AndreaBozzo/ceres-open-data-index huggingface dataset:
BIOGEOCHEMICAL dataset collected during the SOCLIM cruise

The biogeochemical dataset was acquired during the (SOCLIM cruise)-[https://doi.org/10.17600/16003300] to study : The Air-Sea exchange by improving the quantification of important climate relevant parameters such as air-sea fluxes of heat, fresh-water and carbon. The Carbon sequestration with describing and quantifying the physical and biogeochemical processes driving the sequestration of carbon in the Southern Ocean The Bio-optical anomaly while exploring the bio-optical anomaly of Southern Ocean surface waters, which contain less chlorophyll a than their color is actually suggesting The Role of Mesoscale by evaluating the role of mesoscale and submesoscale dynamics in driving physical, biogeochimical and biological processes
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AMOR-Bflux porewater and sediment data

Estuarine regions are generally considered a major source of atmospheric CO2 as a result of the high organic carbon (OC) mineralization rates in their water column and sediments. Yet, the intensity of anaerobic respiration processes in the sediments tempered by the reoxidation of reduced metabolites near the sediment-water interface controls the flux of benthic alkalinity. This alkalinity may partially buffer metabolic CO2 generated by benthic OC respiration in sediments. Thus sediments with high anaerobic respiration rates could contribute less to local acidification than previously thought. In this study, a benthic chamber was deployed in the Rhône River prodelta and the adjacent continental shelf (Gulf of Lions, NW Mediterranean) in late summer to assess the fluxes of total alkalinity (TA) and dissolved inorganic carbon (DIC) from the sediment. Concurrently, in situ O2 and pH microprofiles, voltammetric profiles and pore water composition were measured in surface sediments to identify the main biogeochemical processes controlling the net production of alkalinity in these sediments. Benthic TA and DIC fluxes to the water column, ranging between 14 and 74 mmol m-2 d-1 and 18 and 78 mmol m-2 d-1, respectively, were up to 8 times higher than DOU rates (10.4 ± 0.9 mmol m-2 d-1) close to the river mouth, but their intensity decreased offshore, as a result of the decline in OC inputs. In the zone close to the river mouth, pore water redox species indicated that TA and DIC were mainly produced by microbial sulfate and iron reduction. Despite the complete removal of sulfate from pore waters, dissolved sulfide concentrations were low and significant concentration of FeS were found indicating the precipitation and burial of iron sulfide minerals with an estimated burial flux of 12.5 mmol m-2 d-1 near the river mouth. By preventing reduced iron and sulfide reoxidation, the precipitation and burial of iron sulfide increases the alkalinity release from the sediments during the spring and summer months. Under these conditions, the sediment provides a net source of alkalinity to the bottom waters which mitigates the effect of the benthic DIC flux on the carbonate chemistry of coastal waters and weakens the partial pressure of CO2 increase in the bottom waters that would occur if DIC was produced only.
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Multi-decadal shifts in fish community diversity across a dynamic biogeographic transition zone

Aim: A 21-year fisheries-independent monitoring dataset was used to explore fish community diversity across a latitudinal gradient to quantify how diversity has changed and relate those changes in diversity to changes in the abiotic environment. Additionally, this study spans a biogeographic transition zone, providing insight into future species assemblages across regions of relatively high species diversity. Location: Indian River Lagoon, Florida, USA Methods: Spatial and temporal beta diversity was quantified latitudinally with “best derived breaks” determined by using chronological cluster analyses.  Multiple indices of alpha diversity were quantified, including species richness, Shannon diversity, Simpson diversity, and Pielou’s evenness. AIC model selection and environmental fit tests were performed to link patterns of diversity and species assemblages with the abiotic environment. Results: Evidence of a biogeographic transition zone was supported by data spanning the entire study period; the largest break in species assemblage occurred near 28°N. Fine scale analyses using small and large seine catches were noisier than broad analyses but indicated a northern shift in location of the biogeographic transition zone. Beta-diversity was generally dominated by species turnover/balance versus nestedness/gradient components, implying that changes were driven by species sorting associated with the physical environment. Excluding the summation of all environmental variables, temperature and dissolved oxygen best describe patterns of diversity and species composition. Main Conclusions: Over years less affected by disturbances, large and small seine catch data suggest the fish community assemblage and location of the biogeographic transition zone has shifted 9 km and 21 km to the north. If the trends observed in these years were to continue from 1999 until the year 2100, a 111 km to 243 km shift in fish communities could be expected. Variation in rates of movement based on gear type suggest novel species assemblages could ensue.
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1986-2018 near-surface sea temperature registered daily at the pumping station of the Nuclear Power Station of Flamanville (25 km south west of Cherbourg, Northwest Cotentin, sea Channel)

