Mesoscale dynamics in the Mediterranean Sea have been investigated for years and anticyclonic eddies are regularly observed features in the Algerian Basin. In early spring 2016, a field experiment during the ProtevsMed 2016 cruise thoroughly investigated this specific eddy, when it was located near the North Balearic Front, taking high-resolution (Seasoar) hydrological transects, several CTD casts and LADCP measurements. In addition, four drifting buoys were released in the eddy core. These in situ measurements revealed that the vertical structure of this anticyclone was made of two water lenses of very different origins (Atlantic Water above and Western Intermediate Water below) spinning together. In the vicinity of the North Balearic Front, which may act as a dynamical barrier for structures, the eddy interacted with a subsurface anticyclonic eddy made of modal water, which fostered cross-front exchanges generating filaments by stirring. The high-resolution sampling revealed fine scales structures both adjacent to the eddy and within its core. The eddy has been targeted from 21 March to 1 April 2016 taking advantage of a meteorological window. It has been sampled with:  - a towed undulating vehicle, the SeaSoar designed and built by Chelsea Instruments; it gets mounted on its sides two Sea-bird SBE-9 (SBE 3 temperature and SBE 4 conductivity sensors)  and a Wetlabs Fluorometer of type ChloroA WetStar  - CTD casts performed with a Sea-bird SBE-9 (SBE 3 temperature and SBE 4 conductivity sensor) and an RDI 150 kHz current profiler mounted in a general oceanics 12-place rosette, with12l Niskin bottles  - drifters with holey-sock positioned at 50 m deep below the expected Ekman layer thickness (remaining in the eddy until mid May).

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 description # #############   This dataset have been constructed and used for scientific purpose, available in the paper "Detecting the effects of inter-annual and seasonal changes of environmental factors on the the striped red mullet population in the Bay of Biscay" authored by  Kermorvant C., Caill-Milly N., Sous D., Paradinas I., Lissardy M. and Liquet B. and published in Journal of Sea Research. This file is an extraction from the SACROIS fisheries database created by Ifremer (for more information see https://sextant.ifremer.fr/record/3e177f76-96b0-42e2-8007-62210767dc07/) and from the Copernicus database. Biochemestry comes from the product GLOBAL_ANALYSIS_FORECAST_BIO_001_028 (https://resources.marine.copernicus.eu/?option=com_csw&view=details&product_id=GLOBAL_ANALYSIS_FORECAST_BIO_001_028). Temperature and salinity comes from GLOBAL_ANALYSIS_FORECAST_PHY_001_024 product (https://resources.marine.copernicus.eu/?option=com_csw&view=details&product_id=GLOBAL_ANALYSIS_FORECAST_PHY_001_024). As fisheries landing per unit of effort is only available per ICES rectangle and by month, environmental data have been aggregated accordingly. ############### # Colomns description # ############### rectangle - The 6 ICES statistical rectangles used in the study. time_m - Time in months, from the beginning to the end of the study. annee = year mois = month (from 1 to 12) Poids = Weight of red mullet landed valeur = Temps_peche = fishing time Nb_sequence = number of fishing sequences Moy / Med / Var / StD Quartil_1 / Quartil_3 / min / max / CV / IQR = statistical descriptors of landing by rectangle and by month log_cpue = log of Med colomn mean_surface_s = mean of surface salinity by month and by rectangle median_surface_s = median of surface salinity by month and by rectangle mean_surface_t = mean of surface temperature by month and by rectangle median_surface_t = median of surface temperature by month and by rectangle si / zeu /po4 / pyc / o2/ nppv / no3 and nh4 mean and median concentration by rectangle and by month pc3 / pc2 / pc1 - projections of previous biochemestry variables on the three first axes of a PCA

This folder contains two examples of PAGURE datasets, corresponding to three surveys: -CGFS conducted in 2018 in the English Channel (Northeast Atlantic) -EPIBENGOL conducted in 2019 in the Gulf of Lion (Western Mediterranean) -EVHOE conducted in 2020 in the Bay of Biscay and Celtic Shelf (Northeast Atlantic) Files include metadata for the sampling stations, annotation files. A readme tex file contains the links to the voyage metadata This folder is aimed at providing an example of documented underwater imagery dataset. These data are part of the data exchange conducted in the QuatreA collaboration between the French Research Institute for the Exploitation of the Sea (Ifremer), the Commonwealth Scientific and Industrial Research Organisation (CSIRO), and the University of Tasmania (UTAS).

