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93 results on '"IFREMER - Nantes"'

1. Dynamics of the periodically forced light-limited Droop model

Author: Francis Mairet, Olivier Bernard, Carlos Martínez, Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'océanographie de Villefranche (LOV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), CONICYT doctoral grant BECAS CHILE, IPL Algae in silico (INRIA) project, ANR-14-CE04-0011,Phycover,Durabilité des productions microalgales par recyclage du phosphore et de l'azote des eaux résiduaires : vers la station d'épuration du futur(2014), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Laboratoire d'océanographie de Villefranche (LOV), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), and Université de Nantes (UN)
Subjects: Dynamical systems theory, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Global stability, [MATH.MATH-CA]Mathematics [math]/Classical Analysis and ODEs [math.CA], 01 natural sciences, Cooperative System, Planar, Microalgae, Applied mathematics, Microalgae growth, Voltage droop, Positive periodic solution, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, 0101 mathematics, Mathematics, Applied Mathematics, 010102 general mathematics, Dynamics (mechanics), Variable quota model, Cooperative system, 010101 applied mathematics, Monotone polygon, Population model, Kolmogorov equations, Analysis
Abstract: International audience; The periodically forced light-limited Droop model represents microalgae growth under co-limitation by light and a single substrate, accounting for periodic fluctuations of factors such as light and temperature. In this paper, we describe the global dynamics of this model, considering general monotone growth and uptake rate functions. Our main result gives necessary and sufficient conditions for the existence of a positive periodic solution i.e. a periodic solution characterized by the presence of microalgae) which is globally attractive. In our approach, we reduce the model to a cooperative planar periodic system. Using results on periodic Kolmogorov equations and on monotone sub-homogeneous dynamical systems, we describe the global dynamics of the reduced system. Then, using the theory of asymptotically periodic semiflows, we extend the results on the reduced system to the original model. To illustrate the applicability of the main result, we include an example considering a standard microalgae population model.
Published: 2020
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2. Estimating effective population size using RADseq: Effects of SNP selection and sample size

Author: Marandel, Florianne, Charrier, Grégory, Lamy, Jean‐Baptiste, Le Cam, Sabrina, Lorance, Pascal, Trenkel, Verena M., Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Laboratoire de Génétique et Pathologie des Mollusques Marins - Ifremer (SG2M-LGPMM), ANR-14-CE02-0006,GenoPopTaille,Estimation de la taille absolue de population marines en danger par identification génétique des paires parent-descendant(2014), Écologie et Modèles pour l'Halieutique (EMH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), and Santé, Génétique et Microbiologie des Mollusques (SGMM)
Subjects: generations, ratio, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], NeEstimator, ACL, conservation, markers, RADseq, skates and rays, linkage-disequilibrium, GenoPopTaille, lcsh:QH540-549.5, n-e, lcsh:Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, effective population size, linkage disequilibrium, Original Research
Abstract: Effective population size (Ne) is a key parameter of population genetics. However, N e remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient F IS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Neestimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies., SNP‐based estimates of effective population size were found to be sensitive to SNP filtering threshold values. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates by around 70%. Sample size had a small effect beyond a minimum number.
Published: 2020
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3. Phthalates and organophosphate esters in surface water, sediments and zooplankton of the NW Mediterranean Sea: Exploring links with microplastic abundance and accumulation in the marine food web

Author: Benjamin Oursel, Richard Sempéré, Natascha Schmidt, Javier Castro-Jiménez, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Agence de l’eau Rhône Mediterranee Corse Blue-POLUTproject and from European FEDER Fund under project 1166-39417, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), and Université de Nantes (UN)
Subjects: phthalate, zooplankton, Microplastics, plasticizers, Food Chain, 010504 meteorology & atmospheric sciences, Health, Toxicology and Mutagenesis, Bioconcentration, 010501 environmental sciences, Toxicology, Flame retardants, 01 natural sciences, Zooplankton, Mediterranean sea, plastic, Plasticizers, Mediterranean Sea, Animals, 14. Life underwater, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Water, Sediment, Esters, General Medicine, organophosphate esters, Bioaccumulation, Pollution, Organophosphates, sediment, 13. Climate action, Environmental chemistry, Environmental science, Seawater, Plastics, Surface water, Bay, Water Pollutants, Chemical, Environmental Monitoring
Abstract: In this study, surface seawater, sediment and zooplankton samples were collected from three different sampling stations in Marseille Bay (NW Mediterranean Sea) and were analyzed for both microplastics and organic plastic additives including seven phthalates (PAEs) and nine organophosphate esters (OPEs). PAE concentrations ranged from 100 to 527 ng L−1 (mean 191 ± 123 ng L−1) in seawater, 12–610 ng g−1 dw (mean 194 ± 193 ng g−1 dw) in sediment and 0.9–47 μg g−1 dw (mean 7.2 ± 10 μg g−1 dw) in zooplankton, whereas OPE concentrations varied between 9 and 1013 ng L−1 (mean 243 ± 327 ng L−1) in seawater, 13–49 ng g−1 dw (mean 25 ± 11 ng g−1 dw) in sediment and 0.4–4.6 μg g−1 dw (mean 1.6 ± 1.0 μg g−1 dw) in zooplankton. Microplastic counts in seawater ranged from 0 to 0.3 items m−3 (mean 0.05 ± 0.05 items m−3). We observed high fluctuations in contaminant concentrations in zooplankton between different sampling events. However, the smallest zooplankton size class generally exhibited the highest PAE and OPE concentrations. Field-derived bioconcentration factors (BCFs) showed that certain compounds are prone to bioaccumulate in zooplankton, including some of the most widely used chlorinated OPEs, but with different intensity depending on the zooplankton size-class. The concentration of plastic additives in surface waters and the abundance of microplastic particles were not correlated, implying that they are not necessarily good indicators for each other in this compartment. This is the first comprehensive study on the occurrence and temporal variability of PAEs and OPEs in the coastal Mediterranean based on the parallel collection of water, sediment and differently sized zooplankton samples.
Published: 2021
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4. Rapp. Comm. int. Mer Médit., 42, p 97, 2019

Author: CARLOTTI, Francois, Tronczynski, Jacek, TEDETTI, Marc, Marc, Pagano, Garnier, Cédric, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

5. Biological, socio-economic, and administrative opportunities and challenges to moving aquaculture offshore for small French oyster-farming companies

Author: Barillé, Laurent, LE BRIS, Anthony, Goulletquer, Philippe, Thomas, Yoann, Glize, Philippe, Kane, Frank, Falconer, Lynne, Guillotreau, Patrice, Trouillet, Brice, Palmer, Stéphanie, Gernez, Pierre, Mer, molécules et santé EA 2160 (MMS), Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN)-Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN), Littoral, Environnement, Télédétection, Géomatique (LETG - Nantes), Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), Université de Nantes (UN)-Université de Nantes (UN)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Brest (UBO)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Syndicat Mixte pour le Développement de l'Aquaculture et de la Pêche en Pays de la Loire (SMIDAP), Marine Institute [Ireland], University of Stirling, Laboratoire d'économie et de management de Nantes Atlantique (LEMNA), Institut d'Économie et de Management de Nantes - Institut d'Administration des Entreprises - Nantes (IEMN-IAE Nantes), Université de Nantes (UN)-Université de Nantes (UN)-FR 3473 Institut universitaire Mer et Littoral (IUML), Le Mans Université (UM)-Université d'Angers (UA)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Université de Bretagne Sud (UBS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM)-Université d'Angers (UA)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Université de Bretagne Sud (UBS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), European Project: 678396,H2020,H2020-SFS-2015-2,TAPAS(2016), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Brest (UBO)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Le Mans Université (UM)-Université d'Angers (UA)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Université de Bretagne Sud (UBS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM)-Université d'Angers (UA)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Université de Bretagne Sud (UBS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Le Mans Université (UM)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Normandie Université (NU)-Normandie Université (NU)-École pratique des hautes études (EPHE)-Université de Brest (UBO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement (IGARUN), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Institut national de recherches archéologiques préventives (Inrap), FR 3473 Institut universitaire Mer et Littoral (IUML), Université de Bretagne Sud (UBS)-Le Mans Université (UM)-Université d'Angers (UA)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Université de Bretagne Sud (UBS)-Le Mans Université (UM)-Université d'Angers (UA)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Institut d'Économie et de Management de Nantes - Institut d'Administration des Entreprises - Nantes (IEMN-IAE Nantes), and Université de Bretagne Sud (UBS)-Le Mans Université (UM)-Université d'Angers (UA)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Université de Bretagne Sud (UBS)-Le Mans Université (UM)-Université d'Angers (UA)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Nantes (UN)-École Centrale de Nantes (ECN)
Subjects: Site selection, acl, Dynamic energy budget (DEB) model, Off-shore aquaculture, Remote sensing, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, [SDE.ES]Environmental Sciences/Environmental and Society, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, Pacific oyster, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q2 - Renewable Resources and Conservation/Q.Q2.Q22 - Fishery • Aquaculture, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; Oyster production has historically taken place in intertidal zones, and shellfish farms already occupy large extents of the French intertidal space. The expansion of French shellfish aquaculture within intertidal areas is therefore spatially limited, and moving production to the subtidal offshore environment is considered to be a possible solution to this problem. Finding new sites along the French Atlantic coast was studied here from the perspective of small oyster companies run by young farmers, who are interested in offshore bivalve aquaculture expansion compatible with their investment capacity. In assessing the feasibility of such offshore production, we considered three main issues: (1) bivalve growth potential and (2) technical feasibility and conflicting uses, both within a spatial framework, as well as (3) the steps and barriers of the administrative licensing process. Oyster spat in an experimental offshore cage showed significantly faster growth, in terms of both weight and length, compared to those in an intertidal cage, mainly due to lower turbidity and full-time feeding capacity (i.e., constant immersion in the water). A combination of Earth Observation data and bivalve ecophysiological modelling was then used to obtain spatial distribution maps of growth potential, which confirmed that offshore sites have better potential for oyster growth than the traditionally oyster-farmed intertidal sites overall, but that this is highly spatially variable. Small-scale producers indicated two technical factors constraining where farms could be located: bathymetry must be between 5 and 20 m and the distance from a harbor no more than five nautical miles. These were included along with maps of various environmental and socioeconomic constraints in a Spatial Multi-Criteria Evaluation (SMCE). Touristic traffic and bottom trawling by fisherman were found to be the two other most restrictive variables. The GIS-based SMCE developed in this study showed that there is almost 400 km 2 of highly-to very highly-suitable area within which to develop offshore aquaculture using simple, low-cost bottom-cage techniques, and can be used to assist the shellfish industry in the Marine Spatial Planning decision-making process, still in progress in this coastal area. However, the complexity of the administrative processes necessary to obtain an offshore license is perceived as a stronger barrier by farmers owning small companies than site selection, technical feasibility, and required investments, and will be crucial to address in order to realistically proceed to offshore cultivation. The process demonstrated here, and the results are relevant to other coastal and offshore locations throughout the world and can be adapted for other species.
Published: 2020
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6. Global vulnerability of marine mammals to global warming

Author: Marta M Rufino, Thomas L. Frölicher, Fabien Leprieur, David Mouillot, Camille Albouy, Giulia Donati, Loïc Pellissier, Severine Albouy-Boyer, Valentine Delattre, Écologie et Modèles pour l'Halieutique (EMH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Landscape Ecology Group [ETH Zürich], Institute of Terrestrial Ecosystems (ITES), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Climate and Environmental Physics [Bern] (CEP), Physikalisches Institut [Bern], Universität Bern [Bern] (UNIBE)-Universität Bern [Bern] (UNIBE), Oeschger Centre for Climate Change Research (OCCR), University of Bern, Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida = University Institute of Psychological, Social and Life Sciences (ISPA), Centro de Ciências do Mar [Faro] (CCMAR), Universidade do Algarve (UAlg), Swiss Federal Research Institute, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), IFREMER - Nantes, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Universität Bern [Bern]-Universität Bern [Bern], and Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA)
Subjects: 0106 biological sciences, Aquatic Organisms, Conservation of Natural Resources, Internationality, 010504 meteorology & atmospheric sciences, Dugong, 530 Physics, [SDE.MCG]Environmental Sciences/Global Changes, Biodiversity, lcsh:Medicine, 010603 evolutionary biology, 01 natural sciences, Global Warming, Article, Megafauna, Animals, Marine ecosystem, 14. Life underwater, Author Correction, lcsh:Science, 550 Earth sciences & geology, Phylogeny, 0105 earth and related environmental sciences, Mammals, Multidisciplinary, biology, Ecology, Global warming, Climate-change ecology, fungi, lcsh:R, 15. Life on land, biology.organism_classification, Overexploitation, Geography, Habitat destruction, 13. Climate action, Threatened species, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Although extinctions due to climate change are still uncommon, they might surpass those caused by habitat loss or overexploitation over the next few decades. Among marine megafauna, mammals fulfill key and irreplaceable ecological roles in the ocean, and the collapse of their populations may therefore have irreversible consequences for ecosystem functioning and services. Using a trait-based approach, we assessed the vulnerability of all marine mammals to global warming under high and low greenhouse gas emission scenarios for the middle and the end of the 21st century. We showed that the North Pacific Ocean, the Greenland Sea and the Barents Sea host the species that are most vulnerable to global warming. Future conservation plans should therefore focus on these regions, where there are long histories of overexploitation and there are high levels of current threats to marine mammals. Among the most vulnerable marine mammals were several threatened species, such as the North Pacific right whale (Eubalaena japonica) and the dugong (Dugong dugon), that displayed unique combinations of functional traits. Beyond species loss, we showed that the potential extinctions of the marine mammals that were most vulnerable to global warming might induce a disproportionate loss of functional diversity, which may have profound impacts on the future functioning of marine ecosystems worldwide.
Published: 2020
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7. Supplementary materials : Salt Shock Responses of Microcystis Revealed through Physiological, Transcript, and Metabolomic Analyses

Author: Georges des Aulnois, Maxime, Réveillon, Damien, Robert, Elise, Caruana, Amandine, Briand, Enora, Guljamow, Arthur, Dittmann, Elke, Amzil, Zouher, Bormans, Myriam, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), University of Potsdam, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), and Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: microcystin, Microcystis aeruginosa, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, transcript, salt stress, metabolomic
Abstract: International audience; The transfer of from freshwater to estuaries has been described worldwide and salinity is reported as the main factor controlling the expansion of to coastal environments. Analyzing the expression levels of targeted genes and employing both targeted and non-targeted metabolomic approaches, this study investigated the effect of a sudden salt increase on the physiological and metabolic responses of two toxic strains separately isolated from fresh and brackish waters, respectively, PCC 7820 and 7806. Supported by differences in gene expressions and metabolic profiles, salt tolerance was found to be strain specific. An increase in salinity decreased the growth of with a lesser impact on the brackish strain. The production of intracellular microcystin variants in response to salt stress correlated well to the growth rate for both strains. Furthermore, the release of microcystins into the surrounding medium only occurred at the highest salinity treatment when cell lysis occurred. This study suggests that the physiological responses of involve the accumulation of common metabolites but that the intraspecific salt tolerance is based on the accumulation of specific metabolites. While one of these was determined to be sucrose, many others remain to be identified. Taken together, these results provide evidence that is relatively salt tolerant in the mesohaline zone and microcystin (MC) release only occurs when the capacity of the cells to deal with salt increase is exceeded.
Published: 2020
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8. A global database for metacommunity ecology, integrating species, traits, environment and space

