Recursos de colección

ArchiMer, Institutional Archive of Ifremer (French Research Institute for Exploitation of the Sea) (10.107 recursos)

Archimer, is the institutional repository of Ifremer (French Research Institute for Exploitation of the Sea). It provides freely available scientific or technical documents online (publications, theses, conference proceedings, etc) in all fields related to oceans (oceanography, aquaculture, fisheries, etc). The site is available in French and English.


Mostrando recursos 1 - 20 de 245

  1. Detection and distribution of ostreid herpesvirus 1 in experimentally infected Pacific oyster spat

    Segarra, Amelie; Baillon, Laury; Faury, Nicole; Tourbiez, Delphine; Renault, Tristan
    High mortality rates are reported in spat and larvae of Pacific oyster Crassostrea gigas and associated with ostreid herpesvirus 1 (OsHV-1) detection in France. Although the viral infection has been experimentally reproduced in oyster larvae and spat, little knowledge is currently available concerning the viral entry and its distribution in organs and tissues. This study compares OsHV-1 DNA and RNA detection and localization in experimentally infected oysters using two virus doses: a low dose that did not induce any mortality and a high dose inducing high mortality. Real time PCR demonstrated significant differences in terms of viral DNA amounts between...

  2. Ecological indicators to capture the effects of fishing on biodiversity and conservation status of marine ecosystems

    Coll, M.; Shannon, L. J.; Kleisner, K. M.; Juan-jorda, M. J.; Bundy, A.; Akoglu, A. G.; Banaru, Daniela; Boldt, J. L.; Borges, M. F.; Cook, A.; Diallo, I.; Fu, C.; Fox, C.; Gascuel, D.; Gurney, L. J.; Hattab, T.; Heymans, J. J.; Jouffre, D.; Knight, B. R.; Kucukavsar, S.; Large, S. I.; Lynam, C.; Machias, A.; Marshall, K. N.; Masski, H.; Ojaveer, H.; Piroddi, C.; Tam, J.; Thiao, D.; Thiaw, M.; Torres, M. A.; Travers-trolet, Morgane; Tsagarakis, K.; Tuck, I.; Van Der Meeren, G. I.; Yemane, D.; Zador, S. G.; Shin, Y. -j.
    IndiSeas (“Indicators for the Seas”) is a collaborative international working group that was established in 2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data availability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii) mean maximum life span of surveyed fish species,...

  3. First evidence for a Vibrio strain pathogenic to Mytilus edulis altering hemocyte immune capacities

    Ben Cheikh, Yosra; Travers, Marie-agnes; Morga, Benjamin; Godfrin, Yoann; Rioult, Damien; Le Foll, Franck
    Bacterial isolates were obtained from mortality events affecting Mytilus edulis and reported by professionals in 2010-2013 or from mussel microflora. Experimental infections allowed the selection of two isolates affiliated to V. splendidus/V. hemicentroti type strains: a virulent 10/068 1T1 (76,6% and 90% mortalities in 24h and 96h) and an innocuous 12/056 M24T1 (0% and 23,3% in 24h and 96h). These two strains were GFP-tagged and validated for their growth characteristics and virulence as genuine models for exposure. Then, host cellular immune responses to the microbial invaders were assessed. In the presence of the virulent strain, hemocyte motility was instantaneously enhanced...

  4. Using a spatially structured life cycle model to assess the influence of multiple stressors on an exploited coastal-nursery-dependent population

    Archambault, B.; Rivot, E.; Savina-rolland, Marie; Le Pape, Olivier
    Exploited coastal-nursery-dependent fish species are subject to various stressors occurring at specific stages of the life cycle: climate-driven variability in hydrography determines the success of the first eggs/larvae stages; coastal nursery habitat suitability controls juvenile growth and survival; and fisheries target mostly adults. A life cycle approach was used to quantify the relative influence of these stressors on the Eastern English Channel (EEC) population of the common sole (Solea solea), a coastal-nursery-dependent flatfish population which sustains important fisheries. The common sole has a complex life cycle: after eggs hatch, larvae spend several weeks drifting in open water. Survivors go on...

  5. Low incidence of clonality in cold water corals revealed through the novel use of standardized protocol adapted to deep sea sampling

    Becheler, Ronan; Cassone, Anne-laure; Noël, Philippe; Mouchel, Olivier; Morrison, Cheryl L.; Arnaud-haond, Sophie
    Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata. Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay,...

