@article {8109, title = {Influence of infrastructure material composition and microtopography on marine biofilm growth and photobiology}, journal = {Biofouling}, year = {2021}, month = {Apr-08-2022}, pages = {1 - 17}, issn = {0892-7014}, doi = {10.1080/08927014.2021.1959918}, url = {https://www.tandfonline.com/doi/full/10.1080/08927014.2021.1959918}, author = {Vivier, Baptiste and Pascal Claquin and Lelong, Christophe and Lesage, Quentin and Peccate, Mathias and Hamel, Bastien and Georges, Marine and Bourguiba, Amel and Sebaibi, Nassim and Boutouil, Mohamed and Goux, Didier and Dauvin, Jean-Claude and Francis Orvain} } @article {7854, title = {Marine artificial reefs, a meta-analysis of their design, objectives and effectiveness}, journal = {Global Ecology and Conservation}, year = {2021}, month = {Jan-03-2021}, pages = {e01538}, issn = {23519894}, doi = {10.1016/j.gecco.2021.e01538}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2351989421000883}, author = {Vivier, Baptiste and Dauvin, Jean-Claude and Navon, Maxime and Anne-Marie Rusig and Isabelle Mussio and Francis Orvain and Boutouil, Mohamed and Pascal Claquin} } @article {7376, title = {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}, journal = {Science of The Total Environment}, volume = {733}, year = {2020}, month = {Jan-09-2020}, pages = {139307}, issn = {00489697}, doi = {10.1016/j.scitotenv.2020.139307}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969720328242}, author = {Dairain, Annabelle and Maire, Olivier and Meynard, Guillaume and Francis Orvain} } @article {7195, title = {Evidence for better microphytobenthos dynamics in mixed sand/mud zones than in pure sand or mud intertidal flats (Seine estuary, Normandy, France)}, journal = {PLOS ONE}, volume = {15}, year = {2020}, month = {08/2020}, pages = { e0237211}, abstract = {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{\textendash}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.}, doi = {10.1371/journal.pone.0237211}, author = {Morelle, J{\'e}r{\^o}me and Pascal Claquin and Francis Orvain} } @article {7377, title = {Sediment stability: can we disentangle the effect of bioturbating species on sediment erodibility from their impact on sediment roughness?}, journal = {Marine Environmental Research}, volume = {162}, year = {2020}, month = {Jan-12-2020}, pages = {105147}, issn = {01411136}, doi = {10.1016/j.marenvres.2020.105147}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0141113620305055}, author = {Dairain, Annabelle and Maire, Olivier and Meynard, Guillaume and Richard, Ana{\"\i}s and Rodolfo-Damiano, Tiffany and Francis Orvain} } @article {6668, title = {Modelling the functioning of a coupled microphytobenthic-EPS-bacterial system in intertidal mudflats}, journal = {Marine Environmental Research}, volume = {150}, year = {2019}, abstract = {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. {\textcopyright} 2019 Elsevier Ltd}, keywords = {Bacillariophyta, bacteria, Bacteria (microorganisms), bacterial growth, bacterium, Biogeochemical modeling, biogeochemistry, Biomass, Carbon, Carbon and nitrogen, Carbon and nitrogen ratios, Diatom, diel vertical migration, exopolymer, Experimental conditions, Extracellular polymeric substances, intertidal environment, intertidal zone, light, mesocosm, microbial community, Microphytobenthos, Migration, modeling, mudflat, Nitrogen, nonhuman, Nutrient availability, Nutrients, nutritional requirement, organic carbon, organismal interaction, Photosynthesis, Phytobenthos, Phytoplankton, polymer, Review, simulation, tide, vertical migration}, issn = {01411136}, doi = {10.1016/j.marenvres.2019.104754}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0141113619300704}, author = {Rakotomalala, C and Katell Guizien and Karine Granger{\'e} and S{\'e}bastien Lefebvre and Christine Dupuy and Francis Orvain} } @article {5428, title = {Annual Phytoplankton Primary Production Estimation in a Temperate Estuary by Coupling PAM and Carbon Incorporation Methods}, journal = {Estuaries and Coasts}, year = {2018}, month = {02/2018}, abstract = {

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 {\textpm} 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 {\textpm} 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.

}, keywords = {High frequency . Electron requirement for carbon fixation . Electron transport rate (ETR) . Seine estuary}, author = {Morelle, J{\'e}r{\^o}me and Mathilde Schapira and Francis Orvain and Riou, Philippe and Pascal Jean Lopez and Duplessix, Olivier and Rabiller, Emilie and Maheux, Franc and Simon, Benjamin and Pascal Claquin} } @article {5586, title = {Dynamics of exopolymeric carbon pools in relation with phytoplankton succession along the salinity gradient of a temperate estuary (France)}, journal = {Estuarine, Coastal and Shelf Science}, volume = {209}, year = {2018}, pages = {18-29}, abstract = {

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.