During 33 years, from January 1986 to December 2018, seawater temperature has then been registered daily at 4pm in the pumping station([1])-[#_ftn1] of the Nuclear Power Station of Flamanville located 25 km south west of Cherbourg. In order to cool their condensers, seawater has been drawn off with a water flows of 45 m3s-1. The monthly average seawater temperature minimum has been registered in February (8,90°C), with extremes values in 1986 (6,80°C) and 2016 (10,33°C). The maximum of the seawater temperature has been registered in august (17, 81°C), varying from 16,28°C in 1986 to 18,60°C in 2014. The annual average seawater temperature is 13,09°C when using monthly average values and 13,13°C using all 12053 individuals values. Mean annual values differ from 11,37 °C in 1986 to 14,18 °C in 2014. Before this time-series of 33 years, the only dataset available had been registered between 1904 and 1923 and had been published in 35 by J. R. Lumby([5])-[#_ftn5] at 12 meter depth to get an additional time-series of 999 seawater temperatures recorded from September 1976 to May 1980, in a discontinuous way. An increase of 1,2 °C in the annual mean seawater temperature is observed between the first and the third time-series. A key point when analysing those three time-series is to keep in mind the difference in the location, depth and in the sensor. Conclusions from comparisons of those three time series need to be done carefully. Those data are now updated each year before being published in an annual report for Ifremer and EDF([6])-[#_ftn6] about the ecological and fishery monitoring of Flamanville Nuclear Power Station location.   ([1])-[#_ftnref1] Geographical coordinates of the pumping station : 49,53 N – 1,88 W ([2])-[#_ftnref2] LUMBY, J.R. 1935.- « Salinity and temperature of the English Channel ». Fishery Investigations, series II, vol. XIV, n°3 ([3])-[#_ftnref3] Coordonnées géographiques du R 26 : 49° 37’ N – 02° 14’ W ([4])-[#_ftnref4] Today Laboratoire National d'Hydraulique et Environnement (LNHE) ([5])-[#_ftnref5] Geographical coordinates  of Fertex and Aanderaa : 49° 32’ 29’’N -  001° 53’ 49’’W ([6])-[#_ftnref6] ROPERT M., E. ANTAJAN, G. COURTAY, L. DREVES, A. FOVEAU, T. HERNÀNDEZ FARIÑAS, C. LOOTS, I. SCHLAICH , B. SIMON. (2019). Surveillance écologique et halieutique du site électronucléaire de Flamanville : Année 2018. RST/ODE/UL/LERN-19.001. Conv. EDF C4493C0850. 217 p.
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Gombessa 5 cruise: CTD profiles in western Mediterranean, July 2019

This dataset contains the CTD data collected during the GOMBESSA 5 cruise, from 1 to 25 July 2019, in the western Mediterranean, jointly by the (MEGAFAUNA research project)-[https://reefish.umontpellier.fr/]. The full-depth CTD profiles were performed using an autonomous SeaBird SBE 19plus V2 SeaCAT Profiler CTD, from the Zembra vessel belonging to (Andromède océanologie)-[https://web.facebook.com/page.andromede/?_rdc=1&_rdr] (France). 15 stations, from the depth of 200 m to the surface, were sampled off the French and Monegasque coasts (western Mediterranean basin) between latitude 43.06-43.69 °N and longitude 5.65-7.31 °E. The accuracy, specified by the manufacturer, were ± 0.005 °C for temperature and ± 0.0005 S/m for conductivity. The dataset is provided as an ODV (Ocean Data View) collection, which contains, for each station the following parameters: Depth [salt_water,m] Temperature [ITS-90,deg-C] pH Salinity [PSU] Conductivity [S/m] Density [kg/m^3] Oxygen [mL/L] Oxygen_sat [% saturation] Oxygen_umoll [umol/L] Turbidity [NTU] Fluorescence [mg/m^3] Light [PAR/Irradiance] The ZIP archives contain 1/ a map of stations 2/ the list of the ID stations and geographic coordinates 3/ all raw data acquired, for all parameters, in ODV format, 4/ in NetCDF format, 5/ in CSV format and 6/ one vertical profile graph of the Sea Water Temperature for each station. All data acquired are publicly accessible without any restriction (under CC-BY licence). The extracted data are accessible from this GOMBESSA 5 landing page with a downloadable ZIP file.
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BIOGEOCHEMICAL dataset collected during the PROSOPE cruise