Author: Ramiro de Campos, Julia Ramos Miranda, Sandrine Pavoine, Sylvain Dolédec, Joshua Adam Drew, David Mouillot, Elizabeth C. Lowe, Robin J. Pakeman, Willem Renema, Heloise Gibb, Nicole J. de Voogd, Sen-Her Shieh, Triin Reitalu, Stéphane Chantepie, Jan Żarnowiec, Guillaume Fried, Roel van Klink, Núria Bonada, Sébastien Villéger, Daniel F. R. Cleary, Anthony Eallonardo, Damian Chmura, Bjorn J. M. Robroek, William K. Cornwell, Monika Staniaszek-Kik, Christoph F. J. Meyer, Martin J. Westgate, Valérie Raevel, Cédric Frenette-Dussault, Frank Dziock, Cajo J. F. ter Braak, Alienor Jeliazkov, Nadia Barsoum, Adrià López-Baucells, Philippe Choler, Darko Mijatovic, Anik Brind'Amour, Michal Stanko, Helena Castro, Mark C. Urban, Belinda Gallardo, Maxim Zolotarev, Francesco Pomati, Alessandro Ossola, Andrés Mellado-Díaz, Luc Barbaro, Raphaël Arlettaz, R.M.A. Wegman, Thiago Gonçalves-Souza, Melanie J. Edgar, Alena Bartonova, Francisco Leonardo Tejerina-Garro, Nigel R. Andrew, Burak K. Pekin, Myles H. M. Menz, Karen M. Chong-Seng, Joan Pino, Jonathan M. Chase, Elena Belskaya, Jean-Yves Humbert, Ignacio Ribera, Oliver Purschke, Koenraad Martens, Arnaud Pocheville, Jonas O. Wolff, Boris R. Krasnov, Peter Poschlod, Ricardo Rocha, Peter Meffert, Domingo Flores Hernandez, Rebecca Spake, A. Cormont, Janet Higuti, Rodrigo Assis de Carvalho, Eric Le Saux, Natalie Robinson, Zoë Lindo, Fábio Z. Farneda, Honor C. Prentice, Bryndís Marteinsdóttir, German Centre for Integrative Biodiversity Research, German Research Foundation, Fédération Île de France de Recherche en Environnement, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Swiss National Science Foundation, Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Alice Holt Research Station, Forest Research [Great Britain], University of South Bohemia, Grup de Recerca 'Freshwater Biology and Management' (FEM), Universitat de Barcelona (UB), Severtsov Institute of Ecology and Evolution, Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Forest Research, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Centre for Functional Ecology, University of Coimbra [Portugal] (UC), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Naturalis Biodiversity Center [Leiden], Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut de Recherche pour le Développement (IRD [France-Sud])-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Applied and Restoration Ecology Group, Pyrenean Institute of Ecology, Department of Ecology, State University of Maringá, Ramon Science Center and Mitrani Department of Desert Ecology, Ben-Gurion University of the Negev (BGU), University of Western Ontario (UWO), Aquatic and Terrestrial Ecology, Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences (RBINS), Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), The University of Sydney, Universität Regensburg (REGENSBURG), Universität Regensburg, Lund University [Lund], German Centre for Integrative Biodiversity Research (iDiv), Laboratoire des Sciences de l'Environnement, Universitat Pompeu Fabra [Barcelona], Institute of Zoology, Slovak Academy of Science [Bratislava] (SAS), Université de Montpellier (UM), Peace Research Institute Frankfurt (PRIF), Hessische Stiftung Friedens- und Konfliktforschung, Martin-Luther-University Halle-Wittenberg, Universität Zürich [Zürich] = University of Zurich (UZH), University of New England (UNE), Institute of Ecology and Evolution [Bern, Switzerland], University of Bern, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Ecosystems, Society and Biosecurity, Forest Research, Alice Holt Lodge, Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS), Ural Branch of Russian Academy of Sciences (UB RAS), Institute of Plant and Animal Ecology, Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain] (IRBio UB), Department de Biologia Evolutiva, Ecologia i Ciències Ambientals, University of Barcelona, Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Universidade Estadual de Goiás (UEG), University of Bielsko-Biala, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), ARC Centre of Excellence for Coral Reef Studies (CoralCoE), James Cook University (JCU), Centro de Estudos do Ambiante e do Mar (CESAM), Universidade de Aveiro, National Penghu University of Science and Technology, Wageningen University and Research [Wageningen] (WUR), Wageningen Environmental Research, Evolution and Ecology Research Centre [UNSW Sydney], School of Biological, Earth and Environmental Sciences [Sydney] (BEES), University of New South Wales [Sydney] (UNSW)-University of New South Wales [Sydney] (UNSW), Laboratorio de Ictiología, Instituto Nacional de Limnología [Santa Fe] (INALI), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), Universidade Estadual de Maringà (UEM), Institute of Environmental Sciences [Leiden] (CML), Leiden University, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), SUNY College of Environmental Science and Forestry (SUNY-ESF), State University of New York (SUNY), Dresden University of Applied Sciences, OBG, Part of Ramboll, The Natural History Museum [London] (NHM), State University of Rio de Janeiro, Smithsonian Tropical Research Institute, Centre for Ecology - Evolution and Environmental Changes (cE3c), Universidade de Lisboa (ULISBOA), Universidad Autónoma de Campeche, Institut de Recherches en Biologie Végétale [Montréal] (IRBV), Université de Montréal (UdeM), Unité entomologie et plantes invasives, Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Pyrenean Institute of Ecology (IPE), Spanish National Research Council (CSIC), La Trobe University [Melbourne], Rural Federal University of Pernambuco, The Jacob Blaustein Institutes for Desert Research (BIDR), Mitrani Department of Desert Ecology, Jacob Blaustein Institute for Desert Research, Museu de Ciencies Naturals de Granollers, Macquarie University [Sydney], The soil conservation service of Iceland (SCSI), Universiteit Gent = Ghent University [Belgium] (UGENT), Imprint, Universidad de Murcia, Departamento de Ecología e Hidrología. Facultad de Biología. Universidad de Murcia. 30100 Murcia. Spain, Max Planck Institute for Ornithology, Max-Planck-Gesellschaft, University of Salford, School of Environmental and Life Sciences, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), The James Hutton Institute, Istanbul Technical University (ITÜ), Avrasya Yer Bilimleri Enstitüsü = Eurasia Institute of Earth Sciences [Istanbul] (AYBE), CREAF - Centre for Ecological Research and Applied Forestries, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), University of Regensburg, Department of Ecology and Conservation Biology, Department of Physical Geography and Ecosystem Science [Lund], Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Tallinn University of Technology (TTÜ), Universitat Pompeu Fabra [Barcelona] (UPF), Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, National ecological observatory network, University of Colorado [Boulder], Department of Ecology and Evolutionary Biology [Boulder], University of Southampton, Providence University, School of Geography and Environmental Sciences, University of Lódź, Institute of Parasitology [České Budějovice] (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Institute of Zoology Slovak Academy of Sciences, Centro de Biologia Aquática, Escola de Ciências Agrárias e Biológicas, Pontifícia Universidade Católica de Goiás, Biometris, University of Connecticut (UCONN), Fenner School of Environment and Society, Australian National University (ANU), This work was funded by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (funded by the German Research Foundation, DFG FZT 118). We thank Jitendra Gaikwad for his precious help with the technical aspects of the database storage and management through the iDiv Biodiversity Portal (https://idata.idiv.de/, https://doi.org/10.25829/idiv.286-21-2695) and the iDiv IT Support for their help in the CESTES website development (https://icestes.github.io/).The datasets provided by A. Jeliazkov were collected with financial support from the Federation d'Ile-de-France pour la Recherche en Environnement (FIRE FR-3020). The dataset provided by R. Carvalho and F.L. Tejerina-Garro had financial support from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq No. 471283/2006-1) granted to FLTG. The datasets provided by R. van Klink, J.-Y. Humbert, R. Arlettaz and M.H. M. Menz were collected with financial support from the Swiss National Science Foundation (grants 31003A_125398/2 and 31003A_149656) awarded to RA., Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écologie et Modèles pour l'Halieutique (EMH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre for Functional ecology, Universiteit Leiden, Universidade de Lisboa = University of Lisbon (ULISBOA), Unité entomologie et plantes invasives (LSV Montpellier), Laboratoire de la santé des végétaux (LSV), Instituto Pirenaico de Ecologìa = Pyrenean Institute of Ecology [Zaragoza] (IPE - CSIC), Universiteit Gent = Ghent University (UGENT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Biodiversity, DIVERSITY, computer.software_genre, 01 natural sciences, VARIABLES, Aardobservatie en omgevingsinformatica, Biodiversiteit en Beleid, Taxonomic rank, PLANT FUNCTIONAL TRAITS, lcsh:Science, Macroecology, ComputingMilieux_MISCELLANEOUS, Database, Ecology, Statistics, Community structure, Plants, PE&RC, Biota, Computer Science Applications, Geography, Biometris, Trait, LIFE-HISTORY TRAITS, Statistics, Probability and Uncertainty, COMMUNITY STRUCTURE, Information Systems, Metacommunity, Statistics and Probability, Earth Observation and Environmental Informatics, Life on Land, Ecology (disciplines), BIOLOGICAL TRAITS, MODELS, Library and Information Sciences, 010603 evolutionary biology, Biodiversity and Policy, Life history theory, Education, Database management, ddc:570, Animals, Life Science, Community ecology, Author Correction, Gestió de bases de dades, SPERMONDE-ARCHIPELAGO, Community, 010604 marine biology & hydrobiology, 15. Life on land, Biodiversitat, Research data, Earth and Environmental Sciences, Dades de recerca, lcsh:Q, Probability and Uncertainty, BIODIVERSITY, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, RESPONSES
Abstract: The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology., This work was funded by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (funded by the German Research Foundation; DFG FZT 118). We thank Jitendra Gaikwad for his precious help with the technical aspects of the database storage and management through the iDiv Biodiversity Portal (https://idata.idiv.de/, https://doi.org/10.25829/idiv.286-21-2695) and the iDiv IT Support for their help in the CESTES website development (https://icestes.github.io/). The datasets provided by A. Jeliazkov were collected with financial support from the Fédération d’Ile-de-France pour la Recherche en Environnement (FIRE FR-3020). The dataset provided by R. Carvalho and F.L. Tejerina-Garro had financial support from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq No. 471283/2006-1) granted to FLTG. The datasets provided by R. van Klink, J.-Y. Humbert, R. Arlettaz and M.H.M. Menz were collected with financial support from the Swiss National Science Foundation (grants 31003A_125398/2 and 31003A_149656) awarded to RA.
Published: 2020
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9. Modeling and analysis of an Absorption Column Connected to a Microalgae Culture

Author: Francis Mairet, Andrés I. Ávila, Carlos Martínez, David Jeison, Leslie Meier, Université Côte d'Azur (UCA), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Universidad de la frontera [Chile], Escuela de Ingeniería Bioquímica [Valparaíso], Pontificia Universidad Católica de Valparaíso (PUCV), This work was supported by the project FONDECYT 1120488, by INRIA Chile-CIRIC, by the INRIA associated team Greencore, and by the INRIA Project Lab Algae in silico., COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Gouzé, Jean-Luc
Subjects: Steady state (electronics), Absorption column, 7. Clean energy, 01 natural sciences, global asymptotic behavior, biogas upgrading, Shooting method, Biogas, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Microalgae, Applied mathematics, Uniqueness, Boundary value problem, 0101 mathematics, Mathematics, microalgae, Applied Mathematics, shooting method, State (functional analysis), Global asymptotic behavior, 010101 applied mathematics, boundary value problem, Biogas upgrading, [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering, absorption column
Abstract: International audience; We build and analyze a mathematical model of a system for biogas upgrading: an absorption column connected to a microalgae culture. The construction of the model is based on a chemical engineering approach and classical models of microalgae cultures. In our analysis, we prove the existence and uniqueness of solutions of a boundary value problem describing the absorption column. Some properties of this solution are also proved. Then, we use these results to study the long-term behavior of the mathematical model describing the coupled system. We state sufficient conditions for the existence of a globally attracting steady state characterized by the presence of microalgae. Finally, we find numerically the steady states of the system to test the efficiency of the system for purifying biogas.
Published: 2020
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10. Theory of turbid microalgae cultures

Author: Francis Mairet, Olivier Bernard, Carlos Martínez, Université Côte d'Azur (UCA), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Laboratoire d'océanographie de Villefranche (LOV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), CONICYT doctoral grant, Phycover [ANR-14-CE04-0011], and IPL Algae in silico (INRIA) projects
Subjects: 0106 biological sciences, 0301 basic medicine, Statistics and Probability, Photoinhibition, Materials science, Light, Light limitation, Photobioreactor, 01 natural sciences, Optical depth, Modelling, General Biochemistry, Genetics and Molecular Biology, Turbidity, Photobioreactors, 03 medical and health sciences, Game Theory, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, 010608 biotechnology, Microalgae, Animals, Microalgae growth, Growth rate, Photosynthesis, Population Density, General Immunology and Microbiology, Applied Mathematics, General Medicine, Ray, Culture Media, 030104 developmental biology, Modeling and Simulation, General Agricultural and Biological Sciences, Biological system, Intensity (heat transfer)
Abstract: International audience; Microalgae can be cultivated in closed or open photobioreactors (PBR). In these systems, light rapidly decreases as it passes through the culture due to the turbidity of the medium. Thus, microalgae experiment different light intensities depending on their position in the medium. In this paper, we study theoretically how the growth rate of microalgae is affected by different factors; incident light intensity, form of the PBR, microalgae population density, turbidity of non-microalgae components, and light path-length of the reactor. We show that for different types of PBR the average growth rate is completely determined by the incident light intensity and the optical depth. In the case of vertical cylindrical PBRs illuminated from above (e.g. race-way or panel-type reactors), we described (and we prove under general assumptions) in details the dependence of the AGR on the aforementioned factors. Finally, we discuss some implications of our analysis; the occurrence of the Allee effect, if light ostensibly limits or inhibits the growth rate in outdoor cultures, and how the geometry of the PBR affects microalgae growth rate and productivity.
Published: 2018
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11. Characterization of New Oligosaccharides Obtained by An Enzymatic Cleavage of the Exopolysaccharide Produced by the Deep-Sea Bacterium Alteromonas infernus Using its Cell Extract

Author: Hélène Rogniaux, Katy Akoumany, David Ropartz, Sylvia Colliec-Jouault, Christine Delbarre-Ladrat, Laëtitia Marchand, Mathieu Fanuel, Muriel Pipelier, Corinne Sinquin, Agata Zykwinska, Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies [IFREMER, Nantes], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), and Institut National de la Recherche Agronomique (INRA)
Subjects: glycosaminoglycan-mimetic, Pharmaceutical Science, Polysaccharide, Cleavage (embryo), Alteromonas infernus, 01 natural sciences, Analytical Chemistry, lcsh:QD241-441, Glycosaminoglycan, 03 medical and health sciences, lcsh:Organic chemistry, deep-sea bacterium, Drug Discovery, [CHIM]Chemical Sciences, structural analysis, Physical and Theoretical Chemistry, Lyase activity, 030304 developmental biology, mass spectrometry, chemistry.chemical_classification, 0303 health sciences, biology, 010405 organic chemistry, Depolymerization, Chemistry, exopolysaccharides, Organic Chemistry, Oligosaccharide, biology.organism_classification, 0104 chemical sciences, Enzyme, Biochemistry, 13. Climate action, Chemistry (miscellaneous), wild-type strain, enzymatic depolymerization, Molecular Medicine, Bacteria
Abstract: Bacteria from deep-sea hydrothermal vents constitute an attractive source of bioactive molecules. In particular, exopolysaccharides (EPS) produced by these bacteria become a renewable source of both biocompatible and biodegradable molecules. The low molecular weight (LMW) derivatives of the GY785 EPS produced by the deep-sea hydrothermal vent strain Alteromonas infernus have previously displayed some biological properties, similar to those of glycosaminoglycans (GAG), explored in cancer and tissue engineering. These GAG-mimetic derivatives are obtained through a free radical depolymerization process, which could, however, affect their structural integrity. In a previous study, we have shown that A. infernus produces depolymerizing enzymes active on its own EPS. In the present study, an enzymatic reaction was optimized to generate LMW derivatives of the GY785 EPS, which could advantageously replace the present bioactive derivatives obtained by a chemical process. Analysis by mass spectrometry of the oligosaccharide fractions released after enzymatic treatment revealed that mainly a lyase activity was responsible for the polysaccharide depolymerization. The repeating unit of the GY785 EPS produced by enzyme cleavage was then fully characterized.
Published: 2019
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12. Combining multiple data sets to unravel the spatio-temporal dynamics of a data-limited fish stock

Author: Cecilia Pinto, Youen Vermard, Etienne Rivot, Morgane Travers-Trolet, Jed I. Macdonald, Département Sciences et Technologies Halieutiques / Laboratoire Technologie Halieutique (Ifremer) (STH - LTH), Unité de recherche Sciences et Technologies Halieutiques (STH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Faculty of Life and Environmental Sciences, University of Iceland [Reykjavik], Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Líf- og umhverfisvísindadeild (HÍ), Faculty of Life and Environmental Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), School of Engineering and Natural Sciences (UI), Háskóli Íslands, and University of Iceland
Subjects: Vistkerfi, 0106 biological sciences, [SDV]Life Sciences [q-bio], distributions, population, Aquatic Science, Biology, computer.software_genre, Fish stock, 01 natural sciences, spatial autocorrelation, Sjávarlíffræði, 010104 statistics & probability, 14. Life underwater, mullet, 0101 mathematics, north-sea, uncertainty, species distribution models, climate, Ecology, Evolution, Behavior and Systematics, Data limited, 010604 marine biology & hydrobiology, conservation, approximate bayesian-inference, Multiple data, mullus-surmuletus, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, Data mining, Fiskar, computer, [PHYS.PHYS.PHYS-DATA-AN]Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an]
Abstract: Publisher's version (útgefin grein), The biological status of many commercially exploited fishes remains unknown, mostly due to a lack of data necessary for their assessment. Investigating the spatiotemporal dynamics of such species can lead to new insights into population processes and foster a path towards improved spatial management decisions. Here, we focused on striped red mullet (Mullus surmuletus), a widespread yet data-limited species of high commercial importance. Aiming to quantify range dynamics in this data-poor scenario, we combined fishery-dependent and -independent data sets through a series of Bayesian mixed-effects models designed to capture monthly and seasonal occurrence patterns near the species’ northern range limit across 20 years. Combining multiple data sets allowed us to cover the entire distribution of the northern population of M. surmuletus, exploring dynamics at different spatiotemporal scales and identifying key environmental drivers (i.e., sea surface temperature, salinity) that shape occurrence patterns. Our results demonstrate that even when process and (or) observation uncertainty is high, or when data are sparse, if we combine multiple data sets within a hierarchical modelling framework, accurate and useful spatial predictions can still be made., CP’s postdoc was funded by Ifremer and France Filière Peche. The authors thank Bruno Ernande for suggestions and comments that improved the work during the analysis. The authors also thank two anonymous reviewers for their comments, which helped to improve the manuscript.
Published: 2019
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13. Usability of the bivalves Dreissena polymorpha and Anodonta anatina for a biosurvey of the neurotoxin BMAA in freshwater ecosystems

