AndreaBozzo/ceres-open-data-index huggingface dataset:
Combining Individual Phenotypes of Feed Intake with Genomic Data to Improve Feed Efficiency in Sea Bass

[Lien vers la fiche source] 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.
MOOSE T02_14 (EGO tintin glider) deployment (Mediterranean Sea - Western basin)

[Lien vers la fiche source] The observations of tintin glider on mooset02_14 (Mediterranean Sea - Western basin) : - EGO NetCDF time-series (data, metadata, derived sea water current) - NetCDF profiles extracted from the above time-series - Raw data - JSON metadata used by the decoder The following parameters are provided : - Practical salinity - Sea temperature in-situ ITS-90 scale - Electrical conductivity - Sea water pressure, equals 0 at sea-level
COSTOF, technical data from SeaMoN West, node of the EMSO-Azores observatory, 2013-2014

[Lien vers la fiche source] This dataset contains technical parameters (Voltage in V, current in mA, energy in Ah, internal pressure in mbar, water leak detection) acquired between September 2013 and February 2014 (n=332) by the COSTOF (COmmunication and STOrage Front-end), which is the Electronic core of SeaMoN West, the bottom station of EMSO-Azores dedicated to geophysical observations (data acquired every 6 hours).
Budget and staff for management and protection of coastal environment; wastewater management; response to green algae blooms

[Lien vers la fiche source] The data presented herein are focused on marine and coastal environment management and protection costs as measuring the state's effort in terms of budget and staff in this domain. There is a considerable diversity of actions for marine and coastal envrionment both at the level of the state and of local authorities. So the picture given by the data remains partial. Budget data as sourced from yearly budgets indicate the main actions and there cost in terms of state expenditure. In addition the Environment Satellite Accounts provide data on waste water management (with obvious impacts of the state of sea waters). An example of local problem is analysed in terms of cost: green algae blooms are managed at local level, and collection requires a sizeable budget as shown using data from CEVA Center for Seaweed Study and Processing.
Biogenic and lithogenic particulate silica, diatom abundance and C biomass data during the OUTPACE (2015) cruise

[Lien vers la fiche source] This dataset was collected during the French program OUTPACE: It includes suspended particulate Si matter. Samples were collected from Niskin bottles mounted on a rosette and both biogenic and lithogenic silica were obtained from 2L filtered samples in the 0-200 m surface layer. This dataset also includes diatom abundance and C biomass conversion data. Samples were collected from Niskin bottles at the surface and DCM (Deep Chlorophyll a Maximum) depth.
CAMBIOS Tomography data: level 1 to 3

[Lien vers la fiche source] The primary tomography data are the full reception window received and stored by the tomography receiver. The processing includes the extraction of the acoustic signal transmitted by the source, the correction due to mooring motion and clock drift. Then, the arrival time of the signal along the different paths have to be identified. Changes in the soure-to-receiver travel time along the different ray path are due to changes in te ocean sound velocity structure, mainly related to temperature. In the Canary basin, due to the strong anomaly produced by the Mediterranean water, we first observe a leading, unresolved packet, followed by a few resolved refracted ray arrivals, and at last some bottom reflected rays.
Data related to biogenic dissolution rates quantified in various carbonate substrates exposed to ocean acidification at Ischia (Italy) and Faial (Azores)

