%0 Journal Article %J Biofouling %D 2021 %T Influence of infrastructure material composition and microtopography on marine biofilm growth and photobiology %A Vivier, Baptiste %A Pascal Claquin %A Lelong, Christophe %A Lesage, Quentin %A Peccate, Mathias %A Hamel, Bastien %A Georges, Marine %A Bourguiba, Amel %A Sebaibi, Nassim %A Boutouil, Mohamed %A Goux, Didier %A Dauvin, Jean-Claude %A Francis Orvain %B Biofouling %P 1 - 17 %8 Apr-08-2022 %G eng %U https://www.tandfonline.com/doi/full/10.1080/08927014.2021.1959918 %! Biofouling %R 10.1080/08927014.2021.1959918 %0 Journal Article %J Global Ecology and Conservation %D 2021 %T Marine artificial reefs, a meta-analysis of their design, objectives and effectiveness %A Vivier, Baptiste %A Dauvin, Jean-Claude %A Navon, Maxime %A Anne-Marie Rusig %A Isabelle Mussio %A Francis Orvain %A Boutouil, Mohamed %A Pascal Claquin %B Global Ecology and Conservation %P e01538 %8 Jan-03-2021 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S2351989421000883 %! Global Ecology and Conservation %R 10.1016/j.gecco.2021.e01538 %0 Journal Article %J Science of The Total Environment %D 2020 %T Does parasitism influence sediment stability? Evaluation of trait-mediated effects of the trematode Bucephalus minimus on the key role of cockles Cerastoderma edule in sediment erosion dynamics %A Dairain, Annabelle %A Maire, Olivier %A Meynard, Guillaume %A Francis Orvain %B Science of The Total Environment %V 733 %P 139307 %8 Jan-09-2020 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0048969720328242 %! Science of The Total Environment %R 10.1016/j.scitotenv.2020.139307 %0 Journal Article %J PLOS ONE %D 2020 %T Evidence for better microphytobenthos dynamics in mixed sand/mud zones than in pure sand or mud intertidal flats (Seine estuary, Normandy, France) %A Morelle, Jérôme %A Pascal Claquin %A Francis Orvain %X Understanding the dynamics of microphytobenthos biomass and photosynthetic performances in intertidal ecosystems will help advance our understanding of how trophic networks function in order to optimize ecological management and restoration projects. The main objective of this study was to investigate microphytobenthic biomass and photosynthetic performances as a function of the sedimentary and environmental variabilities in the range of intertidal habitats in the downstream Seine estuary (Normandy, France). Our results highlight higher biomass associated with more stratified biofilms and better photosynthetic performances in areas characterized by a sand/mud mixture (40–60% of mud) compared to pure sand or pure mud environments. This type of sediment probably offers an efficient trade-off between the favorable characteristics of the two types of sediments (sand and mud) with respect to light penetration and nutrient accessibility. Moreover, the large quantities of exopolysaccharides produced in sand/mud mixtures emphasizes the functional role played by microphytobenthos in promoting sediment stability against erosion. This allows us to show that despite the strong increase in sand content of the downstream Seine estuary, intertidal flats are still productive since microphytobenthic biomass, photosynthetic performances and exopolysaccharides secretion are highest in sand-mud mixtures. This study also underlines the impact of ecosystem modifications due to human disturbance and climate change on the dynamics of key primary producers in estuaries. %B PLOS ONE %V 15 %P e0237211 %8 08/2020 %G eng %N 8 %R 10.1371/journal.pone.0237211 %0 Journal Article %J Marine