Author: Grilot, Théo, Jean, Sarah, Faassen, Elisabeth, Amzil, Zouher, Mineaud, Emilien, Brient, Luc, Savar, Véronique, Robert, Elise, Lepoutre, Alexandra, Hervieux, J., Faassen, E.J., Zweers, A.J., Lürling, Miquel, Geffard, Alain, Lance, Emilie, IFREMER - Nantes, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de Reims Champagne-Ardenne (URCA), and Aquatic Ecology (AqE)
Subjects: Aquatic Ecology and Water Quality Management, 010504 meteorology & atmospheric sciences, Health, Toxicology and Mutagenesis, Dreissena polymorpha, BU Contaminanten & Toxines, Fresh Water, 010501 environmental sciences, Toxicology, 01 natural sciences, Dreissena, Freshwater ecosystem, β-Methylamino-L-alanine, BU Contaminants & Toxins, Phytoplankton, Neurotoxin, Animals, 14. Life underwater, Anodonta, Ecosystem, 0105 earth and related environmental sciences, Pollutant, WIMEK, biology, Cyanobacteria Toxins, Aquatic ecosystem, Amino Acids, Diamino, General Medicine, Plan_S-Compliant_NO, Contamination, Aquatische Ecologie en Waterkwaliteitsbeheer, biology.organism_classification, Pollution, Bioaccumulation, 6. Clean water, Biosurvey, 13. Climate action, Environmental chemistry, international, Anodonta anatina, [SDE]Environmental Sciences, Water Pollutants, Chemical, Environmental Monitoring
Abstract: The environmental neurotoxin β-methylamino-L-alanine (BMAA) may represent a risk for human health in case of chronic exposure or after short-term exposure during embryo development. BMAA accumulates in freshwater and marine organisms consumed by humans. It is produced by marine and freshwater phytoplankton species, but the range of producers remains unknown. Therefore, analysing the phytoplankton composition is not sufficient to inform about the risk of freshwater contamination by BMAA. Filter-feeders mussels have accumulation capacities and therefore appear to be relevant to monitor various pollutants in aquatic ecosystems. We investigated the suitability of the freshwater mussels Dreissena polymorpha and Anodonta anatina for monitoring BMAA in water. Both species were exposed to 1, 10, and 50 μg of dissolved BMAA/L daily for 21 days, followed by 42 days of depuration in clean water. On days 0, 1, 7, 14, and 21 of exposure and 1, 7, 14, 21 and 42 of depuration, whole D. polymorpha and digestive glands of A. anatina were sampled, and the total BMAA concentration was measured. D. polymorpha accumulated BMAA earlier (from day 1 at all concentrations) and at higher tissue concentrations than A. anatina, which accumulated BMAA from day 14 when exposed to 10 μg BMAA/L and from day 7 when exposed to 50 μg BMAA/L. As BMAA accumulation by D. polymorpha was time and concentration-dependent, with a significant elimination during the depuration period, this species may be able to reflect the levels and dynamics of water contamination by dissolved BMAA. The species A. anatina could be used for monitoring water concentrations above 10 μg BMAA/L. D. polymorpha and A. anatina could be used to biomonitor BMAA in fresh water.
Published: 2019
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14. Optimal control of bacterial growth for metabolite production: The role of timing and costs of control

Author: H. de Jong, Jean-Luc Gouzé, Eugenio Cinquemani, Francis Mairet, Ivan Yegorov, Modeling, simulation, measurement, and control of bacterial regulatory networks (IBIS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Jean Roget, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), North Dakota State University (NDSU), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Inria IPL project CoSy, Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Inria Grenoble - Rhône-Alpes, and Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique)
Subjects: 0209 industrial biotechnology, Computer science, [SDV]Life Sciences [q-bio], 020208 electrical & electronic engineering, Control (management), 02 engineering and technology, Business process reengineering, Bacterial growth, Optimal control, Bioproduction, Synthetic biology, 020901 industrial engineering & automation, 0202 electrical engineering, electronic engineering, information engineering, Production (economics), Resource allocation, [INFO]Computer Science [cs], Biochemical engineering, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; The growth of microorganisms is controlled by strategies for the dynamical allocation of available resources over different cellular functions. Synthetic biology approaches are considered nowadays to artificially modify these strategies and turn microbial populations into biotechnological factories for the production of metabolites of interest. In our recent work [1], [2] we have studied dynamics of microbial resource allocation and growth in terms of coarse-grained self-replicator models described by ordinary differential equations, and proposed artificial control strategies for the optimization of metabolite production based on the reengineering of resource allocation. In this paper, we elaborate on our earlier results and further investigate synthetic resource allocation control strategies. Using numerical simulation, we study the effect on growth and bioproduction of the (biological or technological) costs associated with discontinuous control strategies, and of the time allotted to optimal substrate utilization. Results provide novel insight into the most favorable synthetic control strategies.
Published: 2019
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15. 3,4-Dideoxy-3,3,4,4-tetrafluoro- and 4-OH epimeric 3-deoxy-3,3-difluoro-α-GalCer analogues: Synthesis and biological evaluation on human iNKT cells stimulation

Author: Arnaud Tessier, Jézabel Rocher, Katy Akoumany, Allan Patinec, Virginie Blot, Didier Dubreuil, Jacques Le Pendu, Jean-Yves Le Questel, Bruno Linclau, Samuel Golten, Jérôme Graton, Muriel Pipelier, Denis Jacquemin, J.Y. Douillard, Jacques Lebreton, Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Host-Pathogen Interactions in the Regulation of Immune Responses (CRCINA-ÉQUIPE 5), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies [IFREMER, Nantes], and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: Models, Molecular, Stereochemistry, [SDV]Life Sciences [q-bio], Molecular Conformation, Receptors, Antigen, T-Cell, Galactosylceramides, 01 natural sciences, Work related, 03 medical and health sciences, chemistry.chemical_compound, Interferon-gamma, Amide, Drug Discovery, Electronic effect, [CHIM]Chemical Sciences, Humans, Receptor, Deoxygenation, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Pharmacology, 0303 health sciences, Interleukin-13, biology, 010405 organic chemistry, Hydrogen bond, Organic Chemistry, T-cell receptor, Hydrogen Bonding, Stereoisomerism, General Medicine, 0104 chemical sciences, chemistry, CD1D, biology.protein, Natural Killer T-Cells, Antigens, CD1d, HeLa Cells, Protein Binding
Abstract: 20 iNKT cells recognize CD1d/-galactosylceramide (-GalCer) complexes via their invariant 21 TCR receptor and stimulate the immune response. Many -GalCer analogues have been 22 investigated to interrogate this interaction. Following our previous work related to the 23 modification of the hydrogen bond network between -GalCer and CD1d, we have now 24 focused our attention on the synthesis of 3-deoxy-3,3-difluoro-and 3,4-dideoxy-3,3,4,4-25 tetrafluoro-α-GalCer analogues, and studied their ability to stimulate human iNKT cells. In 26 2 each case, deoxygenation at the indicated positions was accompanied by difluoro introduction 1 in order to evaluate the resulting electronic effect on the stability of the ternary 2 CD1d/Galcer/TCR complex which has been rationalized by modeling study. With deoxy-3 difluorination at the 3-position, the two epimeric 4-OH analogues were investigated to establish 4 their capacity to compensate for the lack of the hydrogen bond donating group at the 3-position. 5 The 3,4-dideoxytetrafluoro analogue was of interest to highlight the amide NH-bond hydrogen 6 bond properties. 7 8
Published: 2019
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16. A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

Author: Mónica Medina, Arite Bigalke, Ezequiel M. Marzinelli, Eve Toulza, Elena Kazamia, Tilmann Harder, Ulisse Cardini, Soizic Prado, Johan Decelle, François H. Lallier, Fabrice Not, Claire M. M. Gachon, Sarah Griffiths, Enora Briand, Paco Cárdenas, Ehsan Kayal, Marc-André Selosse, José Pintado Valverde, Willem Stock, Derek J. Skillings, Damien Eveillard, Mahasweta Saha, Simon M. Dittami, Enrique Arboleda, Teresa Maria Morganti, Catherine Leblanc, Shinichi Sunagawa, Laura Núñez Pons, Ashwin Engelen, Alexey Vorobev, Jean-Christophe Auguet, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institute for Inorganic and Analytical Chemistry, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of Medicinal Chemistry, Uppsala University, Sweden, Uppsala University, Stazione Zoologica Anton Dohrn (SZN), Laboratoire de physiologie cellulaire végétale, Institut National de la Recherche Agronomique (INRA), Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Scottish Association for Marine Science, Scottish Marine Institute, School of Science and the Environment, Manchester Metropolitan University (MMU), University of Bremen, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Pennsylvania State University (Penn State), Penn State System, Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), IIM CSIC, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Department of Biological Sciences, University of Essex, Origine, structure et évolution de la biodiversité (OSEB), University of Gdansk, University of Pennsylvania, Laboratory of Protistology & Aquatic Ecology, Institute of Microbiology and Swiss Institute of Bioinformatics, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Stazione Zoologica Anton Dohrn, Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Singapore Centre for Environmental Life Sciences Engineering [Singapore, Singapore] (SCELSE), Nanyang Technological University [Singapour]-Interdisciplinary Graduate School [Singapore, Singapore], Helmholtz Center for Ocean Research, University of Pennsylvania [Philadelphia], Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Adaptation and Diversity in the Marine Environment, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0303 health sciences, 010604 marine biology & hydrobiology, media_common.quotation_subject, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Populations and Evolution (q-bio.PE), Complex system, Community perspective, 01 natural sciences, Data science, Holobiont, 03 medical and health sciences, State (polity), 13. Climate action, FOS: Biological sciences, Marine ecosystem, Evolutionary ecology, 14. Life underwater, Sociology, Quantitative Biology - Populations and Evolution, 030304 developmental biology, media_common
Abstract: Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help describe and understand these complex systems. It posits that a host and its associated microbiota, living together in a long-lasting relationship, form the holobiont, and have to be studied together, as a coherent biological and functional unit, in order to understand the biology, ecology and evolution of the organisms. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences with comparisons to terrestrial science whenever appropriate. A deeper understanding of such complex systems, however, will require further technological and conceptual advances. The most significant challenge will be to bridge functional research on simple and tractable model systems and global approaches. This will require scientists to work together as an (inter)active community in order to address, for instance, ecological and evolutionary questions and the roles of holobionts in biogeochemical cycles., PeerJ Preprints, Computer Science Preprints., 2019
Published: 2019
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17. Modelling paralytic shellfish toxins (PST) accumulation in Crassostrea gigas by using Dynamic Energy Budgets (DEB)

Author: Yoann Thomas, Eric Rannou, Jonathan Flye-Sainte-Marie, Philippe Soudant, Emilien Pousse, Marianne Alunno-Bruscia, Hélène Hégaret, Caroline Fabioux, Ludovic Hermabessiere, Zouher Amzil, Gonçalo M. Marques, Justine Castrec, Malwenn Lassudrie, Laure Pecquerie, Fred Jean, Marc Long, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Mathématiques de Bretagne Atlantique (LMBA), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Instituto Superior Técnico, Technical University of Lisbon, School of Chemistry [Wollongong], University of Wollongong [Australia], Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), ANR-13-CESA-0019,ACCUTOX,De la caractérisation des déterminants de l'accumulation des toxines paralysantes (PST) chez l'huître (Crassostrea gigas) au risque sanitaire pour l'homme dans son contexte sociétal(2013), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université de Brest (UBO)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS), Marine, Environment and Technology Center (MARATEC), School of Chemistry, University of Wollongong, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011)
Subjects: 0106 biological sciences, Oyster, Alexandrium minutum, Dynamic energy budget, Paralytic shellfish toxins (PST), Zoology, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, Modelling, chemistry.chemical_compound, biology.animal, medicine, Pacific oyster, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Shellfish, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Saxitoxin, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, biology, 010604 marine biology & hydrobiology, ACL, fungi, Dinoflagellate, food and beverages, Dynamic Energy Budget (DEB), biology.organism_classification, medicine.disease, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Shellfish poisoning, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, chemistry, [SDE]Environmental Sciences, Crassostrea, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Clearance rate
Abstract: International audience; As other filter-feeders, Crassostrea gigas can concentrate paralytic shellfish toxins (PST) by consuming dino-flagellate phytoplankton species like Alexandrium minutum. Intake of PST in oyster tissues mainly results from feeding processes, i.e. clearance rate, pre-ingestive sorting and ingestion that are directly influenced by environmental conditions (trophic sources, temperature). This study aimed to develop a mechanistic model coupling the kinetics of PST accumulation and bioenergetics in C. gigas based on Dynamic Energy Budget (DEB) theory. For the first time, the Synthesizing Units (SU) concept was applied to formalize the feeding preference of oysters between non-toxic and toxic microalgae. Toxin intake and accumulation were both dependent on the physiological status of oysters. The accumulation was modelled through the dynamics of two toxin compartments: (1) a compartment of ingested but non-assimilated toxins, with labile toxins within the digestive gland eliminated via faeces production; (2) a compartment of assimilated toxins with a rapid detoxification rate (within a few days). Firstly, the DEB-PST model was calibrated using data from two laboratory experiments where oysters have been exposed to A. minutum. Secondly, it was validated using data from another laboratory experiment and from three field surveys carried out in the Bay of Brest (France) from 2012 to 2014. To account for the variability in PST content of A. minutum cells, the saxitoxin (STX) amount per energy units in a toxic algae (ppsT) was adjusted for each dataset. Additionally, the effects of PST on the oyster bioenergetics were calibrated during the first laboratory experiment. However, these effects were shown to depend on the strain of A. minutum. Results of this study could be of great importance for monitoring agencies and decision makers to identify risky conditions (e.g. production areas, seawater temperature), to properly assess detoxification step (e.g. duration, modalities) before any commercialization or to improve predictions regarding closing of shellfish areas.
Published: 2019
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18. Microcarriers Based on Glycosaminoglycan-Like Marine Exopolysaccharide for TGF-beta1 Long-Term Protection

Author: Zykwinska, Agata, Marquis, Mélanie, Godin, Mathilde, Marchand, Laëtitia, Sinquin, Corinne, Garnier, Catherine, Jonchère, Camille, Chédeville, Claire, Le Visage, Catherine, Guicheux, Jérôme, Colliec-Jouault, Sylvia, Cuenot, Stéphane, Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies [IFREMER, Nantes], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA), Regenerative Medicine and Skeleton research lab (RMeS), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Nantes - UFR Odontologie, Université de Nantes (UN), Ostéo-articulaire - Tête et cou - Odontologie - Neurochirurgie - Neurotraumatologie [CHU Nantes] (Pôle hospitalo-universitaire PHU4 - OTONN), Centre hospitalier universitaire de Nantes (CHU Nantes), Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), UFR d’Odontologie [CHU Hôtel Dieu, Nantes], Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes microbiens et Molécules Marines pour les Biotechnologies (EM3B), Biotechnologies et Ressources Marines (BRM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Regenerative Medicine and Skeleton (RMeS), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Jehan, Frederic
Subjects: Cartilage, Articular, Drug Compounding, microfluidics, Biological Availability, Article, Cell Line, Transforming Growth Factor beta1, Hydrothermal Vents, Polysaccharides, Humans, Regeneration, lcsh:QH301-705.5, Drug Implants, microparticles, Drug Carriers, [SDV.MHEP.RSOA] Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, Tissue Scaffolds, [SDV.MHEP.GEG] Life Sciences [q-bio]/Human health and pathology/Geriatry and gerontology, [SDV.MHEP.GEG]Life Sciences [q-bio]/Human health and pathology/Geriatry and gerontology, growth factor, Drug Liberation, lcsh:Biology (General), [SDV.MHEP.RSOA]Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, bioactivity, Delayed-Action Preparations, exopolysaccharide, Alteromonas
Abstract: Articular cartilage is an avascular, non-innervated connective tissue with limited ability to regenerate. Articular degenerative processes arising from trauma, inflammation or due to aging are thus irreversible and may induce the loss of the joint function. To repair cartilaginous defects, tissue engineering approaches are under intense development. Association of cells and signalling proteins, such as growth factors, with biocompatible hydrogel matrix may lead to the regeneration of the healthy tissue. One current strategy to enhance both growth factor bioactivity and bioavailability is based on the delivery of these signalling proteins in microcarriers. In this context, the aim of the present study was to develop microcarriers by encapsulating Transforming Growth Factor-&beta, 1 (TGF-&beta, 1) into microparticles based on marine exopolysaccharide (EPS), namely GY785 EPS, for further applications in cartilage engineering. Using a capillary microfluidic approach, two microcarriers were prepared. The growth factor was either encapsulated directly within the microparticles based on slightly sulphated derivative or complexed firstly with the highly sulphated derivative before being incorporated within the microparticles. TGF-&beta, 1 release, studied under in vitro model conditions, revealed that the majority of the growth factor was retained inside the microparticles. Bioactivity of released TGF-&beta, 1 was particularly enhanced in the presence of highly sulphated derivative. It comes out from this study that GY785 EPS based microcarriers may constitute TGF-&beta, 1 reservoirs spatially retaining the growth factor for a variety of tissue engineering applications and in particular cartilage regeneration, where the growth factor needs to remain in the target location long enough to induce robust regenerative responses.
Published: 2019
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19. Oceanic mercury concentrations on both sides of the Strait of Gibraltar decreased between 1989 and 2012

