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).

This dataset contains bio-optical measurements from BioGeoChemical-Argo (BGC-Argo) profiling floats complemented with ocean-colour satellite matchups of variables related to the detection of coccolithophore blooms dominated by Emiliania huxleyi. BGC-Argo float data cover the global ocean from November 2012 to December 2018 and include measurements of the particulate backscattering coefficient (BBP_float in m-1), the concentration of Chlorophyll-a (CHLA_float in mg m-3), and the particulate beam attenuation coefficient (CP_float in m-1) with data processing and quality control described in the manuscript entitled “Detection of coccolithophore blooms with BioGeoChemical-Argo floats” submitted to Geophysical Research Letters. The data represent near-surface ocean conditions, calculated as the average value in the top 15m of the water column. Daily ocean-colour satellite data were downloaded from the GlobColour project (ftp://ftp.hermes.acri.fr) with a spatial resolution of 4km and matched with every BGC-Argo float observation by using a 5x5 pixel box and a 9-day temporal window. For each float observation, we extracted concurrent satellite data of the concentrations of Particulate Inorganic Carbon (PIC_sat in mmol m-3) and Particulate Organic Carbon (POC_sat in mmol m-3), from which we derived the proportion of PIC_sat to the total particulate carbon concentration (PIC_POC_sat in % and defined as PIC_sat / [PIC_sat+POC_sat]). Coccolithophore bloom periods were identified using annual times series of PIC_sat and PIC_POC_sat at each profile location as described in the submitted manuscript, and the column “inside_coccolithophore_bloom” reports the float observations occurring inside such blooms.

Three saltmarshes, Aiguillon, Brouage, Fier d'Ars, located in the Pertuis-Charentais Sea along the south-west coast of France, were studied to evaluate their sediment and mass accumulation rates (SAR; MAR) based on 210Pb and 137Cs profiles in sediments. Coastal saltmarshes play indeed an essential role in providing services such as coastal protection and supporting biodiversity. Saltmarshes are also critical environments for the accumulation of sedimentary organic carbon (blue carbon). However, the number of studies on saltmarshes remains underrepresented compared to studies on mangroves and seagrass. This work is a contribution to the effort to document sediment and mass accumulation rates of saltmarshes.A total of 16 1m sediment cores were collected in the three saltmarshes (Aiguillon, Brouage, Fier d'Ars) in 2021 and 2022 using an Eijkelkamp stainless steel peat sampler. Each sediment core was sampled every 1 cm from the top to the bottom of the core. The sediment layers were used to determine dry bulk density and selected radioisotope activities (210Pb, 226Ra, 137Cs, 228Th, 137Cs). Combining excess 210Pb and 137Cs has allowed to establish a reliable chronology of sediment deposition on a multidecadal timescale.

210Pb, 226Ra and 137Cs were measured by non-destructive gamma spectrometry on marine sediment cores, collected during RIKEAU 2002 cruise on board r/v Thalia, on the shelf of the Bay of Biscay

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.

The West Gironde Mud Patch (WGMP) is a mud deposit located 25 km from the mouth of the Gironde Estuary in the Bay of Biscay. This 4-metre-thick clay-silt feature, which extends over an area of 420 km2, is found at depths between 30 and 80 meters. The main objectives of the JERICObent7 cruise, in July 2019, were to characterise the evolution of the WGMP’s benthic ecosystem in terms of its sedimentary, biogeochemical and ecological properties and to reconstruct climate variations and identify potential anthropogenic impacts over the last few centuries. To this end, a precise chronological framework was established for the sedimentary archives of the last few decades using 210Pbxs (T1/2 = 22.3 years). Interface cores were collected at stations 1, 3 and 4 along a cross-shelf transect. Twin Kullenberg cores were collected at sites 3 and 4 for geochemical (KGL) and palaeoceanographic (JB7-ST) investigations. Each interface core was carefully extruded at 0.5 cm intervals from the top of the core to 4 cm, and then at 1 cm intervals until the bottom was reached. Kullenberg cores were only collected at sites 3 and 4. Depending on their intended use, the Kullenberg cores were sampled at different resolutions, the depth of each sediment layer corresponded to the depth from the top of the core. These layers were then used to determine the dry bulk density and radioisotope activities of interest (210Pb, 226Ra,  228Th, 137Cs, 40K). Excess 210Pb was used to establish the realignment and chronological framework of the interface and Kullenberg cores.

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.

For the 21 years of the study, an examination of trends in chlorophyll concentration revealed a general decline throughout the Gulf over the production period. These trends, extracted from dynamic linear model, also allowed this decline to be quantified. Expressed as a percentage, a large part of the area below the 50 m bathymetric line showed a decrease of at least 10% over the period, corresponding to a value of at least 0.1 µg.l-1. However, the spatial distribution reveals some more local phenomena. In southern Brittany, from Quimper to Vannes, a particular feature appears, with an upward trend over several kilometres along the coast, followed by a pronounced gradient along the coast. This gradient includes a zone where a continuous monotonic increasing trend is observed, then a zone where the trend becomes not significant and finally, about 15 km from the coast, a new zone where a significant continuous monotonic decreasing trend is observed. The increase in chlorophyll a concentration in the very coastal part is greater than 0.1 µg.l-1 over the period. Another peculiarity concerns the central part, located at the edge of the plateau at Cap Ferrat and Pente Aquitaine, where an increase in chlorophyll a was observed, but the variations remained small, being less than 0.1 µg.l-1. About a hundred kilometres south-west of Saint Nazaire, an area of about 40 by 50 km shows a decrease in chlorophyll a of more than 20%, quantified as more than 0.1 µg.l-1 over the period.

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.