sediment organic matter, sediment C content, sediment N content.

The diet and stable isotopic (i.e. δ15N and δ13C values) compositions of eels have been studied during each season of 2019 with a fyke net in six estuaries located along the French coast of the eastern English Channel (Slack, Wimereux, Liane, Canche, Authie and Somme estuaries) (10.1371/journal.pone.0270348).

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/).

Long-term time series of coliform bacteria concentration (fecal coliform or Escherichia coli) in shellfish in four submarine areas (North Sea/Channel, Britany, Atlantic, Mediterranean).

This database contains hauls collated from 1965 to 2019, from fisheries dependent and independent data, from across eastern Atlantic waters and French Mediterranean waters. From this data diadromous fish spatio-temporal data was cleaned and standardised.

Data collected by the Spindrift 2 Sails of Change vessel during its attempt at the round-the-world sailing record, the Jules Verne Trophy. More information at https://spindrift-racing.com/fr/.

SUCHIMED 2021 is the 10th campaign for monitoring chemical contamination and its evolution in the Mediterranean Sea. It has been designed as a platform supporting various surveillance and research activities, with the main pillar being the RINBIO network, which involves active biosurveillance through mussel caging. Regarding chemical contamination, the main results of this campaign are as follows: In Occitania region: - Chronic presence of DDT for 20 years. - Detection of terrigenous markers (Mn, As) between the mouths of the Aude and Hérault rivers, along with contamination of sediments near Port-La-Nouvelle by HAP and TCE (Pt). In PACA region: - PCB markers detected between the Rhône River and Marseille (in all matrices), originating from multiple sources with no significant changes over the past 20 years. - HAP contamination in sediments of the industrial-port zone in Fos. - Presence of TBT at the Carry-le-Rouet station above ecologically acceptable concentrations (EAC), to be confirmed in the next campaign. - Detection of metallic elements and HAP in sediments near the Marseille urban area, partly in plankton, along with TCE near the Cortiou wastewater treatment plant outfall. - Chronic marking of PCB, HAP, metals (Hg, Pb, Cu, TCE), PBDE, and/or organotin compounds (TBT) in Toulon Bay, showing no significant temporal trend over two decades for the first five compounds. - Detection of Cr, Mn, and Ni in the water column and HAP in sediments near the Var River mouth, with differences in contamination between matrices raising questions about organic matter origin. - Metal (including Pb) and HAP marking in the water column and sediment in Villefranche Bay. Around Corsica: - Strong influence of the island's geological background (i.e., high Cr and Ni content) on obtained concentrations. - Chronic marking of Cu in the water column in the ports of Porto-Vecchio and Bonifacio, stable over time, with HAP, metals (Hg, Pb, Zn), and to a lesser extent, PCB detection in Bonifacio sediment. - Marking of HAP and TCE in the sediment of the Bastia coastline. - Detection of Pb and TCE at the Golo River mouth. - Contamination of the Canari site with metals (Cr and Ni in the water column, Cu in sediment), and notably, confirmed ecotoxicity likely linked to these elements. The 2021 campaign highlighted the feasibility of researching effects on caged mussels using biomarkers. Lysosomal markers, less sensitive to trophic differences, proved to best reflect the general stress state of organisms related to their contamination. The study of trophic transfers appears to confirm the decrease in most metallic elements (Cr, Cu, Fe, Mn, Ni, Pb) and HAP, bioamplification of Hg and PCB, and specific bioaccumulation of certain elements by organisms (e.g., As or Zn by mussels, HAP by plankton). Finally, the campaign revealed the presence of micro and mesoplastics at almost all sampled sites. The measured microplastic values align with concentrations observed in the western Mediterranean, with a trend towards reduction based on available 10-year data.

We genotyped 1680 thornback ray Raja clavata sampled in the Bay of Biscay using a DNA chip described in Le Cam et al. (2019). After quality control 4604 SNPs were retained for identifying potential sex-linked SNPs using three methods: i) identification of excess of heterozygotes in one sex, ii) FST outlier analysis between the two sexes and iii) neuronal net modelling. Genotype coding: 0 homozygous for major allele, 1 heterozygous, 2 homozygous for minor allele. Flanking DNA sequences of SNPs identified with methods i) and ii) are also provided.