Author: Bastien Thomas, Francesca Sprovieri, Philippe Courau, Daniel Cossa, Marie Boye, Nicolas Marusczak, Joël Knoery, Institut des Sciences de la Terre (ISTerre), Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Science et Technologie de la Biomasse Marine, Nantes (IFREMER), Laboratoire de Science et Technologie de la Biomasse Marine, Biogéochimie et Ecotoxicologie (IFREMER BE), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institute of Atmospheric Pollution Research (IIA), Consiglio Nazionale delle Ricerche [Roma] (CNR), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-PRES Université de Grenoble-Institut de recherche pour le développement [IRD] : UR219-Institut national des sciences de l'Univers (INSU - CNRS)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Université Joseph Fourier - Grenoble 1 (UJF), Département Biogéochimie et Ecotoxicologie, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), Laboratoire Biogéochimie des Contaminants Métalliques (LBCM), Biogéochimie et Ecotoxicologie (BE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), and European Project: 265113,EC:FP7:ENV,FP7-ENV-2010,GMOS(2010)
Subjects: Mediterranean climate, 010504 meteorology & atmospheric sciences, Natural cycle, chemistry.chemical_element, North east, 010501 environmental sciences, 01 natural sciences, Earth and Planetary Sciences (miscellaneous), Mediterranean Sea, Ecosystem, 14. Life underwater, Atlantic Ocean, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, Gibraltar, Ecology, Aquatic ecosystem, Pelagic zone, Mercury, Mercury (element), Oceanography, chemistry, 13. Climate action, [SDU]Sciences of the Universe [physics], Bioaccumulation, [SDE]Environmental Sciences, Environmental science
Abstract: Mercury (Hg) is a toxic metal that threatens the health of aquatic ecosystems and fish consumers. Its natural cycle has been deeply perturbed by Anthropogenic Hg emissions have deeply perturbed its natural cycle, especially since the start of the Industrial Revolution circa 1850 CE. Anthropogenic Hg emissions from North America and Europe have decreased by a factor of two in the last decades following the implementation of strict regulations. The response of North Atlantic Ocean and Mediterranean waters to this decrease remains poorly documented by field observations. A comparison of results obtained between 1989 and 2012 shows a significant decrease of Hg concentrations in waters on both sides of the Strait of Gibraltar. West of Gibraltar, the Hg decrease ranges from ∼35 % in the upper North East Atlantic Deep Water to ∼50 % in the North East Atlantic Central Water. East of Gibraltar, the observed decrease is ∼30 % in the Western Mediterranean Deep Water. No decrease is observed in the deep Atlantic Ocean layer that formed before the industrial era. These results strongly substantiate the effectiveness of global anti-pollution policies on Hg contamination in oceanic waters. A consequent decline of Hg bioaccumulation in Northeastern Atlantic and Western Mediterranean pelagic ecosystems still requires verification.
Published: 2019
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20. Hide and seek in the Bay of Biscay—a functional investigation of marine megafauna and small pelagic fish interactions

Author: Jérôme Spitz, C. Lambert, Vincent Ridoux, Ghislain Dorémus, Mathieu Doray, Matthieu Authier, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Observatoire PELAGIS UMS 3462 (PELAGIS), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), IFREMER - Nantes, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Ecology, predator-prey interactions, 010604 marine biology & hydrobiology, Hide and seek, predator–prey interactions, Pelagic zone, Aquatic Science, Oceanography, Bay of Biscay, 010603 evolutionary biology, 01 natural sciences, Fishery, cetaceans, prey profitability, marine top predators, Geography, Megafauna, predator avoidance, [SDE]Environmental Sciences, 14. Life underwater, functional traits, Bay, Ecology, Evolution, Behavior and Systematics, seabirds
Abstract: Prey and predator distributions influence one another. Understanding the scale and the orientation of predator–prey spatial correlations is crucial in foraging ecology. Growing evidence suggests that predator–prey interactions are more constrained by functional characteristics of both the predator and the prey. Unfortunately, in marine pelagic systems, the scale and orientation of spatial correlations between predators and prey have been only little explored from a functional point of view. We tested the existence of fine-scale association between predators and fish functional groups. Visual predator sightings and acoustic fish records were collected synchronously during oceanographic surveys from 2004 to 2014. Prey biomass was integrated by nautical miles and split into four size classes (30 cm) and two depth layers (surface, deep). We computed the relative biomass by prey size and depth category from 0 to 12 nm around predator sightings to determine the predators’ proximity to local prey biomass. Two cetaceans (common, bottlenose dolphins) and three seabirds (northern gannets, auks, northern fulmars) were studied. No association was found in fulmars, indicating they probably do not feed on considered fishes in the area. Gannets and auks were positively correlated with local prey biomass for sizes
Published: 2019
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21. Unique Biosynthetic Pathway in Bloom-Forming Cyanobacterial Genus Microcystis Jointly Assembles Cytotoxic Aeruginoguanidines and Microguanidines

Author: Christian Hertweck, Claire Pancrace, Muriel Gugger, Enora Briand, Arthur Guljamow, Keishi Ishida, Nathalie Sassoon, Annika R. Weiz, Thibault Scalvenzi, Douglas Gatte Pichi, Elke Dittmann, Collection des Cyanobactéries, Institut Pasteur [Paris], Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), University of Potsdam, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], DFG-fundedCollaborative Research Centre ChemBioSys (SFB 1127, Institut Pasteur [Paris] (IP), University of Potsdam = Universität Potsdam, Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), and Friedrich Schiller University Jena [Jena, Germany]
Subjects: 0301 basic medicine, Cyanobacteria, Microcystis, Metabolite, [SDV]Life Sciences [q-bio], 01 natural sciences, Biochemistry, Genome, Guanidines, METABOLITES, 03 medical and health sciences, chemistry.chemical_compound, Nonribosomal peptide, ddc:570, RESOURCE, Gene cluster, Axenic, Institut für Biochemie und Biologie, chemistry.chemical_classification, biology, 010405 organic chemistry, Biological activity, PEPTIDES, General Medicine, Eutrophication, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 6. Clean water, 0104 chemical sciences, 3. Good health, Biosynthetic Pathways, 030104 developmental biology, chemistry, 13. Climate action, ESCHERICHIA-COLI, DISCOVERY, Molecular Medicine, GENOMICS
Abstract: International audience; The cyanobacterial genus Microcystis is known to produce an elaborate array of structurally unique and biologically active natural products, including hazardous cyanotoxins. Cytotoxic aeruginoguanidines represent a yet unexplored family of peptides featuring a trisubstituted benzene unit and farnesylated arginine derivatives. In this study, we aimed at assigning these compounds to a biosynthetic gene cluster by utilizing biosynthetic attributes deduced from public genomes of Microcystis and the sporadic distribution of the metabolite in axenic strains of the Pasteur Culture Collection of Cyanobacteria. By integrating genome mining with untargeted metabolomics using liquid chromatography with mass spectrometry, we linked aeruginoguanidine (AGD) to a nonribosomal peptide synthetase gene cluster and coassigned a significantly smaller product to this pathway, microguanidine (MGD), previously only reported from two Microcystis blooms. Further, a new intermediate class of compounds named microguanidine amides was uncovered, thereby further enlarging this compound family. The comparison of structurally divergent AGDs and MGDs reveals an outstanding versatility of this biosynthetic pathway and provides insights into the assembly of the two compound subfamilies. Strikingly, aeruginoguanidines and microguanidines were found to be as widespread as the hepatotoxic microcystins, but the occurrence of both toxin families appeared to be mutually exclusive. M icrocystis is a dominant bloom-forming cyanobacterium occurring in temperate freshwater ecosystems. 1 The genus is infamous for the production of the well-known hepatotoxin microcystin. 2 Both blooms and toxins cause ecosystem disturbance and public health threats and constitute a growing concern in the frame of freshwater eutrophication and global warming. Microcystis has also been described as a producer of a multitude of bioactive natural products, some of interest for biotechnological and pharmaceutical application. 3−5 Cytotoxic aeruginoguanidines (AGDs) represent one of the most remarkable families of compounds described for Microcystis. 6 The three AGD congeners reported for strain Microcystis aeruginosa NIES-98 feature highly unprecedented characteristics such as a 1-(4-hydroxy-3-hydroxymethyl)-phenyl-1-hydroxy-2-propylamine-4′,3′,1-triO -sulfate (Hphpa trisulfate) moiety, along with geranylation and prenylation of arginines (Figure 1A). While bloom-forming Microcystis belong to the most intensively studied cyanobacteria, AGDs were reported only twice from a bloom in Czech Republic and an isolate in Brazil, 7,8 never from any other cyanobacteria. Their intricate features confine AGDs into a unique compound family. 3 Our recent genomic analysis of ten Microcystis strains revealed that the different genotypes share a highly similar core genome, while their biosynthetic gene clusters (BGCs) involved in natural product (NP) formation show a sporadic distribution. Moreover, we uncovered three cryptic BGCs not
Published: 2019
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22. Marine Polysaccharide-Collagen Coatings on Ti6Al4V Alloy Formed by Self-Assembly

Author: Andrei Koptioug, Stéphane Cuenot, Roman A. Surmenev, Corinne Sinquin, Jemma G. Kerns, Sylvia Colliec-Jouault, Oksana I Mishukova, Timothy E.L. Douglas, Agata Zykwinska, Maria A. Surmeneva, Karl Norris, Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN), Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies [IFREMER, Nantes], and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: collagen, lcsh:Mechanical engineering and machinery, 02 engineering and technology, macromolecular substances, engineering.material, marine exopolysaccharide, Fibril, Polysaccharide, Maskinteknik, Article, 03 medical and health sciences, Coating, lcsh:TJ1-1570, Electrical and Electronic Engineering, Cell adhesion, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Chemistry, Mechanical Engineering, Ti6Al4V, Biomaterial, 021001 nanoscience & nanotechnology, Chemical engineering, Control and Systems Engineering, Self-healing hydrogels, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], engineering, Surface modification, Self-assembly, 0210 nano-technology, surface modification
Abstract: Polysaccharides of marine origin are gaining interest as biomaterial components. Bacteria derived from deep-sea hydrothermal vents can produce sulfated exopolysaccharides (EPS), which can influence cell behavior. The use of such polysaccharides as components of organic, collagen fibril-based coatings on biomaterial surfaces remains unexplored. In this study, collagen fibril coatings enriched with HE800 and GY785 EPS derivatives were deposited on titanium alloy (Ti6Al4V) scaffolds produced by rapid prototyping and subjected to physicochemical and cell biological characterization. Coatings were formed by a self-assembly process whereby polysaccharides were added to acidic collagen molecule solution, followed by neutralization to induced self-assembly of collagen fibrils. Fibril formation resulted in collagen hydrogel formation. Hydrogels formed directly on Ti6Al4V surfaces, and fibrils adsorbed onto the surface. Scanning electron microscopy (SEM) analysis of collagen fibril coatings revealed association of polysaccharides with fibrils. Cell biological characterization revealed good cell adhesion and growth on bare Ti6Al4V surfaces, as well as coatings of collagen fibrils only and collagen fibrils enhanced with HE800 and GY785 EPS derivatives. Hence, the use of both EPS derivatives as coating components is feasible. Further work should focus on cell differentiation.
Published: 2019
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23. Foraging behaviour and prey consumption by grey seals (Halichoerus grypus)—spatial and trophic overlaps with fisheries in a marine protected area

Author: Cécile Vincent, Michael A. Fedak, Jérôme Spitz, Vincent Ridoux, Joffrey Jouma’a, Jean-Pierre Leaute, Carole E. Sparling, Bernie J. McConnell, LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Sea Mammal Research Unit (SMRU), University of Saint Andrews, Natural Environment Research Council Sea Mammal Research Unit, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sea Mammal Research Unit [University of St Andrews] (SMRU), School of Biology [University of St Andrews], University of St Andrews [Scotland]-University of St Andrews [Scotland]-Natural Environment Research Council (NERC), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: 0106 biological sciences, Foraging, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, Predation, satellite telemetry, Abundance (ecology), fisheries interactions, 14. Life underwater, Pinnipeds, Sea bass, Iroise Sea, Ecology, Evolution, Behavior and Systematics, Trophic level, Biomass (ecology), Ecology, National park, 010604 marine biology & hydrobiology, Fishery, prey intake, Geography, [SDE]Environmental Sciences, Marine protected area, management
Abstract: International audience; The roles of the marine national park of the Iroise Sea (France) are to maintain marine biodiversity, including the southernmost grey seal colonyin the Eastern Atlantic, whilst managing sustainable human activities. This study compares the fish biomass taken by local seals and thelandings by man in the Iroise Sea. Sixteen seals were satellite tracked from 1999 and 2003, providing location and behavioural (diving) datafrom which foraging locations were estimated. One individual spent a third of its foraging time in direct, long distance trips (200–350 km)across the English Channel, but most seals spent the majority (68.5%) of their foraging time in the Iroise Sea, making return trips within 30 kmof their departure haulout sites. The energetic consumption of the seal colony, taking sex and age classes into account, was assessed and combinedwith seal abundance estimates and dietary data to assess the total prey consumption by seals, for each prey species. We estimated thatduring the study period, the grey seal colony in the Iroise Sea consumed around 115 tons of fish per year. The main source of uncertaintyof this calculation came from the confidence intervals in total seal abundance estimates. This consumption comprised 13.6 tons of sea bass,4.3 tons of pollack and 2.7 tons of sole, representing 16.4, 1.8, and 5.2% of landings in the same areas for these three fish species, respectively.Within the four ICES rectangles where grey seals foraged, overlap between seals and fisheries was greatest in rectangle 25E5 (72.7% of all foragingdives), where grey seals haul out, and less in rectangles 25E4 (11.7%), 26E5 (10.8%), and 26E4 (4.8%).
Published: 2016
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24. Investigation of interactions between the marine GY785 exopolysaccharide and transforming growth factor-β1 by atomic force microscopy

Author: Mélanie Marquis, Corinne Sinquin, Stéphane Cuenot, Agata Zykwinska, Laëtitia Marchand, Sylvia Colliec-Jouault, Institut des Matériaux Jean Rouxel (IMN), Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN), ANR, French National Research Agency [ANR-17-CE08-0001], Pays de la Loire region, and Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique)
Subjects: 0301 basic medicine, Polymers and Plastics, 02 engineering and technology, Plasma protein binding, Nanoassemblies, Glycosaminoglycan, 03 medical and health sciences, chemistry.chemical_compound, Sulfation, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Materials Chemistry, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, AFM imaging, Sulfate, ComputingMilieux_MISCELLANEOUS, Glycosaminoglycans, Sulfated polysaccharides, Atomic force microscopy, Organic Chemistry, Force spectroscopy, 021001 nanoscience & nanotechnology, 030104 developmental biology, chemistry, Single-molecule force spectroscopy, Biophysics, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 0210 nano-technology, Macromolecule, Transforming growth factor
Abstract: International audience; Sulfated polysaccharides, such as glycosaminoglycans (GAG) regulate various biological activities through their interactions with growth factors. Investigating these interactions becomes the key to understand the structurefunction relationship of GAG. Highly sulfated derivatives prepared from the marine GY785 exopolysaccharide (EPS) produced by the deep-sea hydrothermal vent bacterium Alteromonas infernus have previously shown to stimulate the chondrogenic differentiation of mesenchymal stem cells in the presence of Transforming Growth Factor-beta 1 (TGF-beta 1). Here, the interactions between the GAG-mimetic GY785 EPS derivatives and TGF-beta 1 were investigated by Atomic Force Microscopy (AFM). The affinity between slightly sulfated or highly sulfated derivatives and TGF-beta 1 was explored by AFM imaging and single-molecule force spectroscopy experiments. The number of measured interactions and the interaction strength were both higher for highly sulfated derivative compared to the slightly sulfated one. These results clearly emphasize the involvement of sulfate groups in the protein binding and open new ways to tune cellular processes by designing macromolecules with adjustable sulfate charge density.
Published: 2018
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25. Concentration and purification of Porphyridium cruentum exopolysaccharides by membrane filtration at various cross-flow velocities

Author: Marthe Gilbert, Corinne Sinquin, Benjamin Le Gouic, Anthony Massé, Nicolas Brodu, Sophie Le Gall, Romain Le Balc’h, Rafik Balti, Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ifremer, French Regional Council of the 'Pays de la Loire', and Nantes University
Subjects: 0106 biological sciences, 0301 basic medicine, Exopolysaccharides, Concentration, Bioengineering, Polysaccharide, Diafiltration, 01 natural sciences, Applied Microbiology and Biotechnology, Biochemistry, 03 medical and health sciences, [SPI]Engineering Sciences [physics], 010608 biotechnology, Monosaccharide, Dry matter, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Chromatography, biology, Permeation, biology.organism_classification, 6. Clean water, 030104 developmental biology, Ceramic membrane, Membrane, chemistry, Porphyridium cruentum, Membrane filtration, Microalga
Abstract: International audience; Exopolysaccharides (EPS) from cell-free Porphyridiwn cruentum media were concentrated then purified (diafiltration) on a 0.14 ism ceramic membrane. The influence of cross-flow velocities on filtration performances was investigated. Mean permeate fluxes equal to 49.8, 68.9 and 81.9 L h(-1). m(-2) were obtained during the concentration at 4 bars for respectively cross-flow velocities inside the membrane lumen equal to 2.5, 3.3 and 4.2 m s(-1); 49.7 Lm(-1). M-2 for the diafiltration at 3.3 m s(-1). Permeate fluxes were correctly predicted from polysaccharide concentrations (10% deviation). Volume reduction factors higher than 7.8 were reached. Rejection rates of polysaccharides and proteins varied according to the cross-flow velocities. Thus, the EPS recovery rate or time of filtration could be modulated following the cross-flow velocity. Polysaccharides were concentrated 6.3 to 10.4 times in such a way that the final sugars concentration reached 1.74-2.26 g L-1. Rheological behavior of filtered solutions changed following the concentration progress. More than 80% (w/w) of polysaccharides were recovered while 49% and 99% of proteins and salts were removed respectively. The filtrations allowed reaching a final monosaccharide content of dry matter equal to 48.9% against 0.6% (w/w) initially.
Published: 2018
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26. Procédure de qualification des donnnées Quadrige² - Données chimie RNOPHY (Imposex)