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).

Worldwide, shellfish aquaculture and fisheries in coastal ecosystems represent crucial activities for human feeding. But these biological productions are under the pressure of climate variability and global change. Anticipating the biological processes affected by climate hazards remains a vital objective for species conservation strategies and human activities that rely on. Within marine species, filter feeders like oysters are real key species in coastal ecosystems due to their economic and societal value (fishing and aquaculture) but also due to their ecological importance. Indeed oysters populations in good health play the role of ecosystem engineers that can give many ecosystem services at several scales: building reef habitats that contribute to biodiversity, benthic-pelagic coupling and phytoplankton bloom control through water filtration, living shorelines against coastal erosion… The Pacific oyster, Crassostrea gigas (Thunberg, 1793), which is currently widespread worldwide, was introduced into the Atlantic European coasts at the end of the 19th century for shellfish culture purposes and becomes the main marine species farmed in France (around 100 000 tons) despite severe mortalities crisis. But in the same time and because of warming, natural oysters beds has spread significantly along the French coast and are supposed to have reach approximately 500 000 tons. In that context, Pacific oyster populations (natural and cultivated) in France are the subjects of many scientific projects. Among them, a specific long-term biological monitoring focuses on the reproduction of these populations at a national scale: the VELYGER national program. With more than 8 years of weekly data at many stations in France, this field-monitoring program offers a valuable dataset for studying processes underpinning reproduction cycle of this key-species in relation to environmental parameters, water quality and climate change.   Database content: Larval concentration (number of individuals per 1.5 m3) monitored, since 2008, at several stations in six bays of the French coast (from south to north): Thau Lagoon and bays of Arcachon, Marennes Oléron, Bourgneuf, Vilaine and Brest (see map below).   Methods used to monitor larval concentration: An important volume of seawater (1.5 m3) is pumped twice a week throughout the spawning season (june-september), at one meter below the surface at high tide (+/- 2h) in several sites within each VELYGER ecosystem. Water is filtered trough plankton net fitted with 40 µm mesh. After a proper rinsing of the net, the retained material is transferred into a polyethylene bottle (1 liter) and fixed with alcohol. At laboratory, sample is then gently filtered and rinse again and transferred into eprouvette. Two sub-samples of 1 mL are then taken using a pipette and examined on a graticule slide for microscope. The microscopic examination is made with a conventional binocular optical microscope with micrometer stage at a magnification of 10 X (or above). During the counting, a special care is necessary as larvae of other bivalves are also collected and confusion is possible. Larvae of C. gigas are also classified into four stage of development: - Stage I = D-shaped straight hinge larvae (shell length <105 µm) - Stage II = Early umbo evolved larvae (shell length between 105 and 150 µm) - Stage III = Medium umbo larvae (shell length between 150 and 235 µm) - Stage IV*= Large umbo eyed pediveliger larvae (shell length > 235 µm) * Larvae that are very closed to settle are sometimes identified into a separated 5th stage, but generally this stage is included in stage IV.   Illustrations: Location of the different Velyger sites along the French coast. From south to north: Thau Lagoon and bays of Arcachon, Marennes Oléron, Bourgneuf, Vilaine and Brest.   Legend: Pacific Oyster Larvae (left side) and Natural oyster bed (right side). Photos : © S. Pouvreau/Ifremer

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/).

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 Bay of Aiguillon. Measurements are organized into .csv files, with one file per year. Data is collected using a WiMO multiparameter probe, which records the following parameters: •    Temperature (-2 to 35 °C) •    Conductivity (0 to 100 mS/cm) •    Pressure (0 to 30 m) •    Turbidity (0 to 4000 NTU) •    Dissolved Oxygen (0 to 23 mg/L & 0 to 250 %) •    Fluorescence (0 to 500 ppb)  

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/.