The (JGOFS)-[http://ijgofs.whoi.edu/]), 2, focus on small scale biogeochemical processes, in particular at a daily scale, 3, study the influence of nitrogen, phosphorus and iron on oceanic fertility and 4, conduct a calibration/validation operation for the SeaWIFS (Sea-viewing Wide Field-of-View Sensor) color sensor. To reach these objectives, the studied areas, as well as the cruise plan, were designed : To investigate different trophic regimes, to investigate systems characterized by different degrees of limitation in nitrogen and phosphorus and to study stable ("steady state") systems for a sufficiently long period. The cruise track encompassed a variety of trophic systems ranging from eutrophic conditions associated to the Moroccan upwelling to the typical ultra-oligotrophic conditions of the eastern Mediterranean sea during summer stratification. Two main types of stations were occupied : 9 short (4-hour) stations. These sites were occupied around the solar noon and were essentially designed to conduct objectives 1 (JGOFS process studies) and 4 (SeaWIFS validation/calibration) 3 "long" (5-day) stations, where all four objectives were investigated with a particular emphasis on objectives 2 (processes at a daily scale) and 3 (nutrient resources and oceanic fertility). Between each station, continuous multiparametric (hydrological, optical, biological and chemical) surface acquisitions were performed.
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Composition, abundance and biomass of fish assemblages associated to Posidonia oceanica beds sampled by trawling in the north-western Mediterranean Sea

This dataset gathers the names of 86 species of fish as well as their trophic category, abundance and biomass per replicate, sampled by bottom trawling in Posidonia oceanica beds in three main geographic areas (Marseille, Port-Cros Island and Galeria in Corsica) of the Mediterranean French coast. Samples were collected by bottom trawling performed in seagrass meadows between 10 and 40 m depth at different seasons (summer-winter) and period (day-night) at several occasions between 1980 and 2013. This dataset is a witness of the structure, functioning and evolution of fish assemblages in north-western Mediterranean Posidonia oceanica beds.   Image Reference: https://www.seanoe.org/data/00907/101934/illustrations/illustration-236.gif.  
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Turbidity (NTU) data from the EMSO-Azores observatory, 2018-2019

This dataset contains turbidity (NTU) data acquired between August 2018 and June 2019 using a Wetlabs turbidimeter (ECO-BBRTD, serial # 215R) installed horizontally at 1.5 m height at the top of the SeaMoN East frame. The sensor was not calibrated as the sizes of the natural particles are unknown. Data was acquired every 15 minutes. The instrument is part of the SeaMoN East ecological monitoring node deployed at ca 10m away from the active hydrothermal edifice Tour Eiffel. Deployment : 2018/08/23 -Victor 6000 Dive 707-12 (Momarsat 2018 cruise https://doi.org/10.17600/18000514) Recovery : 2019/06/15 - Nautile dive 1942-04 (Momarsat 2019 cruise (https://doi.org/10.17600/18001110)-[https://doi.org/10.17600/18000514]) Location : 37.8N, 36.77S, -31.64E, -32.91W  
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Collection of BGC-Argo single synthetic profile files with improved post processed Chlorophyll-A at the global scale

On January 9, 2024, ((Sauzede et al., 2016)-[https://doi.org/10.1002/2015JC011408]) development, we have applied a specific post-processing that acts similarly to a DM adjustment to improve Chla accuracy, but unlike DM data, data produced are not fully scrutinized. This post-processing procedure aims to apply three main corrections: 1) the median of the minima for dark correction; 2) the Non-Photochemical Quenching (NPQ) correction from (Xing et al. (2018))-[https://doi.org/10.1364/OE.26.024734], based on both Photosynthetically Available Radiation (PAR) and bbp measurements; 3) the physiological correction factor of fluorescence into Chla determined from the method (of Xing et al. (2011))-[https://doi.org/10.1029/2010jc006899], based on the vertical profile of Ed(490), the downwelling irradiance at 490 nm. We applied this procedure to all the BGC-Argo fleet measuring fluorescence, including floats that are non-equipped with a radiometer. For those floats, radiometric parameters [(PAR and Ed(490)] were modelled thanks to the SOCA-light method ((Schmechtig et al., 2023)-[https://doi.org/10.13155/35385]). Schematic representation of the post-processing of Chla data used for SOCA2024 training. The dashed rectangle corresponds to the correction applied using the median of data for the entire lifetime of float estimations. For instance, dark values are corrected by applying the median of all dark values computed across all profiles of the float's lifetime. The satellite indicates where a direct ocean colour matchup is required to obtain a value. Image Reference: https://www.seanoe.org/data/00911/102324/illustrations/illustration-238.gif.
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SOLAB low-cost field surveys of the southern Senegal continental shelf: physical and biogeochemical variables

