cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17882/59658
title: Survival, growth and yield of diploid and triploid oysters Crassostrea gigas tested during the Plan de Sauvegarde from 2011 to 2014

description: 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.
DOI: 10.17882/59517
title: Updated biological traits' scoring and protection status to calculate sensitivity to trawling on mega-epibenthic fauna

description: 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 biological 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. The five categories retained are functional traits that were selected based on the knowledge of the response of benthic taxa to trawling disturbance (de Juan et al., 2009). 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. To expand this approach to that proposed by Certain et al. (2015), the protection status of certain species was also indicated. To enable quantitative analysis, a score was assigned to each category: from low sensitivity (0) to high sensitivity (3). Biological traits of species have been defined, from the BIOTIC database (MARLIN, 2014) and from information given by Garcia (2010), Le Pape et al. (2007) and Brind’Amour et al. (2009). For missing traits, additional information from literature has been considered. The protection status of each taxa was also scored: Atlantic species listed in OSPAR List of Threatened and/or Declining Species and Habitats (https://www.ospar.org/work-areas/bdc/species-habitats/list-of-threatened-declining-species-habitats) and Mediterranean species listed in Vulnerable Marine Ecosystems (FAO, 2018 and Oceana, 2017) were scored 3 and other species were scored 1. The scores of 1085 taxa commonly found in bottom trawl by-catch in the southern North Sea, English Channel and north-western Mediterranean were described.
DOI: 10.17882/59516
title: IAOOS winter hydrographic data during N-ICE 2015 North of Svalbard

description: We gathered ocean profiles during the first two floes of the N-ICE2015 ice camp north of Svalbard with IAOOS ocean profilers. Between January and March 2015, four ocean profilers were deployed: two below a full IAOOS platform (500 m long cable) during floe 1, two on an 800 m long instrumented line in a tent‐covered testing‐hole during floe1 and floe 2. The ocean profilers, from French manufacturer NKE (PROVOR SPI), carried a Seabird SBE41CP CTD (Conductivity, Temperature, Depth) with an Aanderaa 4330 optode for dissolved oxygen (DO). The profilers were set to perform two profiles a day from 500 m upward (800 m from testing hole) starting at 6 am and 6 pm. They provided the first winter data in the region with a total of 138 profiles during floe 1 (January 15- February 21) with 62, 50, and 26 profiles for IAOOS7, IAOOS8, and IAOOS 9, respectively and 16 profiles during floe 2 (February 24 - March 19- IAOOS 11 from testing hole). Following quality control, we retain all the temperature profiles and remove 1% of the salinity profiles. Finally, the accuracy is estimated to be 0.002°C in temperature, and 0.02 g/kg in salinity. Several profiles are missing or incomplete because of high drift speeds (&gt; 0.4 m s−1) impeding the ascent of the profiler. There are no bottle DO measurements during Floe 1 to calibrate the DO data. DO accuracy is estimated comparing the deep values of DO concentration (rather stable at 500m) between the three profilers. A difference of 3 μmol L−1 is observed between IAOOS 8 and 9, and IAOOS 7. An offset of 3 μmol L−1 is then applied to the oxygen data from IAOOS7 and the accuracy of the data is estimated to be at ±3 μmol L−1. The vertical resolution of the processed CTD data is 1 dbar in the upper 400 dbars, 5 dbars from 400 to 550 dbars and 10 dbars from 550 to 850 dbars. The vertical resolution in dissolved oxygen is 2 dbars over all depths.
DOI: 10.17882/59399
title: Arctic Ocean sensitivity tests to doubling of riverine carbon and nutrient delivery simulated by the NEMO-PISCES model

description: This dataset provides model output from idealized NEMO-PISCES simulations on the ORCA1 configuration. The output includes five 80-years simulations: (1) a control run with pre-industrial CO2 concentrations (CTL), (2) a simulation with a 1% increase in atmospheric CO2 per year (CO2), (3) a simulation just like CO2 but with a 1% increase in riverine DOC delivery (DOC), (4) a simulation just like DOC but with a 1% increase in riverine CT delivery (DIC), and (5) a simulation just like DIC but with a 1% increase in riverine nutrient delivery (NUT). The provided variables are annually averaged surface pH, surface aragonite saturation state, depth-integrated CT, air-to-sea CO2 flux, and depth-integrated net primary production.
DOI: 10.17882/59331
title: Matlab Toolbox for Time Series Exploration and Analysis