Author: Enez, Florian, Gauthier, Emilie, Pellouin-Grouhel, Anne, Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ifremer Nantes, Rue de l'Île d'Yeu, 44980 Nantes, and Enez, Florian
Subjects: [SDE.ES] Environmental Sciences/Environmental and Society, [SDE.ES]Environmental Sciences/Environmental and Society
Abstract: La qualification a pour objectif d’attribuer un niveau de qualité aux données : Bon, Douteux ou Faux. Le processus de qualification consiste à rechercher des anomalies plus ou moins complexes dans les données stockées dans la base de données Quadrige², les anomalies étant définies par les responsables de programme Quadrige ou responsables thématiques. Ces recherches d’anomalies sont faites en lien avec la cellule quadrige². La qualification des données peut se faire : • de façon ponctuelle : identification d’un problème de processus analytique pour quelques données • en routine : un processus de qualification dite « automatique » permet de qualifier les enregistrements individuellement (cohérence des informations de chaque résultat individuellement). Puis une qualification dite « experte » permet de vérifier la cohérence d’un résultat par rapport aux autres résultats (séries temporelles, analyse graphique ou statistique). Le présent document décrit les processus de qualification en routine des données du réseau ROCCH – volet IMPOSEX (programme RNOPHY de Quadrige).
Published: 2018

27. The GEOTRACES Intermediate Data Product 2017

Author: Thomas J. Browning, Hans-Jürgen Brumsack, Katharina Pahnke, Saeed Roshan, Stephanie Owens, Rosie Chance, Peter Croot, Steven van Heuven, Alison E. Hartman, Mercedes López-Lora, Pu Zhang, Heather A. Bouman, Géraldine Sarthou, François Lacan, Robyn E. Tuerena, José Marcus Godoy, Ester Garcia-Solsona, Steven L. Goldstein, Hans A. Slagter, Celia Venchiarutti, A. Russell Flegal, Emily Townsend, Ralph Till, Christopher T. Hayes, Melanie Gault-Ringold, Ros Watson, Peter N. Sedwick, Chandranath Basak, Bronwyn Wake, Loes J. A. Gerringa, Noriko Nakayama, Lars-Eric Heimbürger, Paul J. Morris, François Fripiat, Paul B. Henderson, Chris J. Daniels, Catherine Jeandel, Helen M. Snaith, Patrizia Ziveri, Toshitaka Gamo, Yanbin Lu, Oliver J. Lechtenfeld, Yingzhe Wu, Andreas Wisotzki, Hajime Obata, Cynthia Dumousseaud, Ashley T. Townsend, Sebastian Mieruch, Donna Cockwell, Laurent Bopp, Elena Masferrer Dodas, Bernhard Schnetger, J. K. Klar, Sunil K. Singh, Joaquin E. Chaves, Kuo-Fang Huang, Louise A. Zimmer, Laura F. Robinson, Michiel M Rutgers van der Loeff, Corey Archer, Feifei Deng, Karen Grissom, Robert Rember, Nicholas J. Hawco, Jingfeng Wu, Robert M. Sherrell, Rachel U. Shelley, Jan-Lukas Menzel Barraqueta, E. Malcolm S. Woodward, Fanny Chever, Yuichiro Kumamoto, Hélène Planquette, Dorothea Bauch, Frank Dehairs, Daniel C. Ohnemus, Akira Nishiuchi, Paul D. Quay, Sanjin Mehic, Zichen Xue, Maxi Castrillejo, Brian Peters, Michael J. Ellwood, Stephen R. Rintoul, Tobias Roeske, Jing Zhang, Gretchen J. Swarr, Peng Ho, Ken O. Buesseler, Gwenaelle Moncoiffe, Martin Frank, Maureen E. Auro, Abby Bull, David Kadko, Montserrat Roca-Martí, Maeve C. Lohan, Roulin Khondoker, Patricia Cámara Mor, Melissa Gilbert, Sebastian M. Vivancos, Erin E. Black, Santiago R. Gonzalez, Gideon M. Henderson, David J. Janssen, Sylvain Rigaud, Amandine Radic, Maxence Paul, Cyril Abadie, Ana Aguliar-Islas, Seth G. John, Marie Boye, Evgenia Ryabenko, Abigail E. Noble, Luke Bridgestock, Brian Duggan, Hisayuki Yoshikawa, Jun Nishioka, Kathrin Wuttig, Pieter van Beek, Jana Friedrich, Thomas M. Church, Maija Heller, Stephen J.G. Galer, Pier van der Merwe, Claire P. Till, Xin Yuan Zheng, Henning Fröllje, John Niedermiller, Howie D. Scher, Johnny Stutsman, Patricia Zunino, Christel S. Hassler, Ye Zhao, Tim M. Conway, William M. Landing, Yang Xiang, Katrin Bluhm, Maria T. Maldonado, Elena Chamizo, Sabrina Speich, Claudine H. Stirling, Guillaume Brissebrat, Matthew A. Charette, Jeremy E. Jacquot, Yu-Te Hsieh, Pinghe Cai, Ivia Closset, Yoshiki Sohrin, Ejin George, Jong-Mi Lee, Leopoldo D. Pena, Edward Mawji, Damien Cardinal, Catherine Pradoux, Martin Q. Fleisher, Virginie Sanial, Derek Vance, Craig A. Carlson, Pere Masqué, Katlin L. Bowman, Evaline M. van Weerlee, Oliver Baars, Ruifang C. Xie, María Villa-Alfageme, Hein J W de Baar, M. Alexandra Weigand, Tina van de Flierdt, J. Bown, Timothy C. Kenna, Kenneth W. Bruland, Jeroen E. Sonke, Hai Cheng, Mark J. Warner, Sven Ober, Rob Middag, Jessica N. Fitzsimmons, Emilie Le Roy, Yishai Weinstein, Nicholas R. Bates, Joerg Rickli, Daniel M. Sigman, Hendrik M. van Aken, Angela Milne, Cheryl M. Zurbrick, Gregory A. Cutter, Igor Semiletov, Marie Labatut, Torben Stichel, Pascale Lherminier, Gabriel Dulaquais, Jay T. Cullen, Christopher I. Measures, Mark Rosenberg, Tomoharu Minami, Mariko Hatta, Alexander L. Thomas, Gonzalo Carrasco, Karel Bakker, Clifton S. Buck, Maarten B Klunder, Willard S. Moore, Reiner Schlitzer, Tomas A. Remenyi, Susan H. Little, Eberhard Fahrbach, Charles R. McClain, Edward A. Boyle, Ursula Schauer, Linjie Zheng, Alex R. Baker, Emma Slater, Kay Thorne, Patrick Laan, Christina Schallenberg, Reiner Steinfeldt, Benjamin S. Twining, Yolanda Echegoyen-Sanz, Neil J. Wyatt, Alison M. Agather, Viena Puigcorbé, Peter Scott, Gillian Stewart, Matthew P. Humphreys, Frédéric A. C. Le Moigne, Phoebe J. Lam, Núria Casacuberta, Josh Helgoe, Edward C.V. Butler, Mark Rehkämper, Elizabeth M. Jones, Karen L. Casciotti, James W. Moffett, Tristan J. Horner, Sue Velazquez, Yuzuru Nakaguchi, Micha J.A. Rijkenberg, Antje H L Voelker, Joseph A. Resing, Lesley Salt, Eric P. Achterberg, Sven Kretschmer, Jan van Ooijen, Dominik J. Weiss, Moritz Zieringer, Carl H. Lamborg, Rick Kayser, Pierre Branellec, John M. Rolison, Sara Rauschenberg, Walter Geibert, Raja S. Ganeshram, Myriam Lambelet, Janice L. Jones, Chad R. Hammerschmidt, William J. Jenkins, Jordi Garcia-Orellana, Alessandro Tagliabue, Philip W. Boyd, Alan M. Shiller, Marcus Christl, Mark Baskaran, Mak A. Saito, Huong Thi Dieu, Morten B. Andersen, Kenji Isshiki, Taejin Kim, Christian Schlosser, Melanie K. Behrens, Albert S. Colman, Frédéric Planchon, Bettina Sohst, Andrew R. Bowie, Mark A. Brzezinski, R. Lawrence Edwards, Kristen N. Buck, Jeanette O'Sullivan, William M. Smethie, Wafa Abouchami, Valentí Rodellas, Ed C Hathorne, Robert F. Anderson, James H. Swift, Frank J. Pavia, Daniel Cossa, Lauren Kipp, Peter L. Morton, Fabien Quéroué, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Centre for Automotive Safety Research, University of Adelaide, University of California, National Oceanography Centre (NOC), Scottish Association for Marine Science (SAMS), Department of Oceanography [Cape Town], University of Cape Town, Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Chemistry (MPIC), Max-Planck-Gesellschaft, University of Toyama, Department of Marine Chemistry and Geochemistry (WHOI), Woods Hole Oceanographic Institution (WHOI), Royal Netherlands Institute for Sea Research (NIOZ), Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Department of Geology, Wayne State University [Detroit], The Bartlett, University College of London [London] (UCL), Institute for Environmental Research, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris), Department of Earth Sciences [Oxford], University of Oxford [Oxford], Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Cycles biogéochimiques marins : processus et perturbations (CYBIOM), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institute for Research on Learning, Services communs OMP - UMS 831 (UMS 831), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Marine Science Institute [Santa Barbara] (MSI), University of California [Santa Barbara] (UCSB), University of California-University of California, National Oceanography Centre [Southampton] (NOC), University of Southampton, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), University of Victoria [Canada] (UVIC), Massachusetts Institute of Technology (MIT), Universidad de Dakota del Sur, Analytical, Environmental and Geo- Chemistry, Vrije Universiteit [Brussels] (VUB), Wright State University, School of Geography, Earth and Environmental Sciences [Plymouth] (SoGEES), Plymouth University, Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], Alfred Wegener Institute [Potsdam], Institute of Global Environmental Change [China] (IGEC), Xi'an Jiaotong University (Xjtu), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics and Science, National Taiwan Normal University (NTNU), School of Information Technology [Kharagpur], Indian Institute of Technology Kharagpur (IIT Kharagpur), GEOMAR - Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), University of California [Davis] (UC Davis), Institut de Ciencia i Tecnologia Ambientals (ICTA), Universitat Autònoma de Barcelona [Barcelona] (UAB), Institute of Low Temperature Science, Hokkaido University, The University of Tokyo, Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania (UTAS), Joint Institute for the Study of the Atmosphere and Ocean (JISAO), University of Washington [Seattle], Institute of Geochemistry and Petrology, Détection, évaluation, gestion des risques CHROniques et éMErgents (CHROME) / Université de Nîmes (CHROME), Université de Nîmes (UNIMES), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), School of Earth and Ocean Sciences, University of Victoria, Knowledge Media Institute (KMI), The Open University [Milton Keynes] (OU), Bermuda Biological Station for Research (BBSR), Bermuda Biological Station for Research, Department of Geosciences [Princeton], Princeton University, Kyoto University [Kyoto], Géochimie des Isotopes Stables (GIS), Géosciences Environnement Toulouse (GET), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National d'Études Spatiales [Toulouse] (CNES), School of Earth and Environmental Sciences [Queens New York], Queens College [New York], City University of New York [New York] (CUNY)-City University of New York [New York] (CUNY), SOEST, University of Hawai‘i [Mānoa] (UHM), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Bigelow Laboratory for Ocean Sciences, Department of Earth Science and Technology [Imperial College London], Imperial College London, Plymouth Marine Laboratory, Rosenstiel School of Marine and Atmospheric Science (RSMAS), University of Miami [Coral Gables], Tsinghua National Laboratory for Information Science and Technology (TNList), RITE, Research Institute of Innovative Technology for the Earth, Agricultural Information Institute (AII), Chinese Academy of Agricultural Sciences (CAAS), Department of Mathematics [Shanghai], Shanghai Jiao Tong University [Shanghai], University of California [Irvine] (UCI), Institute of Environmental Science and Technology [Barcelona] (ICTA), University of California (UC), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Oxford, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Services communs OMP (UMS 831), Université Toulouse III - Paul Sabatier (UT3), Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France, University of California [Santa Barbara] (UC Santa Barbara), University of California (UC)-University of California (UC), Institut des Sciences de la Terre (ISTerre), Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Vrije Universiteit Brussel (VUB), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Florida International University [Miami] (FIU), Department of Earth Science and Engineering [Imperial College London], Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Universitat Autònoma de Barcelona (UAB), British Oceanographic Data Centre (BODC), Institute of Low Temperature Science [Sapporo], Hokkaido University [Sapporo, Japan], The University of Tokyo (UTokyo), Institute of Geochemistry and Petrology [ETH Zürich], Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), College of Earth, Ocean, and Environment [Newark] (CEOE), University of Delaware [Newark], Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Knowledge Media Institute (KMi), Kyoto University, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Academia Sinica, University of California [Irvine] (UC Irvine), Danish Technological Institute (DTI), Scientific Committee on Oceanic Research (SCOR) from the U.S. National Science Foundation [OCE-0608600, OCE-0938349, OCE-1243377, OCE-1546580], UK Natural Environment Research Council (NERC), Ministry of Earth Science of India, Centre National de Recherche Scientifique, l'Universite Paul Sabatier de Toulouse, Observatoire Midi-Pyrenees Toulouse, Universitat Autonoma de Barcelona, Kiel Excellence Cluster The Future Ocean, Swedish Museum of Natural History, University of Tokyo, University of British Columbia, Royal Netherlands Institute for Sea Research, GEOMAR-Helmholtz Centre for Ocean Research Kiel, Alfred Wegener Institute, Scientific Committee on Oceanic Research, National Science Foundation (US), Natural Environment Research Council (UK), Ministry of Earth Sciences (India), Centre National de la Recherche Scientifique (France), Université Toulouse III Paul Sabatier, Observatoire Midi-Pyrénées (France), Universidad Autónoma de Barcelona, Helmholtz Centre for Ocean Research Kiel, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Germany), Schlitzer, Reiner [0000-0002-3740-6499], Masferrer Dodas, Elena [0000-0003-0879-1954], Chamizo, Elena [0000-0001-8266-6129], Christl, M. [0000-0002-3131-6652], Masqué, Pere [0000-0002-1789-320X], Villa-Alfageme, María [0000-0001-7157-8588], Universitat de Barcelona, Natural Environment Research Council (NERC), Leverhulme Trust, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Carrasco Rebaza, Gonzalo, Echegoyen Sanz, Yolanda, Kayser, Richard A, Isotope Research, Ocean Ecosystems, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Hassler, Christel, Schlitzer, Reiner, Masferrer Dodas, Elena, Chamizo, Elena, Christl, M., Masqué, Pere, and Villa-Alfageme, María
Subjects: Geochemistry & Geophysics, 010504 meteorology & atmospheric sciences, Isòtops, sub-01, Geotraces, MODELS, Digital data, Context (language use), 010502 geochemistry & geophysics, 01 natural sciences, IDP2017, Isotopes, Geochemistry and Petrology, Oceans, Electronic atlas, ddc:550, 0402 Geochemistry, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, NetCDF, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Trace elements, Science & Technology, Information retrieval, ACL, Geology, computer.file_format, Ocean Data View, Metadata, Data processing, GEOTRACES, 0403 Geology, Data extraction, 13. Climate action, Data quality, Physical Sciences, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 0406 Physical Geography and Environmental Geoscience, computer, Processament de dades, Trace elements Isotopes
Abstract: The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González., National Science Foundation (U.S.) (Grant OCE-0608600), National Science Foundation (U.S.) (Grant OCE0938349), National Science Foundation (U.S.) (Grant OCE-1243377), National Science Foundation (U.S.) (Grant OCE-1546580)
Published: 2018
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28. A multiscale study of mercury transformations and dynamics at the chemocline of the Petit-Saut tropical reservoir (French Guiana)

Author: Didier Jézéquel, Daniel Cossa, Edouard Metzger, Bogdan Muresan, Laboratoire de Planétologie et Géodynamique - Angers (LPG-ANGERS), Laboratoire de Planétologie et Géodynamique [UMR 6112] (LPG), Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre d'Enseignement et de Recherche Eau Ville Environnement (CEREVE), AgroParisTech-École des Ponts ParisTech (ENPC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Laboratoire de Planétologie et Géodynamique - Bio-Indicateurs Actuels et Fossiles (LPG-BIAF), Laboratoire de Planétologie et Géodynamique UMR6112 (LPG), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Université d'Angers (UA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Université d'Angers (UA), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), and Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS)
Subjects: Biogeochemical cycle, Environmental Engineering, 010504 meteorology & atmospheric sciences, chemistry.chemical_element, 010501 environmental sciences, Chemocline, 01 natural sciences, Pollution, Redox, Mercury (element), Nutrient, Water column, chemistry, Environmental chemistry, Epilimnion, Dissolved organic carbon, [SDE]Environmental Sciences, Environmental Chemistry, Waste Management and Disposal, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: This study investigated, on both metric and centimetric scales, mercury (Hg) transformations and dynamics within a water column chemocline of a tropical reservoir. Data collected included conventional measurement of Hg in water samples, diffusive gradients in thin-films (DGT) assessments, and thermodynamic speciation modeling in order to portray the biogeochemical processes that control elemental Hg (EM) and dissolved monomethylated Hg (MeHgD) production. The primary contribution of this study is demonstration that the DGT technique can be successfully implemented to examine labile Hg compound mobilization, and estimation of how local substratum facilitates Hg reduction and methylation reactions. DGT profiles with a resolution of 1 cm revealed a fine sequence of prominent Hg reduction/oxidation reactions at the chemocline level. This is interpreted as a manifestation of both: i) kinetic effects capable of arising inside the diffusive layer of DGT devices, and ii) extremely localized production or consumption of reducible and methylable Hg. Another key result obtained at the metric scale is that EM and MeHgD production at a water column chemocline are intricately linked, as both are fueled by nutrients episodically released during the decomposition of falling epilimnetic organic particles or inhibited by dissolved organic matter and inorganic compounds continuously transported from the deeper monimolimnion. Finally, it is worth noting that the chemocline acts as an accumulation and recycling domain for falling MeHg-loaded organic particles, whereas the high primary productivity layer in the epilimnion represents the principal reactor with respect to Hg methylation and reduction.
Published: 2018
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29. Full-scale validation of an algal productivity model including nitrogen limitation

