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A model of fluff layer erosion and subsequent bed erosion in the presence of the bioturbator, Hydrobia ulvae ArchiMer
Orvain, Francis; Le Hir, Pierre; Sauriau, Pierre-guy.
Previous studies have shown that the gastropod Hydrobia ulvae destabilizes the top layers of fine-grained sediments. This process is mediated by the formation of a "biogenic" fluff layer that includes tracks, faecal pellets and mucus. This fluff layer has been shown to be easily resuspended before general bed erosion. In order to examine how fluff layer and bed. erosion interact, flume experiments were performed with fluid sediments of varying water contents. Ten thousand snails were placed and allowed to crawl for 5 h on the sediment surface, and then the resuspended sediment mass was measured in response to step-wise shear stress increases. Two distinct erosion phases were observed: (1) initial resuspension of the fluff layer and (2) the subsequent bed...
Tipo: Text Palavras-chave: Gastropoda; Erosion sediment; Bioturbation; Cohesive sediment; Marine sediment.
Ano: 2003 URL: http://archimer.ifremer.fr/doc/2003/publication-805.pdf
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A model of sediment transport under the influence of surface bioturbation: generalisation to the facultative suspension-feeder Scrobicularia plana ArchiMer
Orvain, Francis.
Flume experiments were designed to study how sediment erodibility was modified by the facultative suspension-feeder Scrobicularia plana living at different densities in sediment beds of various degrees of compaction. Two separate erosion phases were identified from the resuspension kinetics: (1) erosion of an unconsolidated surficial layer (i.e. fluff layer) and (2) the subsequent bed erosion. S. plana were found to influence both erosion phases: (1) erosion rates of the fluff layer were controlled by bioturbation activities, the extents of which were influenced by bivalve density and the degree of compaction of the sediments, and (2) critical thresholds of the subsequent bed erosion decreased as clam density increased, likely due to depressions in the...
Tipo: Text Palavras-chave: Resuspension; Model; Functional groups; Sediment transport; Bioturbation; Scrobicularia plana; Intertidal mudflat.
Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/publication-3776.pdf
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Accounting for Rough Bed Friction Factors of Mud Beds as a Result of Biological Activity in Erosion Experiments ArchiMer
Guizien, Katell; Orvain, Francis; Duchene, Jean-claude; Le Hir, Pierre.
The average bed shear stress and bed friction factor of samples with any roughness was derived from the head loss between upstream and downstream of a test section in an erosion tunnel. The method was validated in both hydraulically smooth (plexiglass; Reynolds number less than 25,000) and rough regimes (calibrated particles with known roughness). As a first step toward using this method on natural sediment, this method was tested with experimental mesocosms assembled from field collected materials (sieved sediments; diatoms). Bed shear stress measurement precision was high enough in the experiments to detect a positive significant relationship between bed friction factor and core roughness. The observed bed friction factor increase could be related to...
Tipo: Text Palavras-chave: Bed roughness; Friction factor; Mud beds; Biological activity; Erosion experiments.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00117/22807/20617.pdf
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Annual Phytoplankton Primary Production Estimation in a Temperate Estuary by Coupling PAM and Carbon Incorporation Methods ArchiMer
Morelle, Jerome; Schapira, Mathilde; Orvain, Francis; Riou, Philippe; Lopez, Pascal Jean; Pierre-duplessix, Olivier; Rabiller, Emilie; Maheux, Frank; Simon, Benjamin; Claquin, Pascal.
Phytoplankton primary production varies considerably with environmental parameters especially in dynamic ecosystems like estuaries. The aim of this study was to investigate short-term primary production along the salinity gradient of a temperate estuary over the course of 1 year. The combination of carbon incorporation and fluorescence methods enabled primary production estimation at short spatial and temporal scales. The electron requirement for carbon fixation was investigated in relation with physical-chemical parameters to accurately estimate primary production at high frequency. These results combined with the variability of the photic layer allowed the annual estimation of primary production along the estuary. Phytoplankton dynamics was closely...
Tipo: Text Palavras-chave: High frequency; Electron requirement for carbon fixation; Electron transport rate (ETR); Seine estuary.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00429/54020/55470.pdf
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Bacterial Dynamics in a Microphytobenthic Biofilm: a Tidal Mesocosm Approach ArchiMer
Agogue, Helene; Mallet, Clarisse; Orvain, Francis; De Crignis, Margot; Mornet, Francoise; Dupuy, Christine.