Environmental Research %D 2020 %T Sediment stability: can we disentangle the effect of bioturbating species on sediment erodibility from their impact on sediment roughness? %A Dairain, Annabelle %A Maire, Olivier %A Meynard, Guillaume %A Richard, Anaïs %A Rodolfo-Damiano, Tiffany %A Francis Orvain %B Marine Environmental Research %V 162 %P 105147 %8 Jan-12-2020 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0141113620305055 %! Marine Environmental Research %R 10.1016/j.marenvres.2020.105147 %0 Journal Article %J Marine Environmental Research %D 2019 %T Modelling the functioning of a coupled microphytobenthic-EPS-bacterial system in intertidal mudflats %A Rakotomalala, C %A Katell Guizien %A Karine Grangeré %A Sébastien Lefebvre %A Christine Dupuy %A Francis Orvain %K Bacillariophyta %K bacteria %K Bacteria (microorganisms) %K bacterial growth %K bacterium %K Biogeochemical modeling %K biogeochemistry %K Biomass %K Carbon %K Carbon and nitrogen %K Carbon and nitrogen ratios %K Diatom %K diel vertical migration %K exopolymer %K Experimental conditions %K Extracellular polymeric substances %K intertidal environment %K intertidal zone %K light %K mesocosm %K microbial community %K Microphytobenthos %K Migration %K modeling %K mudflat %K Nitrogen %K nonhuman %K Nutrient availability %K Nutrients %K nutritional requirement %K organic carbon %K organismal interaction %K Photosynthesis %K Phytobenthos %K Phytoplankton %K polymer %K Review %K simulation %K tide %K vertical migration %X A mechanistic and biogeochemical model was developed to analyze the interactions between microphytobenthos (MPB), bacteria and nutrients in a tidal system. Behavioral vertical migration was hypothesized as being controlled by exogenous factors (tide and light) but also by endogenous factors (carbon and nitrogen requirements). The secretion of Extracellular Polymeric Substances (EPS) during photosynthesis (overflow metabolism) and migration of diatoms was also formulated. Similarities in MPB dynamics between observations and simulations support the assumption that carbon and nitrogen ratios are additional key processes behind the vertical migration of diatoms in the sediment. The model satisfactorily reproduced the three growth phases of the MPB development observed in a mesocosm (the lag phase, the logarithmic growth, and the plateau). Besides, nutrient availability, which could be induced by faunal bioturbation, significantly determined the extent of MPB biomass and development. The plateau phase observed in the last days of simulations appeared to be attributed to a nutrient depletion in the system, emphasizing the importance of nutrient availability. The model, although improvable especially on the formulation of the EPS excretion and bacteria development, already updated understanding of several aspects of benthic-system functioning during experimental conditions. © 2019 Elsevier Ltd %B Marine Environmental Research %V 150 %G eng %U https://www.sciencedirect.com/science/article/abs/pii/S0141113619300704 %R 10.1016/j.marenvres.2019.104754 %0 Journal Article %J Estuaries and Coasts %D 2018 %T Annual Phytoplankton Primary Production Estimation in a Temperate Estuary by Coupling PAM and Carbon Incorporation Methods %A Morelle, Jérôme %A Mathilde Schapira %A Francis Orvain %A Riou, Philippe %A Pascal Jean Lopez %A Duplessix, Olivier %A Rabiller, Emilie %A Maheux, Franc %A Simon, Benjamin %A Pascal Claquin %K High frequency . Electron requirement for carbon fixation . Electron transport rate (ETR) . Seine estuary %X