  6. Compte rendu de la campagne RREX 2015. N/O Thalassa 5 juin 2015 - 10 Juillet 2015

    Thierry, Virginie; Branellec, Pierre; Leizour, Stephane; Hamon, Michel

  7. Sole larval supply to coastal nurseries: Interannual variability and connectivity at interregional and interpopulation scales

    Savina-, Marie; Lunghi, Mathias; Archambault, B.; Baulier, Loic; Huret, Martin; Le Pape, Olivier
    Simulating fish larval drift helps assess the sensitivity of recruitment variability to early life history. An individual-based model (IBM) coupled to a hydrodynamic model was used to simulate common sole larval supply from spawning areas to coastal and estuarine nursery grounds at the meta-population scale (4 assessed stocks), from the southern North Sea to the Bay of Biscay (Western Europe) on a 26-yr time series, from 1982 to 2007. The IBM allowed each particle released to be transported by currents, to grow depending on temperature, to migrate vertically depending on development stage, to die along pelagic stages or to settle...

  8. The interplay between tectonics, sediment dynamics and gateways evolution in the Danube system from the Pannonian Basin to the western Black Sea

    Matenco, Liviu; Munteanu, Ioan; Ter Borgh, Marten; Stanica, Adrian; Tilita, Marius; Lericolais, Gilles; Dinu, Corneliu; Oaie, Gheorghe
    Understanding the natural evolution of a river–delta–sea system is important to develop a strong scientific basis for efficient integrated management plans. The distribution of sediment fluxes is linked with the natural connection between sediment source areas situated in uplifting mountain chains and deposition in plains, deltas and, ultimately, in the capturing oceans and seas. The Danube River–western Black Sea is one of the most active European systems in terms of sediment re-distribution that poses significant societal challenges. We aim to derive the tectonic and sedimentological background of human-induced changes in this system and discuss their interplay. This is obtained by...

  9. Unexpected Levels of Biological Activity during the Polar Night Offer New Perspectives on a Warming Arctic

    Berge, Jorgen; Daase, Malin; Renaud, Paul E.; Ambrose, William G., Jr.; Darnis, Gerald; Last, Kim S.; Leu, Eva; Cohen, Jonathan H.; Johnsen, Geir; Moline, Mark A.; Cottier, Finlo; Varpe, Oystein; Shunatova, Natalia; Balazy, Piotr; Morata, Nathalie; Massabuau, Jean-charles; Falk-petersen, Stig; Kosobokova, Ksenia; Hoppe, Clara J. M.; Weslawski, Jan Marcin; Kuklinski, Piotr; Legezynska, Joanna; Nikishina, Daria; Cusa, Marine; Kedra, Monika; Wlodarska-kowalczuk, Maria; Vogedes, Daniel; Camus, Lionel; Tran, Damien; Michaud, Emma; Gabrielsen, Tove M.; Granovitch, Andrei; Gonchar, Anya; Krapp, Rupert; Callesen, Trine A.
    The current understanding of Arctic ecosystems is deeply rooted in the classical view of a bottom-up controlled system with strong physical forcing and seasonality in primary-production regimes. Consequently, the Arctic polar night is commonly disregarded as a time of year when biological activities are reduced to a minimum due to a reduced food supply. Here, based upon a multidisciplinary ecosystem-scale study from the polar night at 79 degrees N, we present an entirely different view. Instead of an ecosystem that has entered a resting state, we document a system with high activity levels and biological interactions across most trophic levels....

  10. A coupled movement and bioenergetics model to explore the spawning migration of anchovy in the Bay of Biscay

    Politikos, Dimitrios; Huret, Martin; Petitgas, Pierre
    Adult anchovies in the Bay of Biscay perform north to south migration from late winter to early summer for spawning. However, what triggers and drives the geographic shift of the population remains unclear and poorly understood. An individual-based fish model has been implemented to explore the potential mechanisms that control anchovy's movement routes toward its spawning habitats. To achieve this goal, two fish movement behaviors – gradient detection through restricted area search and kinesis – simulated fish response to its dynamic environment. A bioenergetics model was used to represent individual growth and reproduction along the fish trajectory. The environmental forcing...