In intertidal mudflats, during low tide exposure, microphytobenthos (MPB) migrate vertically through the surface sediment and form, with the heterotrophic bacteria, a transient biofilm. Inside this biofilm, multiple interactions exist between MPB and bacteria. These micro-organisms secrete a wide range of extracellular polymeric substances (EPS), which are major components of the biofilm matrix. In this study, we used a tidal mesocosm experiment in order to decipher the interactions of the MPB-EPS-bacteria complex within the biofilm. We tried to determine if the EPS could control bacterial activities and/or production and/or richness according to the age of the biofilm and to the immersion/emersion period. The dynamics of biomasses of MPB and prokaryotes,...
Tipo: Text Palavras-chave: Muddy sediment; Microphytobenthos; Bacteria; Extracellular polymeric substances; Interactions; Mesocosm.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00181/29271/27682.pdf
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Connectivities with shellfish farms and channel rivers are associated with mortality risk in oysters ArchiMer
Gangnery, Aline; Normand, Julien; Duval, Cyrielle; Cugier, Philippe; Grangeré, Karine; Petton, Bruno; Petton, Sebastien; Orvain, Francis; Pernet, Fabrice.
Oyster diseases have major consequences on fisheries and aquaculture. In France, young Pacific oysters Crassostrea gigas are severely hit by the ostreid herpesvirus, whereas adults suffer mortalities presumably caused by pathogenic bacteria. Here we investigated the origin and spread of mortalities that affect both young and adult oysters, and we identified and compared their risk factors. Mortality was monitored in 2 age classes of oysters deployed in early spring at 39 sites spread over a 37 km2 surface area inside and outside of shellfish farms. Environmental data obtained from numerical modelling were used to investigate risk factors. Mortality of young oysters associated with ostreid herpesvirus occurred in the oyster farming area. Hydrodynamic...
Tipo: Text Palavras-chave: Aquaculture; Bivalve; Disease; Epidemiology and health; Ecological modelling; Hydrodynamic connectivity.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00588/69983/67896.pdf
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Dynamics of exopolymeric carbon pools in relation with phytoplankton succession along the salinity gradient of a temperate estuary (France) ArchiMer
Morelle, Jerome; Schapira, Mathilde; Francoise, Sylvaine; Courtay, Gaelle; Orvain, Francis; Claquin, Pascal.
In parallel to phytoplankton community dynamics, transparent exopolymeric particles (TEP) and exopolymeric substances (EPS) were investigated along the salinity gradient of a temperate estuary (Seine estuary, Normandy, France) over the course of a year. The phytoplankton community was mainly dominated by marine diatom species (especially Skeletonema sp., Nitzschia sp., and Paralia sulcata) associated with a spring bloom of pico-eukaryotes and the development of Cryptophyceae in summer. The decreases in species richness and salinity were correlated along the estuary and a significant exponential relationship between species richness and primary production was identified. Concentrations of TEP and EPS (soluble and bound carbohydrates) are highly dynamic in...
Tipo: Text Palavras-chave: Picophytoplankton; Nanophytoplankton; Exopolymeric substances; Species richness.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00440/55189/56645.pdf
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Environmental and behavioural factors affecting activity in the intertidal gastropod Hydrobia ulvae ArchiMer
Orvain, Francis; Sauriau, Pierre-guy.
Laboratory microcosms were used to investigate the mud snail Hydrobia ulvac (Pennant) bioturbation activities and behavioural changes in response to snail density, algal food, sediment moisture content, light regime and water cover conditions. Density-dependent kinetics of bioturbated muddy areas were described by von Bertalanffy equations, which provided reliable estimates of mud surface covering rates by snail tracks (m(2) h(-1) snail(-1)), Snails need a wet habitat to be active either covered by seawater or by moving in fluid layers for low-tide conditions. Light and microphytobenthic biomass, which are less potent to affect snail activity, are positively interrelated to increase covering rates in the tested chl a concentrations within the range of 1 -...
Tipo: Text Palavras-chave: Modelling; Intertidal mudflat; Hydrobia ulvae; Environmental factors; Bioturbation; Behaviour.
Ano: 2002 URL: http://archimer.ifremer.fr/doc/2002/publication-3775.pdf
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Impact of Chronic and Massive Resuspension Mechanisms on the Microphytobenthos Dynamics in a Temperate Intertidal Mudflat ArchiMer
Savelli, Raphael; Bertin, X.; Orvain, Francis; Gernez, P.; Dale, A.; Coulombier, T.; Pineau, P.; Lachaussée, N.; Polsenaere, Pierre; Dupuy, C.; Le fouest, V..