Author: Olivier Bernard, Quentin Béchet, Noémie Coulombier, Thomas Lasserre, Christophe Vasseur, Loic Le Dean, Université Côte d'Azur (UCA), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), La Compagnie du Vent, Université de Nantes (UN)-Université de Nantes (UN), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Gouzé, Jean-Luc, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Full scale, Photobioreactor, Biomass, chemistry.chemical_element, 01 natural sciences, 7. Clean energy, 03 medical and health sciences, 010608 biotechnology, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Raceway, Productivity model, Quota model, 2. Zero hunger, Environmental engineering, Modeling, Nitrogen, Carotenoids, Raceway ponds, Outdoor cultivation, 030104 developmental biology, chemistry, Productivity (ecology), 13. Climate action, Biofuel, Biofuels, Environmental science, Dunaliella salina, [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering, Agronomy and Crop Science
Abstract: International audience; Accurate predictions of algal productivity under nutrient-limiting conditions are needed to assess the economics of full-scale algal cultivation for the developing markets of food, feed, and at longer term, green chemistry and biofuel. In particular, predicting pigments production from micro-algae is a critical milestone in the assessments of high-value chemicals production from micro-algae. This study validates a mathematical model predicting algal biomass productivity in outdoor raceway ponds under nitrogen-limiting conditions. The model was first validated from experimental data collected during Dunaliella salina cultivation in indoor photobioreactors and accounts for the impact of light, temperature, and nitrogen concentration on algal productivity (overall accuracy on algal concentration of ±2.7 mg L−1, N = 48). The model was then validated against data collected in outdoor raceway ponds over a period of 2 years, representing a total of 111 days of cultivation. Biomass and extracellular nitrogen concentrations predictions were accurate within ±0.055 g L−1 (N = 69) and ±0.0024 g L−1 (N = 26), respectively. Model inaccuracies were mostly due to measurement errors and uncertainties on model inputs. Measured carotenoids concentrations were found proportional to the biomass concentrations in the outdoor raceway ponds. By coupling this linear correlation to the productivity model, predicted carotenoids concentrations were in good agreement with experimental data (accuracy within ±0.0046 g L−1, N = 55). The mathematical model developed in this study has therefore the potential to refine previous assessments of algal cultivation for biofuels and pigments production.
Published: 2018
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30. Membrane separation applied to micro-algae: applications to the water treatment and the bio-refinery

Author: Masse, Anthony, Amzil, Zouher, Balti, Rafik, Brodu, Nicolas, Jean Baptiste, Castaing, Fleurence, Joel, Frappart, M., Guilbaud, Julie, Haure, Joël, Jaouen, Pascal, Jubeau, Sébastien, Le Balc’h, Romain, Le Gall, Sophie, Marchal, Luc, Séverine, Plantier, Guillaume, Roelens, Sabiri, Nour-Eddine, Sechet, Véronique, Sinquin, Corinne, Wolff, Francois-Charles, Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Phycotoxines, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Station Ifremer de la Tremblade, Mines Nantes (Mines Nantes)-Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS), Algosource Technologies, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Traitement Eau Air Métrologie (GEPEA-TEAM), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Mines Nantes (Mines Nantes)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), and Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique)
Subjects: [SPI]Engineering Sciences [physics], [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018

31. Impacts of green tides on estuarine fish assemblages

Author: A. Paumier, E. Le Luherne, T. Tatlian, S. Ballu, Elodie Réveillac, O. Le Pape, Mario Lepage, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Centre d'Etude et de Valorisation des Algues (CEVA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), French Fisheries Organization, Loire-Bretagne Water Agency, France Filiere Peche, Institut National de la Recherche Agronomique (INRA), CEVA PLEUBIAN FRA, Partenaires IRSTEA, and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)
Subjects: 0106 biological sciences, Nursery, 010504 meteorology & atmospheric sciences, Estuarine ecology, Aquatic Science, Oceanography, 01 natural sciences, Demersal zone, Nutrient, Macroalgae, Fish community, 14. Life underwater, Green tides, 0105 earth and related environmental sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, Pelagic zone, Estuary, Fishery, Water Framework Directive, Habitat, Benthic zone, [SDE]Environmental Sciences, Guild, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; All around the world, an increasing proportion of estuarine systems are facing massive proliferations of green macroalgae, called green tides, in response to nutrient enrichment. The consequences of this perturbation for ichthyofauna that use estuarine systems as essential fish habitats remain understudied. To estimate these consequences, we combined outputs of both macroalgae proliferation and fish community surveys conducted for the European Water Framework Directive in thirteen estuaries in northwestern France, a region where green tides are of great concern. The approach revealed the influence of green tides on estuarine fish communities. The response of each community to the green tides differed according to their functional guild composition. Benthic and marine juvenile guilds were negatively impacted, while demersal and pelagic fish guilds appeared to be more resilient. Green tides, which significantly affect the suitability of fish habitat, change the composition of the fish community and may hinder the future recruitment of marine fish species that rely on estuaries during the juvenile stage.
Published: 2018
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32. Modeling the influence of eutrophication and redox conditions on mercury cycling at the sediment-water interface in the Berre Lagoon

Author: Joël Knoery, Elizaveta Protsenko, Raoul-Marie Couture, Alice Newton, Olivier Radakovitch, Dominika Krzeminska, Svetlana Pakhomova, Daniel Cossa, Evgeniy Yakushev, Shamil Yakubov, Sylvain Rigaud, Norwegian Institute for Air Research (NILU), Norwegian University of Science and Technology [Trondheim] (NTNU), P.P. Shirshov Institute of Oceanology (SIO), Russian Academy of Sciences [Moscow] (RAS), Norwegian Institute for Water Research (NIVA), Détection, évaluation, gestion des risques CHROniques et éMErgents (CHROME) / Université de Nîmes (CHROME), Université de Nîmes (UNIMES), Institut des Sciences de la Terre (ISTerre), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-PRES Université de Grenoble-Institut de recherche pour le développement [IRD] : UR219-Institut national des sciences de l'Univers (INSU - CNRS)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Université Joseph Fourier - Grenoble 1 (UJF), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Département de Chimie, Université Laval, Université Laval, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Helmholtz-Zentrum Geesthacht (GKSS), Norwegian Institute of Bioeconomy Research (NIBIO), Centro de Investigação Marinha e Ambiental (CIMA), Universidade do Algarve (UAlg), Norwegian University of Science and Technology (NTNU), Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université Laval [Québec] (ULaval), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), PSE-ENV/SRTE/LRTA, Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de recherche sur les transferts des radionucléides dans les écosystèmes aquatiques (IRSN/PSE-ENV/SRTE/LRTA), Service de recherche sur les transferts et les effets des radionucléides sur les écosystèmes (IRSN/PSE-ENV/SRTE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN), and Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO)
Subjects: mercury, lcsh:QH1-199.5, 010504 meteorology & atmospheric sciences, biogeochemical modeling, BROM, chemistry.chemical_element, Ocean Engineering, lcsh:General. Including nature conservation, geographical distribution, 010501 environmental sciences, Aquatic Science, Oceanography, 01 natural sciences, VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440::Miljøkjemi, naturmiljøkjemi: 446, Bottom water, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Water column, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Sediment–water interface, 14. Life underwater, lcsh:Science, 0105 earth and related environmental sciences, Water Science and Technology, Global and Planetary Change, anoxia, Sediment, methylmercury, Eutrophication, Anoxic waters, 6. Clean water, lagoon, Mercury (element), eutrophication, chemistry, 13. Climate action, Bioaccumulation, Environmental chemistry, Mercury Cycling, Environmental science, lcsh:Q, Sediment-Water Interface, Berre Lagoon
Abstract: This study presents a specifically designed Mercury module in a coupled benthic-pelagic reactive-transport model - Bottom RedOx Model (BROM) that allows to study mercury (Hg) biogeochemistry under different conditions. This module considers the transformation of elemental mercury (Hg(O)), divalent mercury (Hg(II)) and methylmercury (MeHg). The behavior of mercury species in the model is interconnected with changes of oxygen, hydrogen sulfide, iron oxides, organic matter, and biota. We simulated the transformation and transport of Hg species in the water column and upper sediment layer under five different scenarios, combining various levels of oxygenation and trophic state in the Berre lagoon, a shallow eutrophic lagoon of the French Mediterranean coast subjected to seasonal anoxia. The first scenario represents the conditions in the lagoon that are compared with experimental data. The four other scenarios were produced by varying the biological productivity, using low and high nutrient (N and P) concentrations, and by varying the redox conditions using different intensity of vertical mixing in the water column. The results of the simulation show that both oxidized and reduced sediments can accumulate Hg, but any shifts in redox conditions in bottom water and upper sediment layer lead to the release of Hg species into the water column. Eutrophication and/or restricted vertical mixing lead to reducing conditions and intensify MeHg formation in the sediment with periodic release to the water column. Oxygenation of an anoxic water body can lead to the appearance of Hg species in the water column and uptake by organisms, whereby Hg may enter into the food web. The comparison of studied scenarios shows that a well-oxygenated eutrophic system favors the conditions for Hg species bioaccumulation with a potential adverse effect on the ecosystem. The research is relevant to the UN Minimata convention, EU policies on water, environmental quality standards and Mercury in particular. VISTA - a basic research program Norwegian Academy of Science and Letters 6164 Statoil 6164 project PREDHYPO A*MIDEX project - Investissements d'Avenir French Government program ANR-11-IDEX-0001-02 Norwegian Research Council SKATTEfunn project Aquatic Modeling Tools 272749 NILU CIMA IMBER Future Earth Coasts Future Earth Ocean KAN info:eu-repo/semantics/publishedVersion
Published: 2018
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33. Introduction to the French GEOTRACES North Atlantic Transect (GA01): GEOVIDE cruise

Author: Géraldine Sarthou, Pascale Lherminier, Eric P. Achterberg, Fernando Alonso-Pérez, Eva Bucciarelli, Julia Boutorh, Vincent Bouvier, Edward A. Boyle, Pierre Branellec, Lidia I. Carracedo, Nuria Casacuberta, Maxi Castrillejo, Marie Cheize, Leonardo Contreira Pereira, Daniel Cossa, Nathalie Daniault, Emmanuel De Saint-Léger, Frank Dehairs, Feifei Deng, Floriane Desprez de Gésincourt, Jérémy Devesa, Lorna Foliot, Debany Fonseca-Batista, Morgane Gallinari, Maribel I. García-Ibáñez, Arthur Gourain, Emilie Grossteffan, Michel Hamon, Lars Eric Heimbürger, Gideon M. Henderson, Catherine Jeandel, Catherine Kermabon, François Lacan, Philippe Le Bot, Manon Le Goff, Emilie Le Roy, Alison Lefèbvre, Stéphane Leizour, Nolwenn Lemaitre, Pere Masqué, Olivier Ménage, Jan-Lukas Menzel Barraqueta, Herlé Mercier, Fabien Perault, Fiz F. Pérez, Hélène F. Planquette, Frédéric Planchon, Arnout Roukaerts, Virginie Sanial, Raphaëlle Sauzède, Rachel U. Shelley, Gillian Stewart, Jill N. Sutton, Yi Tang, Nadine Tisnérat-Laborde, Manon Tonnard, Paul Tréguer, Pieter van Beek, Cheryl M. Zurbrick, Patricia Zunino, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut Cartografic de Catalunya (ICC), Institut Cartografic de Catalunya, Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), Institute for Research on Learning, National Oceanography Centre [Southampton] (NOC), University of Southampton, Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Analytical and Environmental Chemistry and Earth System Sciences, Vrije Universiteit [Brussels] (VUB), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Spanish National Research Council (CSIC), UMS 3113, Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO), Neuropsychopharmacologie, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Ciencia i Tecnologia Ambientals (ICTA), Universitat Autònoma de Barcelona [Barcelona] (UAB), GEOMAR LEGOS, Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), School of Earth and Environmental Sciences [Queens New York], Queens College [New York], City University of New York [New York] (CUNY)-City University of New York [New York] (CUNY), Shenzhen Key Laboratory of Sensor Technology, Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, 03 medical and health sciences, 010504 meteorology & atmospheric sciences, 13. Climate action, [SDE.MCG]Environmental Sciences/Global Changes, 14. Life underwater, 01 natural sciences, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0105 earth and related environmental sciences
Abstract: The GEOVIDE cruise, a collaborative project within the framework of the international GEOTRACES programme, was conducted along the French-led section in the North Atlantic Ocean (Section GA01), between 15 May and 30 June 2014. In this Special Issue, results from GEOVIDE, including physical oceanography and trace element and isotope cyclings, are presented among seventeen articles. Here, the scientific context, project objectives and scientific strategy of GEOVIDE are provided, along with an overview of the main results from the articles published in the special issue.
Published: 2018
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34. Low-Molecular-Weight Fucoidan Induces Endothelial Cell Migration via the PI3K/AKT Pathway and Modulates the Transcription of Genes Involved in Angiogenesis

Author: Sophie Gandrille, Isabelle Galy-Fauroux, Wassila Carpentier, Sylvia Colliec-Jouault, Anna Lokajczyk, Claire Bouvard, Anne-Marie Fischer, Dominique Helley, Françoise Grelac, Thrombose : Épidémiologie, Physiopathologie et Thérapeutiques Innovantes (UMR_S 765), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot - Paris 7 (UPD7), Université Paris Descartes - Paris 5 (UPD5), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Plateforme Post-génomique de la Pitié-Salpêtrière (P3S), UMS omique (OMIQUE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Innovations thérapeutiques en hémostase (IThEM - U1140), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), French Ministry of Research and Education, French Society of Hematology, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Thrombose : Épidémiologie, Physiopathologie et Thérapeutiques Innovantes ( UMR_S 765 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Paris Diderot - Paris 7 ( UPD7 ), Université Paris Descartes - Paris 5 ( UPD5 ), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Plateforme Post-génomique de la Pitié-Salpêtrière ( P3S ), UMS omique ( OMIQUE ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Innovations thérapeutiques en hémostase ( IThEM - U1140 ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes ( IFREMER Nantes ), Université de Nantes ( UN ), and HAL-UPMC, Gestionnaire
Subjects: Vascular Endothelial Growth Factor A, Cell signaling, fucoidan, angiogenesis, vasculogenesis, migration, signaling, transcriptomics, Cytoskeleton organization, Angiogenesis, Neovascularization, Physiologic, Pharmaceutical Science, Biology, Article, chemistry.chemical_compound, Vasculogenesis, Cell Movement, Polysaccharides, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Drug Discovery, Human Umbilical Vein Endothelial Cells, Humans, lcsh:QH301-705.5, Pharmacology, Toxicology and Pharmaceutics (miscellaneous), Cytoskeleton, PI3K/AKT/mTOR pathway, Cell migration, Cell biology, Molecular Weight, Endothelial stem cell, Vascular endothelial growth factor, Gene Expression Regulation, lcsh:Biology (General), chemistry, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Phosphatidylinositol 3-Kinase, Proto-Oncogene Proteins c-akt
Abstract: International audience; Low-molecular-weight fucoidan (LMWF) is a sulfated polysaccharide extracted from brown seaweed that presents antithrombotic and pro-angiogenic properties. However, its mechanism of action is not well-characterized. Here, we studied the effects of LMWF on cell signaling and whole genome expression in human umbilical vein endothelial cells and endothelial colony forming cells. We observed that LMWF and vascular endothelial growth factor had synergistic effects on cell signaling, and more interestingly that LMWF by itself, in the absence of other growth factors, was able to trigger the activation of the PI3K/AKT pathway, which plays a crucial role in angiogenesis and vasculogenesis. We also observed that the effects of LMWF on cell migration were PI3K/AKT-dependent and that LMWF modulated the expression of genes involved at different levels of the neovessel formation process, such as cell migration and cytoskeleton organization, cell mobilization and homing. This provides a better understanding of LMWF's mechanism of action and confirms that it could be an interesting therapeutic approach for vascular repair.
Published: 2015
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35. Effect of vacuum and modified atmosphere packaging on the microbiological, chemical and sensory properties of tropical red drum (Sciaenops ocellatus) fillets stored at 4°C