description: TOOTSEA (Toolbox for Time Series Exploration and Analysis) is a Matlab solftware, developped at LOPS (Laboratoire d'Océanographie Physique et Spatiale), IFREMER. This tool is dedicated to analysing datasets from moored oceanographic instruments (Currentmeter, CTD, Thermistance, ...). TOOTSEA allows the user to explore the data and metadata from various instruments file, to analyse them with multiple plots and stats available, to do some processing/corrections and qualify (automatically and manually) the data, and finally to export the work in a netcdf file.
DOI: 10.17882/59311
title: Oceanic concentrations and emissions toward atmosphere of carbon monoxide simulated by the PISCES biogeochemical model

description: The ocean constitutes a minor source of atmospheric carbon monoxide (CO) at the global scale, but could play an important role far from continental anthropized emission zones. Here we use the NEMO-PISCES (Nucleus for European Modelling of the Ocean, Pelagic Interaction Scheme for Carbon and Ecosystem Studies) ocean general circulation and biogeochemistry model to dynamically assess the oceanic CO budget and its emission to the atmosphere at the global scale. The main bio-chemical sources and sinks of oceanic CO are explicitly represented in the model. The main processes driving the CO concentration are photoproduction and bacterial consumption and are estimated to 19.2 and 21.9 Tg C yr−1 respectively with our best-guess modelling setup. There are however very large uncertainties on their respective magnitude. Despite the scarcity of the in situ CO measurements in terms of spatio-temporal coverage, the proposed best simulation is able to represent most of the data (~ 300 points) within a factor of two. Overall, the global emissions of CO to the atmosphere are 3.6 Tg C yr−1, in the range of recent estimates, but very different from the ones published by Erickson in 1989, which were the only gridded global emission available to date. These oceanic CO emission maps are relevant for use by atmospheric chemical models, especially to study the oxidizing capacity of the atmosphere above the remote ocean.
DOI: 10.17882/59303
title: Acoustic recordings from an ocean glider along the continental shelf break of the Pacific Northwest USA

description: This dataset contains passive acoustic data files recorded from a Slocum G2 ocean glider equipped with a hydrophone and data logging system. The hydrophone was mounted on the dorsal midsection of the vehicle. The acoustic glider recorded continuously at a sample rate of 10 kHz along a 458 km long north to south traverse of the outer continental shelf break of the Pacifc Northwest USA (approximate start and endpoints 46.5N, 125W to 42.75N, 125W). The dataset also includes an html file that describes the acoustic data file format (.DAT) and a matlab file containing the glider navigation information (latitude, longitude, depth, time).
DOI: 10.17882/59232
title: Marine Protected Area Effectiveness

description: Marine protected areas (MPAs) provide biodiversity conservation benefits in a range of marine habitats. Many protected areas are established and governed through top-down or shared governance arrangements, yet little is known about how these governance strategies compare in terms of the protection benefits they provide to MPAs globally. Using an extensive data set of MPA conditions, we developed a set of Bayesian hierarchical models to understand the role of shared governance versus federal governance on reef fish biomass from 218 global MPAs. We find greater reef fish biomass benefits in MPAs with shared governance than with top-down, or federal arrangements. We also find greater benefits in older MPAs and MPAs farther away from shore. Our results highlight the fundamental importance of multi-stakeholder participation for improving conservation outcomes, representing an important conservation opportunity for new or existing MPAs.
DOI: 10.17882/59035
title: Upper ocean profiles of temperature, salinity and turbulent dissipation rate

description: This dataset contains 58 profiles of temperature, conductivity, salinity and turbulent dissipation in the upper ocean (0 - 50m) of a location in the open North Atlantic, off the North American coastal shelf (approximate location 40.27N, 58.9W). The profiles are obtained with the autonomous Air Sea Interaction Profiler (ASIP), which was deployed during a research cruise aboard the RV Knorr (USA) in June 2011. The dataset further contains meteorological observations made from the research vessel during this period. The outcome of the prognostic model by Bellenger et al. 2017, given an input of the combined oceanographic and meteorological observations to simulate seawater temperature and salinity at two depths near the surface, is also included. This dataset forms the basis of the JGR Oceans submission by ten Doeschate et al. 2019 "Upper Ocean Response to Rain Observed from a Vertical Profiler".
DOI: 10.17882/59027
title: Experimental database of the flow past a wall-mounted square cylinder