Phytoplankton primary production varies considerably with environmental parameters especially in dynamic ecosystems like estuaries. The aimof 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 related to salinity and turbidity gradients, which strongly influenced cells physiology and photoacclimatation. The number of electrons required to fix 1 mol of carbon (C) was ranged between 1.6 and 25 mol electron mol C−1 with a mean annual value of 8 ± 5 mol electron mol C−1. This optimum value suggests that in nutrient replete conditions like estuaries, alternative electron flows are low, while electrons transfer from photosystem II to carbon fixation is highly efficient. A statistical model was used to improve the estimation of primary production from electron transport rate as a function of significant environmental parameters. Based on this model, daily carbon production in the Seine estuary (France) was estimated by considering light and photic zone variability. A mean annual daily primary production of 0.12 ± 0.18 g C m−2 day−1 with a maximum of 1.18 g C m−2 day−1 in summer was estimated which lead to an annual mean of 64.75 g C m−2 year−1. This approach should be applied more frequently in dynamic ecosystems such as estuaries or coastal waters to accurately estimate primary production in those valuable ecosystems.

%B Estuaries and Coasts %8 02/2018 %G eng %0 Journal Article %J Estuarine, Coastal and Shelf Science %D 2018 %T Dynamics of exopolymeric carbon pools in relation with phytoplankton succession along the salinity gradient of a temperate estuary (France) %A Morelle, Jérôme %A Mathilde Schapira %A Françoise, Sylvaine %A Courtay Gaëlle %A Francis Orvain %A Pascal Claquin %K Exopolymeric substances Species %K Nanophytoplankton %K Picophytoplankton %K richness %X

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 picoeukaryotes
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 this estuary and can reach respectively 69 mgC L−1, and 33 mgC L−1. TEP distribution was mainly
related to physical factors (hydrodynamics, maximum turbidity zone formation and sediment resuspension)
probably produced by stressed or dying phytoplankton, while EPS appeared to be excreted during the phytoplankton
spring bloom. Soluble and bound EPS appear to be related to Skeletonema sp. and Cryptophyceae occurrences.
This paper presents the dynamic pattern of these carbon pools, which play an important role in the
trophic network and influence the flocculation processes involved in the fate of both organic and inorganic
matter.

%B Estuarine, Coastal and Shelf Science %V 209 %P 18-29 %G eng %0 Journal Article %J Journal of Experimental Marine Biology and Ecology %D 2018 %T A simple, user friendly tool to readjust raw PAM data from field measurements to avoid over- or underestimating of microphytobenthos photosynthetic parameters %A Morelle, Jérôme %A Francis Orvain %A Pascal Claquin %X

Intertidal mudflats are among the most productive ecosystems and microphytobenthic (MPB) biofilms play a key role in primary production. MPB primary production varies at short spatial and temporal scales. Accurate measurements thus require rapid non-intrusive methods like pulse amplitude modulate (PAM) fluorescence. However, the effect of granulometry and chl a concentration profile in light attenuation on irradiance and on fluorescence signal in the photic layer need to be taken into account when primary production is estimated using PAM. We propose a tool to readjust raw photosynthetic parameters (rETRmax, α, Ik) estimated from PAM measurements on the field, to avoid over- or underestimation. To develop the tool, we used models previously designed by Kühl and Jørgensen (1992), Serôdio (2004) and Forster and Kromkamp (2004) by integrating the chl a distribution profiles and sediment granulometry from pure sand to pure mud. The sensitivity of the correction to sediment granulometry and the shape of chl a profile were evaluated theoretically using a typical fluorescence data set obtained using PAM measurements. Our results confirm the importance of accounting for both the chl a profile and sediment granulometry when estimating a light attenuation coefficient. We show that, with the same chl a profile, the photosynthetic parameters are more underestimated in mud than in a sandy environment. Thus, granulometry and the chl a profile need to be systematically quantified and used to correct raw data measured in field studies using PAM before estimating photosynthetic parameters. The numerical tool is available as an e-document that is simple and easy to apply to any PAM data.

%B Journal of Experimental Marine Biology and Ecology %V 503 %P 136-146 %G eng %U https://www.sciencedirect.com/science/article/pii/S0022098117303325 %R https://doi.org/10.1016/j.jembe.2018.02.007 %0 Journal Article %J Journal of Sea Research %D 2017 %T Regional and latitudinal patterns of soft-bottom macrobenthic invertebrates along French coasts: Results from the RESOMAR database %A Régis K. Gallon %A Nicolas Lavesque %A Jacques Grall %A Céline Labrune %A Antoine Grémare %A Guy Bachelet %A Hugues Blanchet %A Paulo Bonifácio %A Vincent M.P. Bouchet %A Jean-Claude Dauvin %A Nicolas Desroy %A Franck Gentil %A Laurent Guerin %A Céline Houbin %A Jérôme Jourde %A Sandrine Laurand %A Michel Le Duff %A Vincent Le Garrec %A Xavier de Montaudouin %A Frédéric Olivier %A Francis Orvain %A Pierre-Guy Sauriau %A Eric Thiébaut %A Olivier Gauthier %K France %K Latitudinal pattern %K Regional pattern %K Soft-bottom %K Species richness %K Zoobenthos %X

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 hosts the lowest number of species. The distribution of species occurrence within and between seaboards was assessed for each major phylum using constrained rarefaction curves. The Mediterranean Sea hosts the highest number of exclusive species. In pairwise comparisons, it also shares a lower proportion of taxa with the Bay of Biscay (34.1%) or the English Channel (27.6%) than that shared between these two seaboards (49.7%). Latitudinal species richness patterns along the Atlantic and English Channel coasts were investigated for each major phylum using partial LOESS regression controlling for sampling effort. This showed the existence of a bell-shaped latitudinal pattern, highlighting Brittany as a hotspot for macrobenthic richness at the confluence of two biogeographic provinces.

