This dataset gathers data used to infer the trophic structure and functioning of fish assemblages in the Eastern English Channel, the Bay of Biscay and the Gulf of Lions : - Biomass data, resulting from accoustic monitoring for pelagic species, or bottom trawling for demersal species, after extrapolation based on stratification scheme - Individual C and N isotopic ratios, length and mass, for all individuals considered - Individual energetic density values

This set of data documents the radiocarbon dates (n=19) obtained thanks to the accelerator mass spectrometry method (AMS) at the LMC14/ARTEMIS French national facility on the cores (Multicorer, Kullenberg) retrieved from the West-Gironde mud patch (WGMP) during the JERICObent-7 cruise (10-15 July 2019; NR Côtes de la Manche, https://doi.org/10.17600/18001022). The WGMP registers very high sedimentation rates since the last 600 years (≥ 0.3 cm/yr) and is thus of great interest for palaeoceanographic investigations. At present, this depocenter marks the mid-shelf of the temperate Bay of Biscay off major French rivers from the Aquitaine basin. The fine mud deposits of the WGMP are of 3 to 4 meters thick and lie on palimpsest levels rich in gravels and shells. They cover a V-shaped structure, oriented SW-NE, which is attributed to the incision(s) of a paleovalley in the Cenozoic substrate, mainly linked to the paleo-Gironde routing changes during past glacials/interglacials, and its potential past convergences with the paleo-rivers of the Antioche perthuis (Seudre, Charente paleovalleys?) at that times. Detailed information on each sample is presented with the 14C results obtained by the Artemis AMS facility at LMC14 laboratory (Dumoulin et al. 2017- https://doi.org/10.1017/RDC.2016.116, Beck et al. 2024- https://doi.org/10.1017/RDC.2023.23). Raw ages are indicated together with calibration calculations using the last two versions of the Calib software (http://calib.org/, Calib 7 and 8) to show the dispersion of ages linked to the updating of calibration curves (Marine13, Intcal13, Marine20, Intcal 20). The calibrated ages finally retained for publications (used in the related Seanoe document - https://doi.org/10.17882/104237 - and published in Eynaud et al., 2025 for the ST3c core, https://doi.org/10.1016/j.gloplacha.2025.105039) are those obtained with the last Calib 8.1 version. Raw 14C ages were calibrated and converted to calendar ages using the IntCal20 calibration curve with a reservoir age correction of 400 years deduced from Radionuclide analyses (137Cs and 210Pb) at the top of the studied cores (see Schmidt, 2025, https://www.seanoe.org/data/00968/107979/). 

The data file present detailed individual congener/compound concentrations  for a large variety of hydrophobic organic contaminants including polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), legacy and alternative brominated flame retardants (BFRs) and per- and polyfluoroalkyl substances (PFASs) in meso- and bathypelagic organisms collected in the Bay of Biscay, northeast Atlantic, in October 2017. The studied species include 3 crustacean species (Pasiphaea sivado, Sergia robusta, Ephyrina figueirai) and 11 fish species (Xenodermichthys copei, Searsia koefoedi, Myctophum punctatum, Notoscopelus kroeyeri, Lampanyctus crocodilus, Argyropelecus olfersii, Arctozenus risso, Stomias boa, Serrivomer beanii, Chauliodus sloani, Aphanopus carbo). The organisms were collected at night during one single trawling using a 25 m vertical opening pelagic trawl in the deep scattering layer (ca 800 m depth in the water column; 1330 m bottom floor). This dataset was used in the article entitled "A large diversity of organohalogen contaminants reach the meso- and bathypelagic organisms in the Bay of Biscay (northeast Atlantic)" published in Marine Pollution Bulletin.