Author: Christine Chopin, Adèle Silbande, Katia Rochefort, Sandra Adenet, Françoise Leroi, Juliette Smith-Ravin, Josiane Cornet, Département Scientifique Interfacultaire (DSI), Université des Antilles (Pôle Martinique), Université des Antilles (UA)-Université des Antilles (UA), Pôle Agroalimentaire Régional de la Martinique (PARM), Ifremer Nantes, STBM, Nantes, France, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies (EM 3 B)
Subjects: Biogenic Amines, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Vacuum, Nitrogen, Organoleptic, Food spoilage, VP, Colony Count, Microbial, Trimethylamine, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Chryseobacterium, Carnobacterium, Microbiology, chemistry.chemical_compound, 0404 agricultural biotechnology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Animals, 14. Life underwater, Food science, ComputingMilieux_MISCELLANEOUS, Cadaverine, biology, Bacteria, Microbiota, Fishes, Food Packaging, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 04 agricultural and veterinary sciences, General Medicine, biology.organism_classification, Biogenic amine, 040401 food science, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Kocuria, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, chemistry, Seafood, Modified atmosphere, NGS, MAP, Food Microbiology, 16S rRNA gene, Metagenomics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Food Science
Abstract: Aims The effect of vacuum (VP – 4 °C) and CO2/N2–atmosphere (MAP – 4 °C) packaging on the quality of red drum fillets compared with whole gutted iced fish was investigated. Methods and results A metagenomic approach, bacterial enumeration and isolation, biochemical and sensory analyses were carried out. The organoleptic rejection of whole fish was observed at day 15 whereas VP and MAP fillets appeared unacceptable only after 29 days. At these dates, total mesophilic counts reached 107–108 CFU g− 1. According to Illumina MiSeq sequencing, Arthrobacter, Chryseobacterium, Brevibacterium, Staphylococcus and Kocuria were the main genera of the fresh red drum fillets. At the sensory rejection time, lactic acid bacteria (LAB), particularly Carnobacterium sp., dominated the microbiota of both types of packaging. The pH value of fresh samples was between 5.96 and 6.37 and did not vary greatly in all trials. Total volatile basic nitrogen (TVBN) and trimethylamine (TMA) concentrations were low and not represent reliable indicators of the spoilage, contrary to some biogenic amines (cadaverine, putrescine and tyramine). Conclusion Chilled packed fillets of red drum have an extended shelf-life compared to whole gutted iced fish. Overall, few differences in sensory and microbial quality were observed between the VP and MAP samples. Significance and impact of the study Next-Generation Sequencing (NGS) provided data on the microbiota of a tropical fish.
Published: 2017
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36. Enriching a cellulose hydrogel with a biologically active marine exopolysaccharide for cell-based cartilage engineering

Author: Rederstorff, E., Réthoré, Gildas, Weiss, Pierre, Sourice, Sophie, Beck-Cormier, Sarah, Mathieu, E., Maillasson, Mike, Jacques, Yannick, Colliec-Jouault, S., Fellah, B., Guicheux, Jérome, VINATIER, Claire, Bernardo, Elizabeth, Laboratoire d'ingénierie osteo-articulaire et dentaire (LIOAD), Université de Nantes (UN)-IFR26-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Nantes - UFR Odontologie, Université de Nantes (UN), Biotechnologie et Molécules Marines (BMM), Biotechnologies et Ressources Marines (BRM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Regenerative Medicine and Skeleton (RMeS), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Ostéo-articulaire - Tête et cou - Odontologie - Neurochirurgie - Neurotraumatologie [CHU Nantes] (Pôle hospitalo-universitaire PHU4 - OTONN), Centre hospitalier universitaire de Nantes (CHU Nantes), Unité de recherche de l'institut du thorax (ITX-lab), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Immunobiology of Human αβ and γδ T Cells and Immunotherapeutic Applications (CRCINA-ÉQUIPE 1), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes), Plateforme IMPACT Nantes (CRCINA-IMPACT), centre de Recherche et d'Investigation Préclinique [Nantes] (CRIP), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), E.R. received a fellowship from the Region Pays de la Loire through a Bioregos grant. This study was supported by grants from the ANR TecSan project Chondrograft, the Art hritis Fondation Courtin and the Société Française de Rhumatologie., Laboratoire de biotechnologie et des molécules marines [IFREMER, Nantes], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Regenerative Medicine and Skeleton research lab (RMeS), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), and Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)
Subjects: body regions, [SDV.CAN] Life Sciences [q-bio]/Cancer, marine polysaccharides, tissue engineering, technology, industry, and agriculture, glycosaminoglycan, chondrocytes, [SDV.CAN]Life Sciences [q-bio]/Cancer, hydrogel, cartilage
Abstract: International audience; The development of biologically and mechanically competent hydrogels is a prerequisite in cartilage engineering. We recently demonstrated that a marine exopolysaccharide, GY785, stimulates the in vitro chondrogenesis of adipose stromal cells. In the present study, we thus hypothesized that enriching our silated hydroxypropyl methylcellulose hydrogel (Si-HPMC) with GY785 might offer new prospects in the development of scaffolds for cartilage regeneration. The interaction properties of GY785 with growth factors was tested by surface plasmon resonance (SPR). The biocompatibility of Si-HPMC/GY785 towards rabbit articular chondrocytes (RACs) and its ability to maintain and recover a chondrocytic phenotype were then evaluated in vitro by MTS assay, cell counting and qRT-PCR. Finally, we evaluated the potential of Si-HPMC/GY785 associated with RACs to form cartilaginous tissue in vivo by transplantation into the subcutis of nude mice for 3 weeks. Our SPR data indicated that GY785 was able to physically interact with BMP-2 and TGFβ. Our analyses also showed that three-dimensionally (3D)-cultured RACs into Si-HPMC/GY785 strongly expressed type II collagen (COL2) and aggrecan transcripts when compared to Si-HPMC alone. In addition, RACs also produced large amounts of extracellular matrix (ECM) containing glycosaminoglycans (GAG) and COL2. When dedifferentiated RACs were replaced in 3D in Si-HPMC/GY785, the expressions of COL2 and aggrecan transcripts were recovered and that of type I collagen decreased. Immunohistological analyses of Si-HPMC/GY785 constructs transplanted into nude mice revealed the production of a cartilage-like extracellular matrix (ECM) containing high amounts of GAG and COL2. These results indicate that GY785-enriched Si-HPMC appears to be a promising hydrogel for cartilage tissue engineering.
Published: 2017
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37. Betaine lipid and neutral lipid production under nitrogen or phosphorus limitation in the marine microalga Tisochrysis lutea (Haptophyta)

Author: Gaël Bougaran, Justine Marchand, Annick Morant-Manceau, Bing Huang, Gregory Carrier, Stanislas Thiriet-Rupert, Virginie Mimouni, Bruno Saint-Jean, Ewa Lukomska, Brigitte Moreau, Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Physiologie et biotechnologie des Algues (PBA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de l’Élevage, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique)
Subjects: 0106 biological sciences, 0301 basic medicine, Betaine lipid, Nitrogen, [SDV]Life Sciences [q-bio], Phospholipid, Photosynthesis, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Betaine, Lipid remodeling, Tisochrysis lutea, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Chemistry, Carbon fixation, Phosphorus, Photosynthetic capacity, Chloroplast, Polyunsaturated fatty acid, 030104 developmental biology, Membrane, Biochemistry, Thylakoid, lipids (amino acids, peptides, and proteins), Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Nitrogen (N) and phosphorus (P) limitations induce neutral lipid accumulation and membrane lipid remodeling in the domesticated oleaginous microalga Tisochrysis lutea. This study compared growth, photosynthetic activity, biochemical and transcriptional responses of T. lutea throughout batch cultures under N or P limitation compared with non-limiting nutrient condition (NP). The results show that, under N limitation, the breakdown and re-use of cellular N-containing compounds contributed to carbohydrates and further triacylglycerol (TAG) accumulation, where the accumulation of docosahexaenoic acid (DHA) in neutral lipids might mainly be derived from the recycling of membrane polar lipids. Conversely, P limitation did not hinder the photosynthetic capacity; a higher efficiency of carbon fixation fueled the allocation of carbon fluxes to the reserves of carbohydrates and neutral lipids. These latter accumulated without massive degradation of essential cellular compounds. Betaine lipids constitute the major compounds of non-plastidial membranes in T. lutea. Given an extremely low constitutive phospholipid level, phospholipids might not be involved in the regulation of P storage. However, transfer of P from non-plastidial to chloroplast membranes might occur, keeping a stable lipid composition of thylakoid membranes and maintaining a relatively high photosynthetic capacity under P deprivation.
Published: 2019
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38. Membrane processes for the microalage biorefinery : example of polysaccharides upgrading

Author: Anthony Masse, Luc Marchal, Jeremy Pruvost, Nicolas Brodu, Lisa Zaouk, Romain Le Balc’h, Rafik Balti, Pascal Jaouen, Corinne Sinquin, Sophie Le Gall, Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Mines Nantes (Mines Nantes)-Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Mines Nantes (Mines Nantes)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: [SPI]Engineering Sciences [physics], [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2016

39. Assembly of HE800 exopolysaccharide produced by a deep-sea hydrothermal bacterium into microgels for protein delivery applications

Author: Corinne Sinquin, Sylvia Colliec-Jouault, Mélanie Marquis, Stéphane Cuenot, Agata Zykwinska, Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), EU Interreg IVA 2 Seas 'Bio-Care Marine', Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), and Université de Nantes (UN)
Subjects: 0301 basic medicine, business.product_category, Polymers and Plastics, Microfluidics, Nanotechnology, 02 engineering and technology, Polysaccharide, Hydrothermal circulation, Divalent, 03 medical and health sciences, Marine exopolysaccharide, Microfiber, Materials Chemistry, Animals, Microparticle, Bovine serum albumin, Microencapsulation, Protein release, ComputingMilieux_MISCELLANEOUS, Glycosaminoglycans, Vibrio, chemistry.chemical_classification, Drug Carriers, biology, Chemistry, Organic Chemistry, Polysaccharides, Bacterial, Microcarrier, Polychaeta, Serum Albumin, Bovine, Microfluidic Analytical Techniques, 021001 nanoscience & nanotechnology, 030104 developmental biology, Microfluidic, Microfibers, biology.protein, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Cattle, Microgel particles, 0210 nano-technology, business, Gels
Abstract: International audience; Assembly of biopolymers into microgels is an elegant strategy for bioencapsulation with various potential biomedical applications. Such biocompatible and biodegradable microassemblies are developed not only to protect the encapsulated molecule but also to ensure its sustained local delivery. The present study describes the fabrication of microassemblies from a marine HE800 exopolysaccharide (EPS), which displays a glycosaminoglycan (GAG)-like structure and biological properties. HE800 EPS was assembled, through physical cross-linking with divalent ions, into microgel particles and microfibers using microfluidics. The microparticle morphology was highly affected by the polysaccharide concentration and its molecular weight. A model protein, namely Bovine Serum Albumin (BSA) was subsequently encapsulated within HE800 microparticles in one-step process using microfluidics. The protein release was tuned by the microparticle morphology with a lower protein amount released from the most homogeneous structures. Our findings demonstrate the high potential of HE800 EPS based microassemblies as innovative protein microcarriers for further biomedical applications.
Published: 2016
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40. Abrupt shifts in the Gironde fish community: an indicator of ecological changes in an estuarine ecosystem

Author: Jérémy Lobry, Arthur Rigaud, Maud Pierre, Aurélie Chaalali, Hilaire Drouineau, Benoît Sautour, Xavier Chevillot, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, CHANGEMENT CLIMATIQUE GLOBAL, Time series, 010504 meteorology & atmospheric sciences, Generalised linear mixed models, ECOSYSTEME, [SDE.MCG]Environmental Sciences/Global Changes, Biodiversity, Climate change, Context (language use), Shift, Aquatic Science, 01 natural sciences, ecological indicators, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Regime shift, Ecosystem, 14. Life underwater, Inter-shift periods, Ecology, Evolution, Behavior and Systematics, Fish diversity, 0105 earth and related environmental sciences, biodiversity, Ecology, 010604 marine biology & hydrobiology, BIODIVERSITE, Global warming, Estuary, Community structure, global climate change, Pelagic zone, 15. Life on land, estuaries, Geography, 13. Climate action, ESTUAIRE, Ecosystem state, INDICATEUR ECOLOGIQUE, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ecosystems, GLMM
Abstract: International audience; For decades, global climate change has directly and indirectly affected the structure and function of ecosystems. Abrupt changes in biodiversity have been observed in response to linear or sudden modifications to the environment. These abrupt shifts can cause long-term reorganizations within ecosystems, with communities exhibiting new functional responses to environmental factors. Over the last 3 decades, the Gironde estuary in southwest France has experienced 2 abrupt shifts in both the physical and chemical environments and the pelagic community. Rather than describing these shifts and their origins, we focused on the 3 inter-shift periods, describing the structure of the fish community and its relationship with the environment during these periods. We described fish biodiversity using a limited set of descriptors, taking into account both species composition and relative species abundances. Inter-shift ecosystem states were defined based on the relationship between this description and the hydro-physico-chemical variables and climatic indices defining the main features of the environment. This relationship was described using generalized linear mixed models on the entire time series and for each inter-shift period. Our results indicate that (1) the fish community structure has been significantly modified, (2) environmental drivers influencing fish diversity have changed during these 3 periods, and (3) the fish-environment relationships have been modified over time. From this, we conclude a regime shift has occurred in the Gironde estuary. We also highlight that anthropogenic influences have increased, which re-emphasizes the importance of local management in maintaining fish diversity and associated goods and services within the context of climate change.
Published: 2016
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41. Abrupt shifts in the Gironde fish community: an indicator of ecological changes in an estuarine ecosystem

Author: Chevillot, X., Pierre, M., Rigaud, A., Drouineau, H., Chaalali, A., Sautour, B., Lobry, J., Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), and Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: CHANGEMENT CLIMATIQUE GLOBAL, ECOSYSTEME, BIODIVERSITE, [SDE.MCG]Environmental Sciences/Global Changes, global climate change, estuaries, ecological indicators, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, ESTUAIRE, INDICATEUR ECOLOGIQUE, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ecosystems, biodiversity
Abstract: International audience; For decades, global climate change has directly and indirectly affected the structure and function of ecosystems. Abrupt changes in biodiversity have been observed in response to linear or sudden modifications to the environment. These abrupt shifts can cause long-term reorganizations within ecosystems, with communities exhibiting new functional responses to environmental factors. Over the last 3 decades, the Gironde estuary in southwest France has experienced 2 abrupt shifts in both the physical and chemical environments and the pelagic community. Rather than describing these shifts and their origins, we focused on the 3 inter-shift periods, describing the structure of the fish community and its relationship with the environment during these periods. We described fish biodiversity using a limited set of descriptors, taking into account both species composition and relative species abundances. Inter-shift ecosystem states were defined based on the relationship between this description and the hydro-physico-chemical variables and climatic indices defining the main features of the environment. This relationship was described using generalized linear mixed models on the entire time series and for each inter-shift period. Our results indicate that (1) the fish community structure has been significantly modified, (2) environmental drivers influencing fish diversity have changed during these 3 periods, and (3) the fish-environment relationships have been modified over time. From this, we conclude a regime shift has occurred in the Gironde estuary. We also highlight that anthropogenic influences have increased, which re-emphasizes the importance of local management in maintaining fish diversity and associated goods and services within the context of climate change.
Published: 2016
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42. Is herbicide toxicity on marine microalgae influenced by the natural dissolved organic matter (DOM)?