[Lien vers la fiche source] Recent studies carried out in coral reef settings or under controlled conditions showed that rising aqueous pCO2 (pH ≥ 7.8 – 7.9, and a saturation state of carbonate minerals > 1) stimulates the growth of reef microboring or euendolithic phototrophs, especially microalgae, and therefore, enhance rates of biogenic dissolution of carbonates. Those micro-organisms play a major role in reef bioerosion and coral reef functioning. In temperate-cold carbonate ecosystems, carbonate dissolution by euendolithic microflora has never been investigated under natural ocean acidification conditions. We thus realized two experiments to investigate the effects of low pH (and saturation states) on early natural microboring communities colonizing various carbonates and their associated rates of biogenic dissolution. One was carried out at Ischia (Italy) with mollusk shells exposed at two CO2 vents (pH < 7.5) vs an ambient site (pH ~ 8) during six months. The other one was realized at Faial (Azores) with various carbonate substrates (both aragonite and calcite) at one CO2 vent (pH ~ 7.4) vs an ambient site (pH ~ 8) over 45 days. Here we provide the data which allowed calculating rates of carbonate biogenic dissolution at all studied sites; i.e. the depth of penetration of euendolithic filaments into carbonates and the % of surface area of substrate colonized by microborers (bioeroded surface area). Rates of biogenic dissolution per site and per location are also provided, as well as environmental data collected at Faial (those collected at Ischia are published elsewhere). A total of 5 excel files is thus provided.
El nino2 deployment (EGO glider : bonpland) (Peru basin)

[Lien vers la fiche source] The observations of bonpland glider on el nino2 deployment (Peru basin) are distributed in 4 files: - EGO NetCDF time-series (data, metadata, derived sea water current) - NetCDF profiles extracted from the above time-series - Raw data - JSON metadata used by the decoder The following parameters are provided : - Practical salinity - Sea temperature in-situ ITS-90 scale - Electrical conductivity - Sea water pressure, equals 0 at sea-level
EMSO-Azores observatory real-time data 2017 deployment

[Lien vers la fiche source] This dataset contains the real-time data acquired from the EMSO-Azores observatory since July 2017. It is daily updated. Data are from the following instruments: Geodesic GPS, Iridium GPS modem, Meteorological station, Ocean Bottom Seismometer, Optode oxygen sensor, Pressure gauges (JP), Turbidity sensor, Benthic and Resistivity Sensors (BARS), video camera and Communication and Storage Front-end (COSTOF2).
COSTOF, technical data from SeaMoN East, node of the EMSO-Azores observatory, 2010-2011

[Lien vers la fiche source] This dataset contains technical parameters (Voltage in V, current in mA, energy in Ah, internal pressure in mbar, water leak detection) acquired between October 2010 and December 2010 (n=332) by the COSTOF (COmmunication and STOrage Front-end), which is the Electronic core of SeaMoN East, the bottom station of EMSO-Azores dedicated to geophysical observations (data acquired every 6 hours).
COSTOF, technical data from SeaMoN West, node of the EMSO-Azores observatory, 2015-2016

[Lien vers la fiche source] This dataset contains technical parameters (Voltage in V, current in mA, energy in Ah, internal pressure in mbar, water leak detection) acquired between April 2015 and September 2016 (n=332) by the COSTOF (COmmunication and STOrage Front-end), which is the Electronic core of SeaMoN West, the bottom station of EMSO-Azores dedicated to geophysical observations (data acquired every 6 hours).
Effect of melt/mantle interactions on MORB chemistry at the easternmost Southwest Indian Ridge (61 to 67°E)

[Lien vers la fiche source] Geochemical data: major, trace element and isotopic (Pb and Nd) compositions of basalts; major and trace element compositions of minerals in ultramafic to gabbroic rocks (clinopyroxenes, orthopyroxenes, plagioclases, olivines and spinels for major elements; clinopyroxenes, orthopyroxenes, plagioclases for trace elements)
MOOSE T00_28 (EGO himilcon glider) deployment (Mediterranean Sea - Western basin)

[Lien vers la fiche source] The observations of himilcon glider on mooset00_28 deployment (Mediterranean Sea - Western basin) are distributed in 4 files: - EGO NetCDF time-series (data, metadata, derived sea water current) - NetCDF profiles extracted from the above time-series - Raw data - JSON metadata used by the decoder The following parameters are provided : - sea water temperature - sea water electrical conductivity - sea water pressure - Quality flag - Sea water salinity
Contribution of benthic microalgae to the temporal variation in phytoplankton assemblages in a macrotidal system. Supplementary Data S1.