Microphytobenthos (MPB) resuspension is a key mechanism in the transfer of organic matter from productive intertidal mudflats to terrestrial and marine systems. In this study, we infer on the contribution of physical and biological factors involved in the MPB resuspension. We use a physical‐biological coupled model forced by realistic meteorological and hydrodynamical forcings to simulate chronic (without any concomitant sediment resuspension) and massive (driven by bed failure) resuspension over a year. The model simulates mud surface temperature, MPB growth, and grazing by the gastropod Peringia ulvae. The model suggests that MPB resuspension is the highest in spring tides and at the flood beginning due to high current velocity and low water heights that...
Tipo: Text Palavras-chave: Microphytobenthos; Mudflat; Resuspension; Physical-biological coupling; Numerical modeling.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00599/71114/69416.pdf
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Interacting effects of Hydrobia ulvae bioturbation and microphytobenthos on the erodibility of mudflat sediments ArchiMer
Orvain, Francis; Sauriau, Pierre-guy; Sygut, A; Joassard, Lucette; Le Hir, Pierre.
Microphytobenthos-macrofauna sediment interactions and their effects on sediment erodability were examined in laboratory experiments. Sediment beds were manipulated in a tidal mesocosm to produce diatom mats in exponential or in stationary phases of development after 6, 8 or 11 d of culture. These sediment beds were used in flume experiments to investigate the influence of bioturbation by the gastropod Hydrobia ulvae on both sediment and pigment resuspension as a function of the physiological state of the microphytobenthic mats. In most experiments, only a surface layer was resuspended. A model was used to analyse in detail the contribution of each variable to this surface-layer erosion. Bioturbation was the major factor controlling resuspension, and its...
Tipo: Text Palavras-chave: Sediment; Bioturbation; Erosion; Model; Hydrobia ulvae; Physiological state; Microphytobenthos; Resuspension.
Ano: 2004 URL: http://archimer.ifremer.fr/doc/2004/publication-3780.pdf
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Microbial interactions in marine water amended by eroded benthic biofilm: A case study from an intertidal mudflat ArchiMer
Montanie, Helene; Ory, Pascaline; Orvain, Francis; Delmas, Daniel; Dupuy, Christine; Hartmann, Hans J..
In shallow macrotidal ecosystems with large intertidal mudflats, the sediment-water coupling plays a crucial role in structuring the pelagic microbial food web functioning, since inorganic and organic matter and microbial components (viruses and microbes) of the microphytobenthic biofilm can be suspended toward the water column. Two experimental bioassays were conducted in March and July 2008 to investigate the importance of biofilm input for the pelagic Microbial and Viral Loops. Pelagic inocula (< 0.6 μ- and < 10 μ filtrates) were diluted either with < 30 kDa-ultrafiltered seawater or with this ultrafiltrate enriched with the respective size-fractionated benthic biofilm or with < 30 kDa-benthic compounds (BC). The kinetics of heterotrophic...
Tipo: Text Palavras-chave: Mudflats; Virus; Bacteria; HNF; Coastal water.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00166/27691/25883.pdf
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Modelling the effects of macrofauna on sediment transport and bed elevation: Application over a cross-shore mudflat profile and model validation ArchiMer
Orvain, Francis; Le Hir, Pierre; Sauriau, Pierre-guy; Lefebvre, Sebastien.
Tipo: Text Palavras-chave: Modelling; Sediment dynamics; Erodability; Bioturbation; Macrofauna; Biota; Sediment stability.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00079/19055/18610.pdf
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Optimising extraction of extracellular polymeric substances (EPS) from benthic diatoms: comparison of the efficiency of six EPS extraction methods ArchiMer
Takahashi, Eri; Ledauphin, Jerome; Goux, Didier; Orvain, Francis.
There is no universal method that can be applied to extract bound extracellular polymeric substances (EPS) from benthic diatoms of intertidal sediments without causing cell lysis. Six extraction methods were tested on a diatom culture of Navicula jeffreyi to establish the best compromise between high yields of carbohydrate extraction and minimum cell lysis. Extraction with distilled water provoked cell lysis (as already known). The five other extraction methods (dowex resin, artificial seawater of half salinity and extractions after pretreatment with gluteraldehyde by three methods: water, dowex water and dowex buffer) did not provoke cell lysis as shown by transmission electronic microscopy. This result was confirmed by the minimum release of internal...