%B Journal of Sea Research %V 130 %P 96 - 106 %G eng %U http://www.sciencedirect.com/science/article/pii/S1385110116302660 %R https://doi.org/10.1016/j.seares.2017.03.011 %0 Conference Proceedings %B Proceedings of the Congress on artificial reefs : from materials to ecosystems %D 2015 %T Artificial reef: Multiscale monitoring of colonization and primary production - Récif artificiel: mise en place d’un suivi de la colonisation a plusieurs échelles %A Pascal Claquin %A Leroy, Fanny %A Anne-Marie Rusig %A Isabelle Mussio %A Eric Feunteun %A Foveau, Aurélie %A Jean-Claude Dauvin %A Régis Gallon %A Lebrun, J-L %A Lestarquit, Mabel %A Francis Orvain %A Anne-Sophie Martinez %A Desoche, E %A Napoléon, Camille %A Roussel, Déborha %A Boutoil, Mohamed %B Proceedings of the Congress on artificial reefs : from materials to ecosystems %7 M. Boutouil & S. Leboulanger %C ESITC Caen %V 1 %P 103-110 %8 01/2015 %@ 978-2-95517664-0-5 %G eng %6 1 %0 Conference Proceedings %B Proceedings of the Congress on artificial reefs : from materials to ecosystems %D 2015 %T Chemical interaction between epilitic microphytobenthic biofilm and larval development of the sea urchin Paracentrotus lividus %A Francis Orvain %A Anne-Sophie Martinez %A Desoche, E %A Pascal Claquin %B Proceedings of the Congress on artificial reefs : from materials to ecosystems %7 M. Boutouil & S. Leboulanger %C ESITC Caen %V 1 %P 239-247 %8 01/2015 %@ 978-2-95517664-0-5 %G eng %6 1 %0 Journal Article %J Journal of Experimental Biology and ecology %D 2015 %T Impact of sediment grain-size and biofilm age on epipelic microphytobenthos resuspension %A Martin Ubertini %A Sébastien Lefebvre %A Rakotomalala, C %A Francis Orvain %B Journal of Experimental Biology and ecology %V 467 %P 52-64 %8 03/2015 %G eng %9 Journal article %0 Journal Article %J Ecological Modelling %D 2015 %T Modelling the effect of Cerastoderma edule bioturbation on microphytobenthos resuspension towards the planktonic food web of estuarine ecosystem %A Rakotomalala, C %A Karine Grangeré %A Martin Ubertini %A Forêt, M %A Francis Orvain %X

Microphytobenthos (MPB) represents an important food source for primary consumers in estuarine ecosystems and the availability of MPB as food items results from complex physical, chemical, and biological interactions. In Baie des Veys (Lower Normandy, France), the common cockle Cerastoderma edule constitutes the major bioturbator in the ecosystem in terms of biomass. In this ecosystem, cockle bioturbation is a key process regulating the MPB erosion flux in the water column. This bivalve intensely modifies the top layer of the sediment by increasing the sediment erodibility and the fluxes of suspended chlorophyll a through the valve movements. More precisely, cockle bioturbation destabilizes the sediment surface by creating a biogenic layer that is easily eroded with tidal hydrodynamic forces. Associated MPB can then be exported to the water column to fuel higher trophic levels of the planktonic food web. The aim of this study was to develop a numerical model that reproduces the export of MPB associated to the biogenic layer erosion. Kinetics of suspended MPB, in response to increasing stress, were obtained from flume experiments in lab controlled conditions and in situ natural conditions. Following this, the suspended MPB were analyzed to respectively parameterize the model by (1) a calibration approach, and (2) an independent validation. The analysis has highlighted that the higher the biomass of cockles, the higher the MPB resuspension rates. Our model consistently reproduces the tendency encountered in laboratory analysis and with in situ natural conditions. During the validation, a small site-specific lack of adjustment was identified, but, among the macrozoobenthic community, the model can be significantly improved by considering the bioturbation activities of another ecosystem engineer, Pygospio elegans. This study thus provides reliable estimates of the daily food availability from benthic primary consumers in an estuarine system where cockles dominate the bioturbating assemblage. This model can be inserted in various model designs (0D, 1D-vertical or 3D).