[Lien vers la fiche source] Suspended benthic microalgae in the water column reflect the strong benthic-pelagic coupling in coastal ecosystems and particularly in turbid macrotidal systems. Nevertheless, the temporal pattern of benthic microalgae contribution to phytoplankton assemblages has been largely overlooked, and yet it may provide significant clues for trophic studies, water quality assessment and understanding of toxic shellfish outbreaks related to phycotoxins produced by benthic species. The study, based on data acquired in a macrotidal system along the French Atlantic coast, analyze the seasonal contribution of benthic microalgal growth-forms to phytoplankton using a 12-year time-series from the Phytoplankton and Phycotoxin Monitoring Network (REPHY) implemented and managed by the French Research Institute for the Exploitation of the Sea (IFREMER). Here we provide all the information gathered in order to estimate microalgal biovolumes and carbon biomass. The table (.xls format) comprise four spreadsheet: i) a main table with all the information regarding the taxa-volume-carbon calculations, ii) equations for geometric forms, iii) a and b coefficients for the biovolume-to-carbon conversion and iv) all the references used.
Complementarity and discriminatory power of genotype and otolith shape in describing the fine-scale population structure of an exploited fish, the common sole of the Eastern English Channel

[Lien vers la fiche source] Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution. We have assessed the discriminatory power of genetic markers and otolith shape to reveal the population structure of the common sole (Solea solea), living in the Eastern English Channel stock off France and the UK. The aims were to (i) inform the short and long-term population structure by comparing genetic and otolith shape approaches, and (ii) combine the tracers in a single analysis to assess the interest of a combined approach. First, we applied Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subpopulations using otolith shape as an integrative tracer of life history. Finally, we combined the genotypes and otolith phenotypes in a supervised machine learning framework to probabilistically assign adults to subpopulations. Genetic assignments and otolith shape analyses provided congruent results suggestive of a metapopulation structure for the common sole of the Eastern English Channel. Despite congruent results from genetics and otolith shape, the combined analysis did not provide realistic reallocation probabilities. Our findings support the idea that independent analyses of tracers provide fruitful insights and that a combined approach should be preferred when a large and balanced number of fish is available for each tracer analyzed.
Antarctic blue whales in the southern Indian Ocean: a multi-year and multi-site database of Z-call detections

[Lien vers la fiche source] As part of the OHASISBIO project, since January 2010, a network of 6 to 8 autonomous hydrophones is deployed in the southern Indian Ocean (Fig. 1) to monitor the low-frequency sounds (0-120 Hz) carried by the ocean. These acoustic data provide unique information on the seasonal presence of several species and sub-species of large baleen whales. Among them, the Antarctic blue whale (Balaenoptera musculus intermedia) has a distinct call between 18 and 26 Hz, easily recognizable by its Z-shape in a time-frequency diagram. We designed an automatic Z-detector (Socheleau et al., 2015) to cense the Z-calls in our multi-year, multi-site acoustic dataset. The resulting database consists of several metrics: time of detection of each individual call, the ambient noise level between 40 and 60 Hz, and the ratio between the whale chorus between 25 and 27 Hz over the noise level between 30 and 33 Hz. The rationale for these metrics and the interpretation of the results can be found in the paper by Leroy et al. (2016; see reference below). Figure 1: Acoustic records available for Antarctic blue whale Z-call detections. © E Leroy / CNRS-U.Brest LGO Figure 2: Acoustic records available for Antarctic blue whale Z-call detections. © E Leroy / CNRS-U.Brest LGO
COSTOF, technical data from SeaMoN West, node of the EMSO-Azores observatory, 2014-2015

[Lien vers la fiche source] This dataset contains technical parameters (Voltage in V, current in mA, energy in Ah, internal pressure in mbar, water leak detection) acquired between July 2014 and April 2015 by the COSTOF (COmmunication and STOrage Front-end), which is the Electronic core of SeaMoN West, the bottom station of EMSO-Azores dedicated to geophysical observations (data acquired every 6 hours).
MOOSE T00_37 (EGO tintin glider) deployment (Mediterranean Sea - Western basin)