  11. Trophic niche overlap of sprat and commercial small pelagic teleosts in the Gulf of Lions (NW Mediterranean Sea)

    Le Bourg, B.; Banaru, Daniela; Saraux, Claire; Nowaczyk, A.; Le Luherne, E.; Jadaud, Angelique; Bigot, Jean-louis; Richard, P.
    Increasing abundance of non-commercial sprats and decreasing biomass and landings of commercial anchovies and sardines justify the need to study the feeding ecology and trophic niche overlap of these planktivorous species in the Gulf of Lions. Their diet has been investigated on the basis of stomach content and stable isotope analyses in 2011 and 2012 according to different depths and regions in the study area. The main prey were Corycaeidae copepods, Clauso/Paracalanus, Euterpina acutifrons and Microsetella, for sprats and small copepods, such as Microsetella, Oncaea and Corycaeidae, for anchovies and sardines. This is the first time that the diet of...

  12. Assessment of SARAL/AltiKa Wave Height Measurements Relative to Buoy, Jason-2, and Cryosat-2 Data

    Hito Sepulveda, Hector; Queffeulou, Pierre; Ardhuin, Fabrice
    SARAL/AltiKa GDR-T are analyzed to assess the quality of the significant wave height (SWH) measurements. SARAL along-track SWH plots reveal cases of erroneous data, more or less isolated, not detected by the quality flags. The anomalies are often correlated with strong attenuation of the Ka-band backscatter coefficient, sensitive to clouds and rain. A quality test based on the 1Hz standard deviation is proposed to detect such anomalies. From buoy comparison, it is shown that SARAL SWH is more accurate than Jason-2, particularly at low SWH, and globally does not require any correction. Results are better with open ocean than with...

  13. Geochemistry and mineralogy of a silica chimney from an inactive seafloor hydrothermal field (East Pacific Rise, 18°S)

    Dekov, V. M.; Lalonde, Stefan; Kamenov, G. D.; Bayon, Germain; Shanks, W. C., Iii; Fortin, D.; Fouquet, Yves; Moscati, R. J.
    An inactive vent field comprised of dead chimneys was discovered on the ultrafast East Pacific Rise (EPR) at 18°S during the research campaign NAUDUR with the R/V Le Nadir in December 1993. One of these chimneys was sampled, studied and found to be largely composed of silica-mineralized bacterial-like filaments. The filaments are inferred to be the result of microbial activity leading to silica (± Fe-oxyhydroxide) precipitation. The chimney grew from the most external layer (precipitated 226 ± 4 yr. B.P.) towards the central chimney conduit. Hydrothermal activity ceased 154 ± 13 yr. B.P. and the chimney conduit was completely sealed....

  14. Effects of density dependence, zooplankton and temperature on blue whiting Micromesistius poutassou growth

    Trenkel, Verena; Lorance, Pascal; Fassler, S. M. M.; Hoines, A. S.
    Blue whiting Micromesistius poutassou mean total length at age in the north-east Atlantic Ocean was found to vary by around ±6% during the period 2004–2011 and mean mass at age by ±22% during the years 1981–2013. Linear modelling provided strong evidence that these phenotypic growth variations can be explained by trophic conditions, mainly negative density dependence and also food availability, and a negative long-term temperature effect on asymptotic siz

  15. Nickel isotope fractionation during laterite Ni ore smelting and refining: implications for tracing the sources of Ni in smelter-affected soils

    Ratie, G.; Quantin, C.; Jouvin, D.; Calmels, D.; Ettler, V.; Sivry, Y.; Cruz Vieira, L.; Ponzevera, Emmanuel; Garnier, J.
    Nickel isotope ratios were measured in ores, fly ash, slags and FeNi samples from two metallurgical plants located in the Goiás State, Brazil (Barro Alto, Niquelândia). This allowed investigating the mass-dependent fractionation of Ni isotopes during the Ni-laterite ore smelting and refining. Feeding material exhibits a large range of δ60Ni values (from 0.02 ± 0.10 ‰ to 0.20 ± 0.05 ‰, n=7), explained by the diversity of Ni-bearing phases, and the average of δ60Nifeeding materials was found equal to 0.08 ± 0.08‰ (2SD, n=7). Both δ60Ni values of fly ash (δ60Ni = 0.07 ± 0.07‰, n=10) and final FeNi produced...

  16. Observations of turbulence within the surf and swash zone of a field-scale sandy laboratory beach

    Brinkkemper, J.a.; Lanckriet, T.; Grasso, Florent; Puleo, J.a.; Ruessink, B.g.
    Current coastal-evolution models generally lack the ability to accurately predict bed level change in shallow (<~2 m) water, which is, at least partly, due to the preclusion of the effect of surface-induced turbulence on sand suspension and transport. As a first step to remedy this situation, we investigated the vertical structure of turbulence in the surf and swash zone using measurements collected under random shoaling and plunging waves on a steep (initially 1:15) field-scale sandy laboratory beach. Seaward of the swash zone, turbulence was measured with a vertical array of three Acoustic Doppler Velocimeters (ADVs), while in the swash zone...