%B Ecological Modelling %V 316 %P 155-167 %8 09/2015 %G eng %0 Journal Article %J Journal of Sea Research %D 2014 %T Bacterial dynamics in a microphytobenthic biofilm: A tidal mesocosm approach %A Hélène Agogué %A Clarisse Mallet %A Francis Orvain %A Margot de Crignis %A Françoise Mornet %A Christine Dupuy %B Journal of Sea Research %V 92 %P 144-157 %8 09/2014 %G eng %0 Journal Article %J Journal of Sea Research %D 2014 %T How does the resuspension of the biofilm alter the functioning of the benthos-pelagos coupled food web of a bare mudflat in Marennes-Oléron Bay (NE Atlantic)? %A Saint-Béat, B. %A Christine Dupuy %A Agogué, H. %A Alexandre Carpentier %A Chalumeau, J. %A Como, S. %A David, V. %A De Crignis, M. %A Duchêne, J.-C. %A Fontaine, C. %A Eric Feunteun %A Katell Guizien %A Hartmann, H. %A Lavaud, J. %A Sébastien Lefebvre %A Lefrançois, C. %A Mallet, C. %A Montanié, H. %A Mouget, J.-L. %A Francis Orvain %A Ory, P. %A Pascal, P.-Y. %A Radenac, G. %A Richard, P. %A Vézina, A.F. %A Nathalie Niquil %B Journal of Sea Research %V 92 %P 144-157 %G eng %U https://www.sciencedirect.com/science/article/pii/S138511011400029X %R 10.1016/j.seares.2014.02.003 %0 Journal Article %J Journal of Sea Research %D 2014 %T Relevance of macrozoobenthic grazers to understand the dynamic behaviour of sediment erodibility and microphytobenthos resuspension in sunny summer conditions %A Francis Orvain %A Katell Guizien %A Sébastien Lefebvre %A Martine Bréret %A Christine Dupuy %B Journal of Sea Research %V 92 %P 46-55 %8 09/2014 %G eng %0 Journal Article %J Journal of Sea Research %D 2014 %T Seasonal dynamics of extracellular polymeric substances (EPS) in surface sediments of a diatom-dominated intertidal mudflat (Marennes–Oléron, France) %A Guillaume Pierre %A Jean-Michel Zhao %A Francis Orvain %A Christine Dupuy %A Géraldine Klein %A Marianne Graber %A Thierry Maugard %B Journal of Sea Research %V 92 %P 26-35 %8 09/2014 %G eng %0 Journal Article %J Journal of Sea Research %D 2014 %T Sequential resuspension of biofilm components (viruses, prokaryotes and protists) as measured by erodimetry experiments in the Brouage mudflat (French Atlantic coast) %A Christine Dupuy %A Clarisse Mallet %A Katell Guizien %A Hélène Montanié %A Martine Bréret %A Françoise Mornet %A Camille Fontaine %A Caroline Nérot %A Francis Orvain %B Journal of Sea Research %V 92 %P 56-65 %8 09/2014 %G eng %0 Journal Article %J Journal of Sea Research %D 2014 %T Structures of benthic prokaryotic communities and their hydrolytic enzyme activities resuspended from samples of intertidal mudflats: An experimental approach %A Clarisse Mallet %A Hélène Agogué %A Frédérique Bonnemoy %A Katell Guizien %A Francis Orvain %A Christine Dupuy %B Journal of Sea Research %V 92 %P 158-169 %8 09/2014 %G eng %0 Journal Article %J Journal of Sea Research %D 2014 %T Tidal and seasonal effects on the short-term temporal patterns of bacteria, microphytobenthos and exopolymers in natural intertidal biofilms (Brouage, France) %A Francis Orvain %A Margot de Crignis %A Katell Guizien %A Sébastien Lefebvre %A Clarisse Mallet %A Takahashi, E %A Christine Dupuy %B Journal of Sea Research %V 92 %P 6-18 %8 09/2014 %G eng