description: In high flow velocity areas like those suitable for tidal applications, turbulence intensity is high and flow variations may have a major impact on tidal turbines behaviour. Large boils that can be observed at the sea surface are emitted from the sea floor and may interact with the tidal turbine. These boils have then to be characterized. The Reynolds number, based on the rugosity height and mean flow velocity, is rather high in this context: Re = 2.5 × 107 . For that purpose, experiments are carried out in a flume tank with Re as high as achievable in Froude similitude (in the tank: Re = 2.5 × 105 and Fr = 0.23) in order to study coherent flow structures emitted behind seabed obstacles. The obstacle is here a canonical square wall-mounted cylinder chosen to be representative of specific in-situ bathymetric variations. Using PIV and LDV measurements, the flow past the cylinder is investigated. The database created is presented in this report.
DOI: 10.17882/58817
title: Camera sled and beam trawl data for the Maryland offshore wind areas

description: Offshore wind farms are a crucial component for the improvement of renewable energy in the United States. The Bureau of Ocean Energy Management (BOEM) designated ~170 km2 of shelf area for wind energy development off the coast of Maryland, USA. In order to understand potential environmental impacts of wind turbine installation on the benthic ecosystem within the designated area, we conducted a study to visually characterize bottom habitats and epibenthic communities in the Mid-Atlantic Outer Continental Shelf blocks of the Maryland wind energy area. Seven 5 km long transects were sampled using a towed camera sled with a downward-facing digital camera that captured images at 5 frames∙s-1s. Additional small-mesh beam trawling was also conducted at selected locations complementary for species identification.. Image data were analyzed using two image selection methods, random and systematic (i.e. video frames were selected at various intervals). For both methods, estimates of community diversity (Hill’s N2) stabilized with sample sizes ranging from 316 to 398 frames. Our results allowed us to define distinct epibenthic communities and bottom habitats that are associated with offshore wind energy sites and to develop a sampling technique for digital images that can be applied to other research programs.
DOI: 10.17882/58767
title: Environmental, biomass and biotic interactions data of Spartina sp. niches in the Bay of Arcahon

description: 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.
DOI: 10.17882/58697
title: Thermohaline Staircases in the Tyrrhenian Sea Experimental data-set (2003-2016)

description: This time series has been collected by the Italian Consiglio Nazionale delle Ricerche (CNR) in a station located at about 3500 m depth in the central Tyrrhenian Sea (39° 46.85 N, 011° 53.00 E) over the period 2003-2016. The dataset contains 21 hydrological profiles (Pressure (dbar), Temperature (ITS-90, °C) and Salinity) performed on average every six months, with a lack of data in the period 2007-2010. The dataset is highly homogeneous in technical characteristics and quality, since the instrument used to collect most of the data is the same CTD probe (SBE911plus) and data quality procedures have been performed. The calibration of the probe was performed at the NATO-CMRE Centre of La Spezia up to 2014, and by the manufacturer (SeaBird) or by the Oceanographic Calibration Center of OGS in Trieste thereafter. To verify the post calibration performance of the probe, redundant sensors were often used for both temperature and salinity measurements, and on board salinity analysis of the water samples was performed using a Guideline Autosal or a Portasal salinometer. Raw data are post-processed and averaged at 1 dbar. Until 2014, the data were collected by the Italian R/V URANIA, those of 2015 by the Italian R/V MINERVA UNO, and those of 2016 by the Spanish R/V Angeles Alvarino. This is the longest time series (fourteen years) of temperature and salinity of thermohaline staircases due to double diffusion in the salt finger regime ever observed. Parameters included in the .csv data file: - Cruise name (Cruise) - Time as julian days (Time_julian day) - Latitude - Longitude - Pressure in dbar (Pressure_dbar) - Practical Salinity (Salinity) - Temperature ITS-90 in °C (Temperature_ITS-90_°C)
DOI: 10.17882/58407
title: Carbon parameters along VOS lines

description: Carbon parameters along the track of merchant ships
DOI: 10.17882/58280
title: High-Frequency physical, biogeochemical and meteorological data of Coastal Mediterranean Thau Lagoon Observatory