Sardine physiological measurments from september to november 2020

As part of the European Horizon Europe FOCCUS project (https://foccus-project.eu/), the metadata inventory of European coastal platforms has been extracted. The inventory was based on the following History and Latest products, downloaded from the CMEMS website (https://marine.copernicus.eu/fr/acces-donnees) at: 1) Global Ocean-In-Situ Near-Real-Time Observation, 2) Atlantic Iberian Biscay Irish Ocean-In-Situ Near Real Time Observations, 3) Mediterranean Sea-In-Situ Near Real Time Observations, 4) Atlantic-European North West Shelf-Ocean In-Situ Near Real Time Observations. To carry out this inventory, it was decided to target only coastal platforms, located less than 200km from the coast and at a depth of less than 400m. For mobile platforms, it was also decided to focus only on the first position in the file. This data must be located within 200 km of the coast and at a depth of less than 400 m. In this inventory, FerryBox platforms have all been considered as coastal platforms. The following platforms were extracted from the products: BO (Bottles), CT (CTD), DB (Drifting Buoys), FB (Ferry Box), GL (Gliders), HF (High Frequency Radar), MO (Mooring), PF (Profiling Float), TG (Tide Gauge) and XB (XBT). Once the metadata had been extracted from the files, duplicates were removed (files with the same names). Duplicate platforms of type _TS_ and _WS_ were merged (date and parameters). Latest‘ files have been merged with ’History" files. Missing metadata have been replaced in the Excel file by ‘Missing Data’. Some old dates were also revised by hand because they had been badly extracted, as well as some institution names that included special characters. Platforms located on estuaries/rivers/lakes/ponds have also been removed by hand. This inventory identified a total of 10,479 coastal platforms.

Particularly suited to the purpose of measuring the sensitivity of benthic communities to trawling, a trawl disturbance indicator (de Juan and Demestre, 2012, de Juan et al. 2009) was proposed based on benthic species life history traits to evaluate the sensibility of mega- and epifaunal community to fishing pressure known to have a physical impact on the seafloor (such as dredging and bottom trawling). The selected biological traits were chosen as they determine vulnerability to trawling: mobility, fragility, position on substrata, average size and feeding mode that can easily be related to the fragility, recoverability and vulnerability ecological concepts. Life history traits of species have been defined from the BIOTIC database (MARLIN, 2014) and from information given by Le Pape et al. (2007), Brindamour et al. (2009) and Garcia (2010). For missing life history traits, additional information from literature has been considered. The five categories retained are life history functional traits that were selected based on the knowledge of the response of benthic taxa to trawling disturbance (de Juan and Demestre, 2012). They reflect respectively the possibility to avoid direct gear impact, to benefit from trawling for feeding, to escape gear, to get caught by the net and to resist trawling/dredging action, each of these characteristics being either advantageous or sensitive to trawling. Then, to allow quantitative analysis, a score was assigned to each category: from low vulnerability (0) to high vulnerability (3). The five categories scores were then summed for each taxon (the highly vulnerable taxon could reach the maximum score is 15) and this value may be considered as a species index of sensitivity to trawling disturbance. The scores of 812 taxa commonly found in bottom trawl by-catch in the southern North Sea, English Channel and north-western Mediterranean were described.

Survival was recorded at the endpoint for all batches of each group (2n-control, 2n-wild, 2n-commercial, 2nR, 3nR and 3n-commercial). Similarly, initial and final yield were recorded, corresponding to the total weight of the live oysters at deployment and at the endpoint. Finally, shell length and total weight for individually recorded at reception and at the endpoint.

Questions: Invasiveness depends in part on the ability of exotic species to either exclude native dominants or to fill an empty niche. Comparisons of niches and effects of closely related native and invasive species enable the investigation of this topic. Does Spartina anglica invade European salt marshes through competitive exclusion of the native Spartina maritima or due to the occurrence of an empty ecological niche in highly anoxic conditions? Location: The Arcachon Bay (France). Methods: At three intertidal levels, we quantified competitive response and effect abilities of the two species through a cross-transplantation removal experiment. We also compared at three intertidal levels the biomass, root/shoot ratio, productivity and environmental conditions (elevation, salinity, potential redox and soil moisture) of salt marsh communities dominated by the exotic Spartina anglica or the native Spartina maritima. Results: Both established species showed similar biotic resistance to the invasion of the other species, but the exotic showed important intraspecific facilitation for growth. Species had similar niches and total biomass along a gradient of anoxic conditions, but the exotic had a much higher root/shoot ratio and productivity than the native. Owing to its rhizome density, the exotic showed a high ability to increase sediment oxygenation, likely to explain its important intraspecific facilitation. Conclusions: Our results showed that the invasion success of S. anglica cannot be explained by the competitive exclusion of the native or by its ability to fill an empty niche along a gradient of anoxia. Its behaviour as a self-facilitator invasive engineer is very likely to explain its rapid spread in the Bay and biotic resistance to the colonization of other congeneric species when established in dense patches. Additionally, we suggest that physical disturbance in the marsh communities dominated by the native S. maritima may disrupt its biotic resistance against the invasion of S. anglica.