Author: Coquillé, N., Stachowski Haberkorn, S., Morin, Soizic, Parlanti, E., Menard, D., Rouxel, Julien, Haugarreau, L., Dupraz, V., Eon, Mélissa, Vedrenne, Jacky, Boutry, Sébastien, Tison-Rosebery, Juliette, Ezzedine, Jade, Gregoire, J.C., Budzinski, H., Tapie, N., Pardon, Patrick, Chevance Demars, L., IRSTEA BORDEAUX UR EABX FRA, IFREMER NANTES FRA, UNIVERSITE DE BORDEAUX CNRS UMR 5805 EPOC TALENCE FRA, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: TOXICITE, ALGUE, MATIERE ORGANIQUE, HERBICIDES, INTERACTION CHIMIQUE, TOXICITY, MICROALGAE, DISSOLVED ORGANIC MATTER, PESTICIDES, ORGANIC MATTER, [SDE]Environmental Sciences, PESTICIDE, EPIPHYTES, HERBICIDE, SYNERGISM
Abstract: International audience; As primary producers, microalgae can be directly affected by herbicides. These organisms can also be impacted by other environmental elements such as the dissolved organic matter (DOM), that may also interact with pesticides. Indeed, MOD can affect pollutant transport, fate, biodegradation, bioavailability, and toxicity on organisms. Therefore, the present study aimed to investigate whether natural DOM influence the toxicity of three herbicides (irgarol (I), diuron (D) and S-metolachlor (S)), single and in mixture, on two marine microalgae, Chaetoceros calcitrans (Cc) and Tetraselmis suecica (Ts). After 6-day exposures to each herbicide (I0.05 and I0.5 µg.L-1; D0.05 and D0.5 µg.L-1; S0.5 and S5 µg.L-1) and to mixtures (M1: I0.05+D0.05+S0.5 and M2: I0.5+D0.5+S5), the effects of herbicides were assessed on growth (doubling time TD), photosynthetic yield (Yeff), reactive oxygen species presence and intracellular relative lipid content. For each condition, two sets of triplicates were run: one with natural DOM added to the culture media, another without DOM. Without DOM, I0.5 and M2 significantly affected almost all parameters with similar trends in both species: an increase of TD by more than twice (+125% and +129% for Cc and Ts respectively, at I0.5), a decrease of Yeff (approximately 30%) and a decrease of the relative lipid content. The M2 impacts observed in Cc were similar to the effects induced by irgarol at 0.5 µg.L-1, however a higher toxicity was shown for Ts (+167% for TD), suggesting a possible synergistic effect of mixture. When DOM was added in the culture media, significant effects were also observed with I0.5 and M2 conditions for both species: while the effects of I0.5 in TD of Cc were decreased (+101%), they were strongly enhanced for Ts (+178%), as were the effects of M2 (+298%). The presence of DOM decreased the herbicide toxicity for Cc whereas toxic effects were increased for Ts. These results may partly be due to the complexation between DOM and herbicides, leading to a lower bioavailability of herbicides. However, the difference in toxicity between the two species remains to be explained. Analysis of herbicide concentrations, dissolved organic carbon concentration and DOM, which are still ongoing, will help to improve the understanding of interactions between microalgae, herbicides and DOM. Finally, this study demonstrates the importance to consider DOM as a major factor possibly involved in toxicity modulation in the environment.
Published: 2016

43. 210 Po and 210 Pb trophic transfer within the phytoplankton–zooplankton–anchovy/sardine food web: a case study from the Gulf of Lion (NW Mediterranean Sea)

Author: Jacek Tronczynski, Olivier Radakovitch, Mireille Harmelin-Vivien, Emilie Strady, Jean François Chiffoleau, Alain Veron, Centre Asiatique de Recherche sur l'Eau CARE-HCMUT, Vietnam, Université Paris Diderot - Paris 7 (UPD7), Diversité, évolution et écologie fonctionnelle marine (DIMAR), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Biogéochimie des contaminants organiques (LBCO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire d'étude des transferts en hydrologie et environnement (LTHE), Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Grenoble (INPG)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire Biogéochimie des Contaminants Organiques (LBCO), Biogéochimie et Ecotoxicologie (BE), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: Polonium, Water Pollutants, Radioactive, Food Chain, Health, Toxicology and Mutagenesis, [SDE.MCG]Environmental Sciences/Global Changes, [SDV]Life Sciences [q-bio], [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Pb-210, Biology, Zooplankton, Engraulis, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Anchovy, Phytoplankton, Mediterranean Sea, Environmental Chemistry, Animals, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Waste Management and Disposal, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Trophic level, Po-210, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Ecology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Fishes, Pelagic zone, Pelagic fishes, General Medicine, Lead Radioisotopes, Plankton, biology.organism_classification, Pollution, Food web, Oceanography, [SDU]Sciences of the Universe [physics], [SDE]Environmental Sciences, France, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: The transfer of (210)Po and (210)Pb in the food web of small pelagic fishes (from phytoplankton and zooplankton to anchovy Engraulis encrasicolus and sardine Sardina pilchardus) is investigated in the Gulf of Lion (GoL). We present original data of (210)Po and (210)Pb activity concentrations, C and N stable isotope ratios, measured (i) from different size classes of phytoplankton and zooplankton during spring and winter in different environments of the GoL, and (ii) in two fish species. Significant spatial patterns based on (210)Po, (210)Pb activity concentrations and (210)Po/(210)Pb ratios in the different plankton size classes are evidenced by hierarchical clustering, both in spring and winter. This variability, also observed for C and N stable isotopes ratios, is connected to local specific pelagic habitats and hydrodynamics. The sampling strategy suggests that (210)Po bioaccumulation in the GoL remains at a constant level from the first (dominated by phytoplankton) to the second trophic level (zooplankton), while (210)Pb bioaccumulation shows an increase in winter. Based on stable N isotope ratios and (210)Po activity concentrations measured in anchovies and sardines, we evidence (210)Po bio-magnification along the trophic food web of these two planktivorous pelagic fishes.
Published: 2015
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44. Point de vue sur l'échantillonnage passifs pour la surveillance des contaminants dans les milieux aquatiques : réalisations et perspectives

Author: Miege, C., Mazzella, N., Allan, I., Dulio, V., Smedes, F., Tixier, C., Vermeirssen, E., Brant, J., O'Toole, S., Budzinski, H., Ghestem, Jean Philippe, Staub, P.F., Lardy Fontan, S., Gonzalez, J.L., Coquery, M., Vrana, B., Milieux aquatiques, écologie et pollutions (UR MALY), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Ecosystèmes aquatiques et changements globaux (UR EABX), Norwegian Institute for Water Research (NIVA), Institut National de l'Environnement Industriel et des Risques (INERIS), Masaryk University [Brno] (MUNI), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Centre for Environment, Fisheries and Aquaculture Science [Lowestoft] (CEFAS), Environmental Protection Agency, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture, IRSTEA, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Office national de l'eau et des milieux aquatiques (ONEMA), Ministère de l'écologie, du développement durable et de l'énergie, IFREMER - Laboratoire Provence Azur Corse, Réseaux épuration et qualité des eaux (UR REBX), Masaryk University, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Swiss Federal Institute for Environmental Science and Technology [Dübendorf] (EAWAG), and Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: EMERGING SUBSTANCE, AQUATIC ENVIRONMENT, SUBSTANCE EMERGENTE, ECHANTILLONNEUR PASSIF, SUBSTANCE PRIORITAIRE, EUROPEAN WATER FRAMEWORK DIRECTIVE, SURVEILLANCE, [SDE]Environmental Sciences, PRIORITY SUBSTANCE, DIRECTIVE CADRE EUROPEENNE SUR L'EAU, MONITORING, MILIEU AQUATIQUE
Abstract: International audience; This paper, based on the outcome of discussions at a NORMAN Network-supported workshop in Lyon (France) in November 2014 aims to provide a common position of passive sampling community experts regarding concrete actions required to foster the use of passive sampling techniques in support of contaminant risk assessment and management and for routine monitoring of contaminants in aquatic systems. The brief roadmap presented here focusses on the identification of robust passive sampling methodology, technology that requires further development or that has yet to be developed, our current knowledge of the evaluation of uncertainties when calculating a freely dissolved concentration, the relationship between data from PS and that obtained through biomonitoring. A tiered approach to identifying areas of potential environmental quality standard (EQS) exceedances is also shown. Finally, we propose a list of recommended actions to improve the acceptance of passive sampling by policy-makers. These include the drafting of guidelines, quality assurance and control procedures, developing demonstration projects where biomonitoring and passive sampling are undertaken alongside, organising proficiency testing schemes and interlaboratory comparison and, finally, establishing passive sampler-based assessment criteria in relation to existing EQS.
Published: 2015
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45. Propidium monoazide PCR, a method to determine OsHV-1 undamaged capsids and to estimate virus Lethal Dose 50.

Author: Renault T, Faury N, and Morga B
Subjects: Animals, DNA, Viral genetics, Capsid, Lethal Dose 50, Polymerase Chain Reaction, Herpesviridae genetics, Crassostrea genetics, Virus Diseases, Azides, Propidium analogs & derivatives
Abstract: Ostreid herpes virus 1 (OsHV-1) has been classified within the Malacoherpesviridae family from the Herpesvirales order. OsHV-1 is the etiological agent of a contagious viral disease of Pacific oysters, C. gigas, affecting also other bivalve species. Mortality rates reported associated with the viral infection vary considerably between sites and countries and depend on the age of affected stocks. A variant called μVar has been reported since 2008 in Europe and other variants in Australia and in New Zealand last decade. These variants are considered as the main causative agents of mass mortality events affecting C. gigas. Presently there is no established cell line that allows for the detection of infectious OsHV-1. In this context, a technique of propidium monoazide (PMA) PCR was developed in order to quantify "undamaged" capsids. This methodology is of interest to explore the virus infectivity. Being able to quantify viral particles getting an undamaged capsid (not only an amount of viral DNA) in tissue homogenates prepared from infected oysters or in seawater samples can assist in the definition of a Lethal Dose (LD) 50 and gain information in the experiments conducted to reproduce the viral infection. The main objectives of the present study were (i) the development/optimization of a PMA PCR technique for OsHV-1 detection using the best quantity of PMA and verifying its effectiveness through heat treatment, (ii) the definition of the percentage of undamaged capsids in four different tissue homogenates prepared from infected Pacific oysters and (iii) the approach of a LD50 during experimental viral infection assays on the basis of a number of undamaged capsids. Although the developped PMA PCR technique was unable to determine OsHV-1 infectivity in viral supensions, it could greatly improve interpretation of virus positive results obtained by qPCR. This technique is not intended to replace the quantification of viral DNA by qPCR, but it does make it possible to give a form of biological meaning to the detection of this DNA., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)
Published: 2024
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46. Production and composition of extracellular polymeric substances by a unicellular strain and natural colonies of Microcystis: Impact of salinity and nutrient stress.

Author: Reignier O, Bormans M, Marchand L, Sinquin C, Amzil Z, Zykwinska A, and Briand E
Subjects: Extracellular Polymeric Substance Matrix, Salinity, Polysaccharides, Microcystis, Cyanobacteria
Abstract: The transfer of toxic cyanobacterial Microcystis blooms from freshwater to estuaries constitutes a serious environmental problem worldwide that is expected to expand in scale and intensity with anthropogenic and climate change. The formation and maintenance of Microcystis in colonial form is conditioned to the presence of extracellular polymeric substances (EPS). In this study, we attempted to better understand how the mucilaginous colonial form of Microcystis evolves under environmental stress conditions. In particular, we studied and compared the production and the composition of EPS fractions (attached and free) from natural colonies of a Microcystis bloom and from a unicellular M. aeruginosa strain under salinity and nutrient stress (representing a land-sea continuum). Our results highlighted a greater production of EPS from the natural colonies of Microcystis than the unicellular one under nutrient and combined stress conditions dominated by the attached form. In comparison to the unicellular Microcystis, EPS produced by the colonial form were characterized by high molecular weight polysaccharides which were enriched in uronic acids and hexosamines, notably for the free fraction in response to increased salinities. This complex extracellular matrix gives the cells the ability to aggregate and allows the colonial cyanobacterial population to cope with osmotic shock., (© 2023 The Authors. Environmental Microbiology Reports published by Applied Microbiology International and John Wiley & Sons Ltd.)
Published: 2023
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47. Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits.

Author: Berthelier J, Saint-Jean B, Casse N, Bougaran G, and Carrier G
Subjects: DNA Transposable Elements genetics, Phenotype, Lipids genetics, Microalgae genetics, Microalgae metabolism, Haptophyta genetics
Abstract: Microalgal domestication is an expanding research field that aims to multiply and accelerate the potential of microalgae for various biotechnological purposes. We investigated the stability of improved lipid traits and genetic changes of a domesticated strain of the haptophyte Tisochrysis lutea, TisoS2M2, previously obtained by a mutation-selection improvement program. After 7 years of maintenance, TisoS2M2 still displayed improved lipid traits compared with the native strain, demonstrating that a mutation-selection improvement program is suitable for obtaining a domesticated strain with stable, improved phenotype over time. We identified specific genetic variations between the native and domesticated strains and focused on the dynamics of transposable elements (TEs). DNA transposons mainly caused specific TE indels of the domesticated strain TisoS2M2, and some specific TE indels may have impacted genes associated to the neutral lipid pathway. We revealed transposition events for TEs in T. lutea and discussed on the potential role of the improvement program on their activity., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Berthelier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2023
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48. Human Sapovirus Replication in Human Intestinal Enteroids.

Author: Euller-Nicolas G, Le Mennec C, Schaeffer J, Zeng XL, Ettayebi K, Atmar RL, Le Guyader FS, Estes MK, and Desdouits M
Subjects: Humans, Bile Acids and Salts pharmacology, Gastroenteritis virology, Intestine, Small virology, Host Microbial Interactions, Culture Media chemistry, Cell Line, Tumor, Cell Differentiation, Caliciviridae Infections virology, Sapovirus growth & development, Sapovirus immunology, Virus Replication drug effects, Virus Replication physiology, Culture Techniques methods
Abstract: Human sapoviruses (HuSaVs), like human noroviruses (HuNoV), belong to the Caliciviridae family and cause acute gastroenteritis in humans. Since their discovery in 1976, numerous attempts to grow HuSaVs in vitro were unsuccessful until 2020, when these viruses were reported to replicate in a duodenal cancer cell-derived line. Physiological cellular models allowing viral replication are essential to investigate HuSaV biology and replication mechanisms such as genetic susceptibility, restriction factors, and immune responses to infection. In this study, we demonstrate replication of two HuSaV strains in human intestinal enteroids (HIEs) known to support the replication of HuNoV and other human enteric viruses. HuSaVs replicated in differentiated HIEs originating from jejunum, duodenum and ileum, but not from the colon, and bile acids were required. Between 2h and 3 to 6 days postinfection, viral RNA levels increased up from 0.5 to 1.8 log 10 -fold. Importantly, HuSaVs were able to replicate in HIEs independent of their secretor status and histo-blood group antigen expression. The HIE model supports HuSaV replication and allows a better understanding of host-pathogen mechanisms such as cellular tropism and mechanisms of viral replication. IMPORTANCE Human sapoviruses (HuSaVs) are a frequent but overlooked cause of acute gastroenteritis, especially in children. Little is known about this pathogen, whose successful in vitro cultivation was reported only recently, in a cancer cell-derived line. Here, we assessed the replication of HuSaV in human intestinal enteroids (HIEs), which are nontransformed cultures originally derived from human intestinal stem cells that can be grown in vitro and are known to allow the replication of other enteric viruses. Successful infection of HIEs with two strains belonging to different genotypes of the virus allowed discovery that the tropism of these HuSaVs is restricted to the small intestine, does not occur in the colon, and replication requires bile acid but is independent of the expression of histo-blood group antigens. Thus, HIEs represent a physiologically relevant model to further investigate HuSaV biology and a suitable platform for the future development of vaccines and antivirals.
Published: 2023
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49. Trajectories of nutrients concentrations and ratios in the French coastal ecosystems: 20 years of changes in relation with large-scale and local drivers.

Author: Lheureux A, David V, Del Amo Y, Soudant D, Auby I, Bozec Y, Conan P, Ganthy F, Grégori G, Lefebvre A, Leynart A, Rimmelin-Maury P, Souchu P, Vantrepote V, Blondel C, Cariou T, Crispi O, Cordier MA, Crouvoisier M, Duquesne V, Ferreira S, Garcia N, Gouriou L, Grosteffan E, Le Merrer Y, Meteigner C, Retho M, Tournaire MP, and Savoye N
Subjects: Humans, Human Activities, Nutrients, Ecosystem, Climate Change
Abstract: Along with their important diversity, coastal ecosystems receive various amounts of nutrients, principally arising from the continent and from the related human activities (mainly industrial and agricultural activities). During the 20th century, nutrients loads have increased following the increase of both the global population and need of services. Alongside, climate change including temperature increase or atmospheric circulation change has occurred. These processes, Ecosystem state changes are hard to monitor and predict. To study the long-term changes of nutrients concentrations in coastal ecosystems, eleven French coastal ecosystems were studied over 20 years as they encompass large climatic and land pressures, representative of temperate ecosystems, over a rather small geographical area. Both univariate (time series decomposition) and multivariate (relationships between ecosystems and drivers) statistical analyses were used to determine ecosystem trajectories as well as typologies of ecosystem trajectories. It appeared that most of the French coastal ecosystems exhibited trajectories towards a decrease in nutrients concentrations. Differences in trajectories mainly depended on continental and human influences, as well as on climatic regimes. One single ecosystem exhibited very different trajectories, the Arcachon Bay with an increase in nutrients concentrations. Ecosystem trajectories based on ordination techniques were proven to be useful tools to monitor ecosystem changes. This study highlighted the importance of local environments and the need to couple uni- and multi-ecosystem studies. Although the studied ecosystems were influenced by both local and large-scale climate, by anthropogenic activities loads, and that their trajectories were mostly similar based on their continental influence, non-negligible variations resulted from their internal functioning., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)
Published: 2023
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50. Impact of Putative Probiotics on Growth, Behavior, and the Gut Microbiome of Farmed Arctic Char ( Salvelinus alpinus ).

Author: Knobloch S, Skírnisdóttir S, Dubois M, Kolypczuk L, Leroi F, Leeper A, Passerini D, and Marteinsson VÞ
Abstract: Beneficial bacteria promise to promote the health and productivity of farmed fish species. However, the impact on host physiology is largely strain-dependent, and studies on Arctic char ( Salvelinus alpinus ), a commercially farmed salmonid species, are lacking. In this study, 10 candidate probiotic strains were subjected to in vitro assays, small-scale growth trials, and behavioral analysis with juvenile Arctic char to examine the impact of probiotic supplementation on fish growth, behavior and the gut microbiome. Most strains showed high tolerance to gastric juice and fish bile acid, as well as high auto-aggregation activity, which are important probiotic characteristics. However, they neither markedly altered the core gut microbiome, which was dominated by three bacterial species, nor detectably colonized the gut environment after the 4-week probiotic treatment. Despite a lack of long-term colonization, the presence of the bacterial strains showed either beneficial or detrimental effects on the host through growth rate enhancement or reduction, as well as changes in fish motility under confinement. This study offers insights into the effect of bacterial strains on a salmonid host and highlights three strains, Carnobacterium divergens V41, Pediococcus acidilactici ASG16, and Lactiplantibacillus plantarum ISCAR-07436, for future research into growth promotion of salmonid fish through probiotic supplementation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Knobloch, Skírnisdóttir, Dubois, Kolypczuk, Leroi, Leeper, Passerini and Marteinsson.)
Published: 2022
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