Tipo: Text Palavras-chave: Transmission electron microscopy; Protein; Navicula jeffreyi; Intertidal sediments; Immuno staining; Immunostaining; GCMS analysis; Dowex; Cell lysis; Biofilm.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-7418.pdf
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Regional and latitudinal patterns of soft-bottom macrobenthic invertebrates along French coasts: Results from the RESOMAR database ArchiMer
Gallon, Regis K.; Lavesque, Nicolas; Grall, Jacques; Labrune, Celine; Gremare, Antoine; Bachelet, Guy; Blanchet, Hugues; Bonifacio, Paulo; Bouchet, Vincent M. P.; Dauvin, Jean-claude; Desroy, Nicolas; Gentil, Franck; Guerin, Laurent; Houbin, Celine; Jourde, Jerome; Laurand, Sandrine; Le Duff, Michel; Le Garrec, Vincent; De Montaudouin, Xavier; Olivier, Frederic; Orvain, Francis; Sauriau, Pierre-guy; Thiebaut, Eric; Gauthier, Olivier.
This study aims to describe the patterns of soft bottom macrozoobenthic richness along French coasts. It is based on a collaborative database developed by the “Réseau des Stations et Observatoires Marins” (RESOMAR). We investigated patterns of species richness in sublittoral soft bottom habitats (EUNIS level 3) at two different spatial scales: 1) seaboards: English Channel, Bay of Biscay and Mediterranean Sea and 2) 0.5° latitudinal and longitudinal grid. Total observed richness, rarefaction curves and three incidence-based richness estimators (Chao2, ICE and Jacknife1) were used to compare soft bottom habitats species richness in each seaboard. Overall, the Mediterranean Sea has the highest richness and despite higher sampling effort, the English Channel...
Tipo: Text Palavras-chave: Zoobenthos; Species richness; Regional pattern; Latitudinal pattern; Soft-bottom; France.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00376/48769/49166.pdf
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Sequential resuspension of biofilm components (viruses, prokaryotes and protists) as measured by erodimetry experiments in the Brouage mudflat (French Atlantic coast) ArchiMer
Dupuy, Christine; Mallet, Clarisse; Guizien, Katell; Montanie, Helene; Breret, Martine; Mornet, Francoise; Fontaine, Camille; Nerot, Caroline; Orvain, Francis.
Resuspension thresholds in terms of friction velocity were experimentally quantified for the prokaryotes, protists and for the first time, viruses of intertidal mudflat biofilms. Differences in resuspension thresholds could be related to the type, behaviour and size of microorganisms and their association with particles. Free microorganisms (viruses, bacteria and some nanoflagellates) were resuspended by weak flow at friction velocities lower than 2 cm s- 1. Chlorophyll a, some nanoflagellates and attached bacteria were resuspended together with the bed’s muddy sediment, which required friction velocities larger than 3 cm s- 1. Diatoms smaller than 60 μm were resuspended at velocities between 3 and 5 cm s- 1, while those larger than 60 μm were resuspended...
Tipo: Text Palavras-chave: Viruses; Microorganisms; Resuspension; Benthic-pelagic coupling; Spatial distribution; Mudflat.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00168/27922/26196.pdf
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Small-scale spatial variability of food partitioning between cultivated oysters and associated suspension-feeding species, as revealed by stable isotopes ArchiMer
Dubois, Stanislas; Orvain, Francis; Marin Leal, Julio César; Ropert, Michel; Lefebvre, Sébastien.
Oyster culture structures support a host of epibionts belonging to the same suspension-feeding guild, which are considered to be potential competitors for food with cultivated oysters. In an intertidal shellfish ecosystem on the northern French coast, an approach based on stable isotopes (C-13 and N-15) was used to investigate intra- and interspecific food resource partitioning among cultivated oysters and the main associated wild sessile epibionts such as polychaetes, barnacles, mussels and ascidians. The main objective of the present study was to determine inter- and intraspecific food partitioning, along with small-scale spatial variability, within the guild of suspension feeders. We demonstrated that interspecific competition was limited among...
Tipo: Text Palavras-chave: Trophic plasticity; Spatial variability; Stable isotopes; Sessile epibionts; Oysters; Shellfish.