Ifremer conducts numerous fisheries surveys dedicated to benthic and demersal populations (commercial / non-commercial fishes and invertebrates). For several years, in application of the ecosystem approach, all benthic invertebrate fauna collected in fishing gear has been systematically monitored: megabenthic invertebrates captured have been sorted, identified, counted and weighted. All these surveys are based on fixed or random stratified sampling strategy with varying intensity depending on the covered survey area. These data are stored, in historical access-based databases or for the most recent years in the centralised “Harmonie” database held in the Ifremer Fishery Information Systeme (SIH). The species nomenclature used was standardized using WoRMS database. Taxa caught at least once a year are listed for each monitoring area on the basis of already available data series. In order to facilitate the identification of individuals sampled on board vessels and to improve the training of onboard scientists, the present work aims to define the minimum level of identification for each of them. The analysis identifies taxa that appears recurrently on available historical series or gathers them on less precise taxonomic levels if this is not the case, which may indicate potential identification difficulties. The following procedure was used: all taxa expressed at the species level were first aggregated at genus level if they occurred less 90% of the years over the available time series. For MEDITS, EPIBENGOL and ORHAGO, the occurrence threshold was set to 70% and to only 50% for NOURMONT because the datasets were less than 10 years long. Then to be kept at that taxonomic level, a given genus had to be observed over 90% of the time (for example over at least 9 years if the dataset contains 10 years). Otherwise it was iteratively regrouped into a higher taxonomic level (family, order, class, division) following the same criteria (Foveau et al, 2017). For instance, for the NOURSEINE survey, this resulted into the aggregation of the 103 origin taxa into 35 taxonomic groups. The name of the final taxon after data processing represents the minimum level of identification defined by the analysis. However, these results are very theoretical. This is why they were sent to scientists who embark regularly in order to refine the level of taxonomic identification with field experience. The first dataset is composed of 8 tables relevant to the different vessel surveys. The first column of each table represents the permanent code of the taxon in the Ifremer taxonomic referential, the second the systematic number and the third the species abbreviated code. The other columns are the different taxonomic levels of the taxon. The minimum level of identification at sea defined by the data processing appears in blue. The level determined by feedback of scientist’s field experience, which is the one to use at sea, appears in green. The second dataset summaries the results detailed in the first table and indicates directly for each taxon identified to far, the minimum level of identification required for the benthic invertebrates by-catch of each fisheries surveys studied.

Good Environmental Status assessment (GES) for descriptor 8 (contaminants, D8) of the Marine Strategy Framework Directive (MSFD) is reached when concentrations of contaminants are at levels not giving rise to pollution effects. It is described by 4 criteria among which the first one focus on the concentration of the contaminants in the environment (criteria 1 of the D8, D8C1). The environmental status for D8 in France includes assessment of contaminant concentrations in sediment, bivalves, fish, birds, mammals to cover the French marine area the continental shelf from the coast line). The 8 tables below present the assessment of the chemical contamination in sediment and bivalves on the coastal area of the 4 French marine subregions for D8 as part of the 2024 GES assessment. These tables report the status and temporal trends of each station x matrice x substance triplet in each of the 4 French marine subregions. Explanation on how to read the cells is given in the “read file”. The environmental assessment for D8 in France can be found in Mauffret al., 2023 (DOI:10.13155/97214). It includes 17 national indicator assessments, 4 OSPAR indicators and integrated assessment in selected assessment units at the level of the criteria 1 and 2.