  17. X-Linked Retinitis Pigmentosa 2 Is a Novel Maternal-Effect Gene Required for Left-Right Asymmetry in Zebrafish

    Desvignes, Thomas; Nguyen, Thaovi; Chesnel, Franck; Bouleau, Aurelien; Fauvel, Christian; Bobe, Julien
    Retinitis pigmentosa 2 (RP2) gene is responsible for up to 20% of X-linked retinitis pigmentosa, a severe heterogeneous genetic disorder resulting in progressive retinal degeneration in humans. In vertebrates, several bodies of evidence have clearly established the role of Rp2 protein in cilia genesis and/or function. Unexpectedly, some observations in zebrafish have suggested the oocyte-predominant expression of the rp2 gene, a typical feature of maternal-effect genes. In the present study, we investigate the maternal inheritance of rp2 gene products in zebrafish eggs in order to address whether rp2 could be a novel maternal-effect gene required for normal development. Although both...

  18. The estuarine geochemical reactivity of Zn isotopes and its relevance for the biomonitoring of anthropogenic Zn and Cd contaminations from metallurgical activities: Example of the Gironde fluvial-estuarine system, France

    Petit, Jerome C. J.; Schafer, Jörg; Coynel, Alexandra; Blanc, Gerard; Chiffoleau, Jean-francois; Auger, Dominique; Bossy, Cecile; Derriennic, Herve; Mikolaczyk, Mathilde; Dutruch, Lionel; Mattielli, Nadine
    Zinc stable isotopes measurements by MC-ICP-MS, validated by laboratory intercalibrations, were performed on wild oysters, suspended particles and filtered river/estuarine water samples to provide new constraints for the use of Zn isotopes as environmental tracers. The samples selected were representative of the long range (400 km) transport of metal (Zn, Cd, etc.) contamination from former Zn-refining activities at Decazeville (i.e. δ66Zn > 1 ‰) and its phasing out, recorded during 30 years in wild oysters from the Gironde Estuary mouth (RNO/ROCCH sample bank). The study also addresses additional anthropogenic sources (urban and viticulture) and focuses on geochemical reactivity of Zn...

  19. Rare earth elements and neodymium isotopes in world river sediments revisited

    Bayon, Germain; Toucanne, Samuel; Skonieczny, Charlotte; Andre, L.; Bermell, Sylvain; Cheron, Sandrine; Dennielou, Bernard; Etoubleau, Joel; Freslon, Nicolas; Gauchery, T.; Germain, Yoan; Jorry, Stephan; Menot, G.; Monin, L.; Ponzevera, Emmanuel; Rouget, M. -l.; Tachikawa, K.; Barrat, Jean-alix
    Over the past decades, rare earth elements (REE) and their radioactive isotopes have received tremendous attention in sedimentary geochemistry, as tracers for the geological history of the continental crust and provenance studies. In this study, we report on elemental concentrations and neodymium (Nd) isotopic compositions for a large number of sediments collected near the mouth of rivers worldwide, including some of the world’s major rivers. Sediments were leached for removal of non-detrital components, and both clay and silt fractions were retained for separate geochemical analyses. Our aim was to re-examine, at the scale of a large systematic survey, whether or...

  20. Two “pillars” of cold-water coral reefs along Atlantic European margins: Prevalent association of Madrepora oculata with Lophelia pertusa, from reef to colony scale

    Arnaud-haond, Sophie; Van Den Beld, Inge; Becheler, Ronan; Orejas, C.; Menot, Lenaick; Frank, N.; Grehan, A.; Bourillet, Jean-francois
    The scleractinian coral Lophelia pertusa has been the focus of deep-sea research since the recognition of the vast extent of coral reefs in North Atlantic waters two decades ago, long after their existence was mentioned by fishermen. These reefs where shown to provide habitat, concentrate biomass and act as feeding or nursery grounds for many species, including those targeted by commercial fisheries. Thus, the attention given to this cold-water coral (CWC) species from researchers and the wider public has increased. Consequently, new research programs triggered research to determine the full extent of the corals geographic distribution and ecological dynamics of...

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