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95 Research products

  • SDSN - Greece
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  • Hal-Diderot
  • HAL Descartes
  • European Marine Science

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  • Authors: Vandeputte, Marc;

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  • Authors: Vandeputte, Marc;

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    Authors: Ferreira Araujo, Beatriz; Osterwalder, Stefan; id_orcid0000-0001-8775-0813; Szponar, Natalie; Lee, Domenica; +19 Authors

    Nature Communications, 13 ISSN:2041-1723

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    Research Collection
    Article . 2022
    License: CC BY
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    Authors: Chenais, Nathalie; Henriquenobrega, Rafael; Thomas, Manon; Porcon, Beatrice; +5 Authors

    International audience

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    Other literature type . 2022
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      Other literature type . 2022
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    Authors: Denvil-Sommer, Anna; Gehlen, Marion; Vrac, Mathieu;

    To derive an optimal observation system for surface ocean pCO2 in the Atlantic Ocean and the Atlantic sector of the Southern Ocean, 11 observation system simulation experiments (OSSEs) were completed. Each OSSE is a feedforward neural network (FFNN) that is based on a different data distribution and provides ocean surface pCO2 for the period 2008–2010 with a 5 d time interval. Based on the geographical and time positions from three observational platforms, volunteering observing ships, Argo floats and OceanSITES moorings, pseudo-observations were constructed using the outputs from an online-coupled physical–biogeochemical global ocean model with 0.25∘ nominal resolution. The aim of this work was to find an optimal spatial distribution of observations to supplement the widely used Surface Ocean CO2 Atlas (SOCAT) and to improve the accuracy of ocean surface pCO2 reconstructions. OSSEs showed that the additional data from mooring stations and an improved coverage of the Southern Hemisphere with biogeochemical ARGO floats corresponding to least 25 % of the density of active floats (2008–2010) (OSSE 10) would significantly improve the pCO2 reconstruction and reduce the bias of derived estimates of sea–air CO2 fluxes by 74 % compared to ocean model outputs.

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    Ocean Science (OS)
    Other literature type . 2021
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    Ocean Science (OS)
    Other literature type . 2021
    Hal-Diderot
    Article . 2021
    License: CC BY
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      Ocean Science (OS)
      Other literature type . 2021
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      Ocean Science (OS)
      Other literature type . 2021
      Hal-Diderot
      Article . 2021
      License: CC BY
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    Authors: Tourneroche, Anne; Lami, Raphaël; Burgaud, Gaëtan; Domart-Coulon, Isabelle; +5 Authors

    The sugar kelp Saccharina latissima dominates many temperate coastal ecosystems, plays key ecological roles and presents important economic potential. However, its microbiota remains poorly investigated, although it could play an important role in algal fitness. In this study, we combined high throughput Illumina-based DNA sequencing and Fluorescence In Situ Hybridization to perform a culture-independent investigation of the S. latissima bacterial and fungal microbiota. Up to 600 bacterial and 100 fungal Amplicon Sequence Variants were identified per algal individual, revealing diverse bacterial and fungal communities associated to S. latissima . Overall, bacterial communities were dominated by Proteobacteria, Actinobacteria, and Bacteroidetes, in particular Hyphomonadaceae and Cyclobacteriaceae . Fungal communities were dominated by Ascomycota and Basidiomycota , in particular Mycosphaerellaceae, Psathyrellaceae , and Bulleribasidiaceae . Our results also revealed a variable distribution of S. latissima microbiota, as two adjacent tissue samples typically contained distinct fungal and bacterial assemblages, and CARD-FISH analysis detected microbial endosymbionts (with a few epibionts). Complementary analyses showed that despite achieving a good sequencing coverage for each tissue sample, the unexpected diversity and variability of ASVs made the definition of a core fungal and bacterial microbiota difficult, and highlights novel avenues to overcome the limitations of current surface-sterilization and metabarcoding protocols.