[Lien vers la fiche source] The observations of tintin glider on mooset00_37 (Mediterranean Sea - Western basin) : - EGO NetCDF time-series (data, metadata, derived sea water current) - NetCDF profiles extracted from the above time-series - Raw data - JSON metadata used by the decoder The following parameters are provided : - Practical salinity - Sea temperature in-situ ITS-90 scale - Electrical conductivity - Sea water pressure, equals 0 at sea-level
Chemical contamination in Mytilus galloprovincialis with metals, PAHs, PCBs and organochlorine pesticides

[Lien vers la fiche source] The MYTIAD project focused on the assessment of chemical contamination (metals, PAHs, PCBs and organochlorine pesticides) in the Adriatic coastal waters by active mussel watching. Its purpose was harmonising and standardising strategies and methodologies used to assess the contamination status of the Adriatic Sea, in the framework of the WFD, the MSFD and UNEP/MAP Integrated Monitoring and Assessment Programme. Data on metals pointed out some hotspots along the eastern and western Adriatic Sea coasts, with the highest values of total PAH concentration detected in Split, Trieste, and Taranto (Ionian Sea). PCB and endrin contamination was higher in the Adriatic Sea than in the western Mediterranean Sea. This is the first comprehensive overview of contamination in the Adriatic Sea with critical comparisons of related studies over the Mediterranean Sea. It provides a useful harmonised dataset to support a coordinated definition of baselines, targets and thresholds, and further management of chemical contamination.
Life history traits' scoring to calculate a trawl disturbance indicator on mega- epibenthic fauna

[Lien vers la fiche source] 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 773 taxa commonly found in bottom trawl by-catch in the southern North Sea, English Channel and north-western Mediterranean were described.
ELISA (1997-1998) mesoscale survey in the Algerian sub-basin (Western Mediterranean): hydrological data set of the cruise ELISA-4 (summer 1998)

[Lien vers la fiche source] The Eddies and Leddies Interdisciplinary Study in the Algerian sub-basin (ELISA) experiment (1997–1998) was a multidisciplinary and multiplatform experiment designed to study the anticyclonic Algerian Eddies (AEs) generated by the instability of the Algerian Current, and their influence on the general circulation and biological phenomena. The data collected confirmed for instance the eastward path of LIW along the Algerian slope, and showed that these anticyclones correspond to the richer areas in spring. Following the daily analysis of satellite thermal images to track the AEs, the sampling scheme was adapted in real time, using transects with CTD casts every ~10km. So that the data are strongly "biased" toward describing (moving) eddies at high resolution: they are likely to be unadequate for a few purposes. The ELISA hydrological data sets have been obtained during the four cruises ELISA-1 to 4, from summer 1997 to summer 1998. This data set includes the ELISA-4 cruise (summer 1998) with 90 CTD profiles plus associated water bottles samples. Data sets are delivered in both netcdf and ODV formats.
Anchovy and Sardine egg abundances and zooplankton biomass within the Gironde plume in 2008

[Lien vers la fiche source] This dataset gathers results of monthly sampling with a WP2 plankton net within the Gironde plume (Bay of Biscay) in 2008 from March to August, as part of the ECLAIR suite of surveys. The sampling in May was part of the ECLAIR time-series but was performed onboard the THALASSA vessel during the PELGAS 2008 survey. Results are made of anchovy and sardine egg abundances, as well as size-fractionnated zooplankton biomass.
Genotyping of 4 European sea bass families with the DlabCHIP SNPs genotyping array

[Lien vers la fiche source] Four experimental backcross full-sib families (378, 454, 291 and 211 individuals) were produced by in vitro fertilization at Ifremer (Palavas-les-Flots, France). All 1334 individuals were genotyped with a ThermoFisher AxiomTM Sea Bass 57k SNP DlabChip at the genotyping platform Gentyane (INRAE, Clermont-Ferrand, France). SNP calling was done using ThermoFisher software AxiomAnalysisSuiteTM. Preliminary quality controls were applied with threshold values of 95% for SNP call rate and 90% for sample call rate.
AMOR-Bflux porewater and sediment data

[Lien vers la fiche source] 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.