Ano: 2007 URL: http://archimer.ifremer.fr/doc/2007/publication-2626.pdf
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Spatial and temporal interaction between sediment and microphytobenthos in a temperate estuarine macro-intertidal bay ArchiMer
Orvain, Francis; Lefebvre, Sebastien; Montepini, J.; Sebire, M.; Gangnery, Aline; Sylvand, B..
Intertidal flats of the estuarine macro-intertidal Baie des Veys (France) were investigated to identify spatial features of sediment and microphytobenthos (MPB) in April 2003. Gradients occurred within the domain, and patches were identified close to vegetated areas or within the oyster-farming areas where calm physical conditions and biodeposition altered the sediment and MPB landscapes. Spatial patterns of chl a content were explained primarily by the influence of sediment features, while bed elevation and compaction brought only minor insights into MPB distribution regulation. The smaller size of MPB patches compared to silt patches revealed the interplay between physical structure defining the sediment landscape, the biotic patches that they contain,...
Tipo: Text Palavras-chave: Benthic diatoms; Benthos; Coastal ecosystems; Intertidal flats; Baie des Veys; Normandie; Spatial pattern; Geostatistics; Kriging.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00088/19945/17598.pdf
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Spatial Variability of Benthic-Pelagic Coupling in an Estuary Ecosystem: Consequences for Microphytobenthos Resuspension Phenomenon ArchiMer
Ubertini, Martin; Lefebvre, Sebastien; Gangnery, Aline; Grangere, Karine; Le Gendre, Romain; Orvain, Francis.
The high degree of physical factors in intertidal estuarine ecosystem increases material processing between benthic and pelagic compartments. In these ecosystems, microphytobenthos resuspension is a major phenomenon since its contribution to higher trophic levels can be highly significant. Understanding the sediment and associated microphytobenthos resuspension and its fate in the water column is indispensable for measuring the food available to benthic and pelagic food webs. To identify and hierarchize the physical/biological factors potentially involved in MPB resuspension, the entire intertidal area and surrounding water column of an estuarine ecosystem, the Bay des Veys, was sampled during ebb tide. A wide range of physical parameters (hydrodynamic...
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Ano: 2012 URL: http://archimer.ifremer.fr/doc/00090/20126/17775.pdf
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Spatio-temporal variations in intertidal mudflat erodability: Marennes-Oleron Bay, western France ArchiMer
Orvain, Francis; Sauriau, Pierre-guy; Le Hir, Pierre; Guillou, Gael; Cann, Philippe; Paillard, Michel.
A portable erosion device (ERIS) was deployed in November 2000 and May 2001 to investigate the spatio-temporal variation of fine-grained sediment erosion over a transect on the intertidal mudflats of Marennes-Oleron Bay, western France. The objective was to relate changes in bed erodability over diurnal emersion periods to bioturbation, rapid changes in sediment characteristics, and microphytobenthos biomass. Macrofaunal assemblages were dominated by the bivalve, Scrobicularia plana, on the upper mudflat, and by the gastropod, Hydrobia ulvae. on the middle mudflat. A power relationship was obtained where tau(cr) was plotted as a function of sediment density. Results from the upper part of the mudflat deviated from this relationship due to bioturbation by...
Tipo: Text Palavras-chave: EPS; Microphytobenthos; Erodability; Intertidal mudflat; Sediment; Scrobicularia plana; Hydrobia ulvae; Bioturbation; Resuspension; Eris.
Ano: 2007 URL: http://archimer.ifremer.fr/doc/2007/publication-3779.pdf
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Stable isotopes (delta C-13, delta N-15) and modelling as tools to estimate the trophic ecology of cultivated oysters in two contrasting environments ArchiMer
Leal, J; Dubois, Stanislas; Orvain, Francis; Galois, Robert; Blin, J; Ropert, Michel; Bataille, M; Ourry, A; Lefebvre, S.
Food sources for cultivated marine bivalves generally are not well identified, although they are essential for a better understanding of coastal ecosystems and for the sustainability of shellfish farming activities. In addition to phytoplankton, other organic matter sources (OMS), such as microphytobenthos and detritus (of terrestrial or marine origins), can contribute significantly to the growth of marine bivalves. The aim of this study was to identify the potential food sources and to estimate their contributions to the growth of the Pacific oyster (Crassostrea gigas) in two contrasting trophic environments of Normandy (France): the Baie des Veys (BDV) and the Lingreville area (LIN). Two sites were studied in the BDV area (BDV-S and BDV-N) and one in the...
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Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4621.pdf
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