description: High-Frequency (from minutes to hour) physical, biogeochemical and meteorological data were recorded in “Coastal Mediterranean Thau Lagoon Observatory” (43°24’53” N, 3°41’16” E). This observatory is located in the Northwestern Mediterranean Thau Lagoon near the pontoon of MEDIMEER (Mediterranean platform for Marine Ecosystems Experimental Research) in proximity of the “Marine Station (OSU OREME)” in the city of Sète in south of France. The physical and biogeochemical sensors were immerged in the water column at approximately 1.5 m below the water surface (max. depth of the site 3 m). The date, hour and minute of data acquisition, type of sensors and unity for each variable are mentioned in each data file.
DOI: 10.17882/58265
title: MaRINET2 Tidal "Round Robin" dataset: comparisons between towing and circulating tanks test results for a tidal energy converter submitted to wave and current interactions

description: This dataset comes from a comparative "Round Robin" testing programme, which has been conducted as part of the MaRINET2 program. The main purpose of this investigation is to evaluate the impact of different experimental facilities on a horizontal axis tidal turbine model when it is exposed to wave and current interactions. The aim of the trials was to test the turbine in five different test facilities to explore the sensitivity of the results to the choice of facility. The facilities comprised two towing tanks, two circulating water channels and one open-sea facility. Performance assessments in terms of torque, drag, blade root forces, wave and inflow speed are recorded for various wave and current conditions.
DOI: 10.17882/58267
title: Combining Individual Phenotypes of Feed Intake with Genomic Data to Improve Feed Efficiency in Sea Bass

description: Measuring individual feed intake of fish in farms is complex and precludes direct selective breeding for feed conversion ratio (FCR). Here, we estimated the individual FCR of 588 sea bass using individual rearing under restricted feeding. These fish were also phenotyped for their weight loss at fasting and muscle fat content as possible indirect indicators of FCR. The 588 fish were from a full factorial mating between parental lines divergently selected for high (F+) or low (F-) weight loss at fasting. The pedigree was known back to the great grandparents. A subset of 400 offspring and their ancestors were genotyped for 1,110 SNPs, which allowed estimating the genomic heritability of traits. Individual FCR and growth rate in aquarium were both heritable (genomic h² = 0.47 and 0.76, respectively) and strongly genetically correlated (-0.98), meaning that under restricted feeding, faster growing fish were more efficient. FCR in aquariums was significantly better for fish with two F- parents (1.38), worse for fish with two F+ parents (1.51) and intermediate (1.46) for crossbred fish (F+/F- or F-/F+). Muscle fat content was positively genetically correlated to growth rate in aquarium and during fasting. Thus, higher growth rate in aquariums, lower weight loss at fasting and fat content are all traits that could improve FCR in aquarium. Improving these traits would also improve FCR of fish in normal group rearing conditions, as we showed that groups composed of fish with good individual FCR were significantly more efficient in groups. The FCR of groups was also better when the fish composing the groups had, on average, lower estimated breeding values for growth rate during fasting (losing less weight). Thus, FCR in aquarium and weight loss at fasting are both promising to improve FCR of fish in groups. Finally, we showed that the reliability of estimated breeding values was higher (from +10% to +125%) with single-step genomic BLUP than with pedigree-based BLUP, showing that genomic data would enhance the accuracy of EBV prediction o in selection candidates from a limited number of sibs individually phenotyped for FCR in aquariums.
DOI: 10.17882/58149
title: Three tidal turbines in interaction: an experimental data-set on wake and performances

description: The development of marine current turbine arrays depends on the understanding of the interaction effects that exist between turbines in close proximity. Moreover, the ambient turbulence intensity also plays a major role in the behaviour of tidal turbines. Thus it is necessary to take ambient turbulence into account when studying interactions between several turbines. In order to highlight these interaction effects, experiments were carried out in the IFREMER flume tank of Boulogne-sur-mer (France). These experiments focused on elementary interactions between 3-bladed horizontal axis turbines. This data-set provides the experimental measurements obtained for three configurations with two ambient turbulence intensity rates. The measurements are divided in terms of turbine performances and flow velocity measurements. For the flow velocity measurements, a special care was taken in the zone of interest, i.e. where the turbine wakes are interacting. For the turbine performances, only the downstream turbine parameters, e.g. torque, rotation speed and drag force, are recorded in order to quantify the upstream turbine row masking effect. These measurements are provided so that to serve as a benchmark test case for numerical validation.