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    Frontiers in Marine Science
    Article
    License: CC BY
    Data sources: Sygma
    Hal-Diderot
    Article . 2020
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    Authors: Bonny, Patrice; Desdouits, Marion; Schaeffer, Julien; Garry, Pascal; +2 Authors

    Shellfish constitute an important protein source but may be contaminated by viruses from various origins. A study performed on clams collected in Cameroon showed a high prevalence of norovirus and hepatitis A virus. After sequencing, the hepatitis A virus showed similarities with the genotype V simian strains. The need for a one-health approach to protect humans from emerging diseases is evident by the high number of microbial pathogens that become zoonotic following insect bites or consumption of contaminated meat. This is particularly well documented for infectious disease transmission from non-human primates to human (Devaux et al. 2019). Environmental issues are critical in such events, especially for RNA viruses that may be excreted at high concentrations by infected hosts and are very resistant outside their hosts (De Graaf et al. 2017). Transmission can occur directly by ingestion of contaminated waters or via contaminated food. For example, shellfish growing in coastal areas or rivers are known to concentrate microorganisms by their ability to filter large volume of waters and thus may favor the transmission of zoonotic strains to humans when consumed.

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    Authors: Girard, Fanny; Sarrazin, Jozee; Olu, Karine;

    Cold seeps are widespread in the deep sea and, like other chemosynthesis-based ecosystems, often host high faunal biomass. Temporal changes at seeps have been inferred by comparing communities at different successional stages; nonetheless, temporal studies in seep ecosystems are rare. Using data collected as part of a benthic observatory, we characterized intra-annual microbial and faunal dynamics in a microbial mat habitat on the Håkon Mosby mud volcano (1256 m depth; Barents Sea), and evaluated the effects of a mud eruption on the biota. Video sequences recorded twice daily for 4.5 months with an autonomous imaging module were analyzed to quantify changes in microbial mat cover and megafaunal density and behavior. In addition, time series data for pressure, bottom currents, and seabed temperature were analyzed to characterize environmental changes. Of the five taxa observed on the video footage, the zoarcid Lycodes squamiventer, the pycnogonid Nymphon macronyx, and the skate Amblyraja hyperborea were the most common. Zoarcids made frequent incursions on microbial mats, but were more often documented on the adjacent sediments. The cyclic behavior of common trends identified between microbial mat cover, zoarcid densities, and abiotic variables using dynamic factor analysis suggested that seep ecosystem dynamics at the Håkon Mosby mud volcano may be modulated by tides and the activity of the volcano. Moreover, the eruption that occurred about 2 months after the start of the study had a significant impact on faunal densities, microbial activity, and environmental variables. The eruption was preceded by a steady increase in seabed temperatures, density of small holes (indicative of gas emissions), and microbial mat cover. It was followed by 3- and 5-fold increase in zoarcid and pycnogonid densities, respectively. To our knowledge, this study is the first to analyze intra-annual temporal data in a cold-seep ecosystem and to present data on the effects of a mud eruption on seep microbial and faunal dynamics. Overall, our results provide the first insight into ecosystem dynamics at a high-latitude cold seep and highlight the need to collect high-resolution temporal data to evaluate seep communities’ response to a warming Arctic and their potential role in mitigating methane emissions.

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  • Authors: Palmer, Stephanie; Gernez, Pierre; Thomas, Yoann; Simis, Stefan, H.G.; +3 Authors

    International audience; Aquaculture increasingly contributes to global seafood production, requiring new farm sites for continued growth. In France, oyster cultivation has conventionally taken place in the intertidal zone, where there is little or no further room for expansion. Despite interest in moving production further offshore, more information is needed regarding the biological potential for offshore oyster growth, including its spatial and temporal variability. This study shows the use of remotely-sensed chlorophyll-a and total suspended matter concentrations retrieved from the Medium Resolution Imaging Spectrometer (MERIS), and sea surface temperature from the Advanced Very High Resolution Radiometer (AVHRR), all validated using in situ matchup measurements, as input to run a Dynamic Energy Budget (DEB) Pacific oyster growth model for a study site along the French Atlantic coast (Bourgneuf Bay, France). Resulting oyster growth maps were calibrated and validated using in situ measurements of total oyster weight made throughout two growing seasons, from the intertidal zone, where cultivation currently takes place, and from experimental offshore sites, for both spat (R-2 = 0.91; RMSE = 1.60 g) and adults (R-2 = 0.95; RMSE = 4.34 g). Oyster growth time series are further digested into industry-relevant indicators, such as time to achieve market weight and quality index, elaborated in consultation with local producers and industry professionals, and which are also mapped. Offshore growth is found to be feasible and to be as much as two times faster than in the intertidal zone (p < 0.001). However, the potential for growth is also revealed to be highly variable across the investigated area. Mapping reveals a clear spatial gradient in production potential in the offshore environment, with the northeastern segment of the bay far better suited than the southwestern. Results also highlight the added value of spatiotemporal data, such as satellite image time series, to drive modeling in support of marine spatial planning. The current work demonstrates the feasibility and benefit of such a coupled remote sensing-modeling approach within a shellfish farming context, responding to real and current interests of oyster producers.