Many developing countries of the global South have limited field experiment programs to monitor the state of their marine environment. As part of the laboratoire mixte international ECLAIRS a monitoring program was initiated in 2017 whose aim was to design and experiment low-cost strategies (field plans, instrumentation) for the monitoring of the southern Senegal coastal ocean. Over 50 field trips, most of them from shore to the shelf break (i.e., ~ 30 to 80 km cross-shore distance) were conducted between fall 2017 and present-day. Among the collected observations are physics and biogeochemistry vertical profiles made with RBR CTD loggers equipped with up to 7 sensors (temperature, salinity, pressure, fluorescence, dissolved oxygen, turbidity, CDOM, photosynthetic available radiation) which are gathered in this dataset (. Nautical vehicules we used mostly consisted in a 25 footer sailing boat (16 field trips), fishing canoes (23 field trips) and, more occasionally sportfishing and work boats of size < 30 feet. Sampling was spatially concentrated along two cross-shore transects at ~ 14.5oN and 13.55N.The trial and error approach and the constraints associated with the boats we used for the program led to some spread/variability in the exact location of the observation stations. The data is also biased toward low-wind/fair weather conditions during which field trips were easier to conduct. Nevertheless, this dataset offers, to date, the most comprehensive insitu description of the southern Senegal seasonal cycle for essential variables temperature, salinity, fluorescence, and dissolved oxygen. Metadata are provided in each netcdf file. Whenever possible up and down profiles are provided (down profile first) so that temperature-salinity misalignments affecting the determination of salinity can be identified (temperature gradients are generally one-signed so the manifestations of misalignment errors are opposite during the up and down profiles). The field DIR provides indication on whether one of the profiles, up or down, shall be preferred (e.g., use upcast when surface data is missing for the downcast; conversely use downcast when water samples were made during the upcast  ...). 
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Global scale surface meso-plankton dataset collected with High-Speed Net and imaged with ZooScan during the Tara Pacific Expedition

This dataset consists of a quantitative imaging dataset of ZooScan-imaged mesoplankton (> 200 µm), collected with high-speed net aboard the schooner Tara during the Tara Pacific Expedition (2016-2018). Samples were collected at the surface, generally on a daily frequency, across the Atlantic and Pacific Oceans from open-ocean stations (151 samples; open-ocean label: [i00_oa###]) and from stations in coastal waters of 32 Pacific islands (54 samples; island label: [i##_oa###]). The full description and discussion of this dataset can be found in the associated data paper Mériguet et al. (in rev). This dataset consists of 256 352 plankton individuals, plankton parts, non-living particles and imaging artefacts, ranging from 300 µm to a few mm, individually imaged and measured with the ZooScan (Gorsky et al., 2010). The objects were classified into 159 taxonomic and morphological groups. All images and their taxonomic annotations are available in the open-access EcoTaxa (Picheral et al., 2017) project at this link: https://ecotaxa.obs-vlfr.fr/prj/11292. The 'EcoTaxa ZooScan Tara Pacific HSN 300 microns export' dataset contains the EcoTaxa tsv exports which associate each object with these metadata (station name, sampling coordinates, sampling date and time, etc., the main metadata are found in the Classic Metadata ZooScan Tara Pacific HSN 330 microns.csv table) and describe it by numerous morphological features extracted from each individual object by ZooProcess. The csv table named 'Export EcoTaxa ZooScan read me.csv' defines the 160 metadata and data found in the EcoTaxa tsv export. The 'Descriptors ZooScan Tara Pacific HSN 330 microns.csv' table combined the data from which we calculated quantitative descriptors of the planktonic communities: abundance (ind.m-3), biovolume (mm3.m-3; as a proxy of biomass) calculated from the area, riddled area and ellipsoidal measurement of each object (see Vandromme et al., 2012 for the 3 calculations of biovolume), and Shannon diversity index. This was done for all taxonomic annotations and for several levels of grouping; living or non-living, plankton groups and trophic association. The individual biovolumes of organisms were arranged in Normalised Biomass Size Spectra (NBSS) as described by Platt (1978), with size expressed as Equivalent Spherical Diameter (ESD, µm). NBSS calculations were made for all taxonomic annotations and for the different levels of grouping. There are available for each station in the NBSS ZooScan Tara Pacific HSN 330 microns csv tables.
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