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    Authors: Daniel, Anne; Laës-Huon, Agathe; Barus, Carole; Beaton, Alexander; +8 Authors

    International audience; Improved comparability of nutrient concentrations in seawater is required to enhance the quality and utility of measurements reported to global databases. Significant progress has been made over recent decades in improving the analysis and data quality for traditional laboratory measurements of nutrients. Similar efforts are required to establish high-quality data outputs from in situ nutrient sensors, which are rapidly becoming integral components of ocean observing systems. This paper suggests using the good practices routine established for laboratory reference methods to propose a harmonized set of deployment protocols and of quality control procedures for nutrient measurements obtained from in situ sensors. These procedures are intended to establish a framework to standardize the technical and analytical controls carried out on the three main types of in situ nutrient sensors currently available (wet chemical analyzers, ultraviolet optical sensors, electrochemical sensors) for their deployments on all kinds of platform. The routine reference controls that can be applied to the sensors are listed for each step of sensor use: initial qualification under controlled conditions in the laboratory, preparation of the sensor before deployment, field deployment and finally the sensor recovery. The fundamental principles applied to the laboratory reference method are then reviewed in terms of the calibration protocol, instrumental interferences, environmental interferences, external controls, and method performance assessment. Data corrections (linearity, sensitivity, drifts, interferences and outliers) are finally identified along with the concepts and calculations for qualification for both real time and time delayed data. This paper emphasizes the necessity of future collaborations between research groups, reference-accredited laboratories, and technology developers, to maintain comparability of the concentrations reported for the various nutrient parameters measured by in situ sensors.

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    e-Prints Soton
    Article . 2020 . Peer-reviewed
    Data sources: e-Prints Soton
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      e-Prints Soton
      Article . 2020 . Peer-reviewed
      Data sources: e-Prints Soton
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  • Authors: Vandeputte, Marc;

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  • Authors: Vandeputte, Marc;

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    Authors: Ferreira Araujo, Beatriz; Osterwalder, Stefan; id_orcid0000-0001-8775-0813; Szponar, Natalie; Lee, Domenica; +19 Authors

    Nature Communications, 13 ISSN:2041-1723

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    NILU Brage
    Article . 2022
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    Research Collection
    Article . 2022
    License: CC BY
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      Article . 2022
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      Research Collection
      Article . 2022
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Chenais, Nathalie; Henriquenobrega, Rafael; Thomas, Manon; Porcon, Beatrice; +5 Authors

    International audience

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    Other literature type . 2022
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      Other literature type . 2022
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    Authors: Denvil-Sommer, Anna; Gehlen, Marion; Vrac, Mathieu;

    To derive an optimal observation system for surface ocean pCO2 in the Atlantic Ocean and the Atlantic sector of the Southern Ocean, 11 observation system simulation experiments (OSSEs) were completed. Each OSSE is a feedforward neural network (FFNN) that is based on a different data distribution and provides ocean surface pCO2 for the period 2008–2010 with a 5 d time interval. Based on the geographical and time positions from three observational platforms, volunteering observing ships, Argo floats and OceanSITES moorings, pseudo-observations were constructed using the outputs from an online-coupled physical–biogeochemical global ocean model with 0.25∘ nominal resolution. The aim of this work was to find an optimal spatial distribution of observations to supplement the widely used Surface Ocean CO2 Atlas (SOCAT) and to improve the accuracy of ocean surface pCO2 reconstructions. OSSEs showed that the additional data from mooring stations and an improved coverage of the Southern Hemisphere with biogeochemical ARGO floats corresponding to least 25 % of the density of active floats (2008–2010) (OSSE 10) would significantly improve the pCO2 reconstruction and reduce the bias of derived estimates of sea–air CO2 fluxes by 74 % compared to ocean model outputs.

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    Ocean Science (OS)
    Other literature type . 2021
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    Ocean Science (OS)
    Other literature type . 2021
    Hal-Diderot
    Article . 2021
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      Ocean Science (OS)
      Other literature type . 2021
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      Ocean Science (OS)
      Other literature type . 2021
      Hal-Diderot
      Article . 2021
      License: CC BY
      Data sources: Hal-Diderot
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