}, keywords = {Exopolymeric substances Species, Nanophytoplankton, Picophytoplankton, richness}, author = {Morelle, J{\'e}r{\^o}me and Mathilde Schapira and Fran{\c c}oise, Sylvaine and Courtay Ga{\"e}lle and Francis Orvain and Pascal Claquin} } @article {5435, title = {A simple, user friendly tool to readjust raw PAM data from field measurements to avoid over- or underestimating of microphytobenthos photosynthetic parameters}, journal = {Journal of Experimental Marine Biology and Ecology}, volume = {503}, year = {2018}, pages = {136-146}, abstract = {

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 K{\"u}hl and J{\o}rgensen (1992), Ser{\^o}dio (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.

}, doi = {https://doi.org/10.1016/j.jembe.2018.02.007}, url = {https://www.sciencedirect.com/science/article/pii/S0022098117303325}, author = {Morelle, J{\'e}r{\^o}me and Francis Orvain and Pascal Claquin} } @article {5366, title = {Regional and latitudinal patterns of soft-bottom macrobenthic invertebrates along French coasts: Results from the RESOMAR database}, journal = {Journal of Sea Research}, volume = {130}, year = {2017}, pages = {96 - 106}, abstract = {

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 {\textquotedblleft}R{\'e}seau des Stations et Observatoires Marins{\textquotedblright} (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{\textdegree} 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.

}, keywords = {France, Latitudinal pattern, Regional pattern, Soft-bottom, Species richness, Zoobenthos}, issn = {1385-1101}, doi = {https://doi.org/10.1016/j.seares.2017.03.011}, url = {http://www.sciencedirect.com/science/article/pii/S1385110116302660}, author = {R{\'e}gis K. Gallon and Nicolas Lavesque and Jacques Grall and C{\'e}line Labrune and Antoine Gr{\'e}mare and Guy Bachelet and Hugues Blanchet and Paulo Bonif{\'a}cio and Vincent M.P. Bouchet and Jean-Claude Dauvin and Nicolas Desroy and Franck Gentil and Laurent Guerin and C{\'e}line Houbin and J{\'e}r{\^o}me Jourde and Sandrine Laurand and Michel Le Duff and Vincent Le Garrec and Xavier de Montaudouin and Fr{\'e}d{\'e}ric Olivier and Francis Orvain and Pierre-Guy Sauriau and Eric Thi{\'e}baut and Olivier Gauthier} } @proceedings {3545, title = {Artificial reef: Multiscale monitoring of colonization and primary production - R{\'e}cif artificiel: mise en place d{\textquoteright}un suivi de la colonisation a plusieurs {\'e}chelles}, volume = {1}, year = {2015}, month = {01/2015}, pages = {103-110}, edition = {M. Boutouil \& S. Leboulanger}, address = {ESITC Caen}, isbn = {978-2-95517664-0-5}, author = {Pascal Claquin and Leroy, Fanny and Anne-Marie Rusig and Isabelle Mussio and Eric Feunteun and Foveau, Aur{\'e}lie and Jean-Claude Dauvin and R{\'e}gis Gallon and Lebrun, J-L and Lestarquit, Mabel and Francis Orvain and Anne-Sophie Martinez and Desoche, E and Napol{\'e}on, Camille and Roussel, D{\'e}borha and Boutoil, Mohamed} } @proceedings {3549, title = {Chemical interaction between epilitic microphytobenthic biofilm and larval development of the sea urchin Paracentrotus lividus}, volume = {1}, year = {2015}, month = {01/2015}, pages = {239-247}, edition = {M. Boutouil \& S. Leboulanger}, address = {ESITC Caen}, isbn = {978-2-95517664-0-5}, author = {Francis Orvain and Anne-Sophie Martinez and Desoche, E and Pascal Claquin} } @article {3790, title = {Impact of sediment grain-size and biofilm age on epipelic microphytobenthos resuspension}, journal = {Journal of Experimental Biology and ecology}, volume = {467}, year = {2015}, month = {03/2015}, pages = {52-64}, type = {Journal article}, author = {Martin Ubertini and S{\'e}bastien Lefebvre and Rakotomalala, C and Francis Orvain} } @article {4232, title = {Modelling the effect of Cerastoderma edule bioturbation on microphytobenthos resuspension towards the planktonic food web of estuarine ecosystem}, journal = {Ecological Modelling}, volume = {316}, year = {2015}, month = {09/2015}, pages = {155-167}, abstract = {

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).

}, author = {Rakotomalala, C and Karine Granger{\'e} and Martin Ubertini and For{\^e}t, M and Francis Orvain} } @article {3418, title = {Bacterial dynamics in a microphytobenthic biofilm: A tidal mesocosm approach}, journal = {Journal of Sea Research}, volume = {92}, year = {2014}, month = {09/2014}, pages = {144-157}, author = {H{\'e}l{\`e}ne Agogu{\'e} and Clarisse Mallet and Francis Orvain and Margot de Crignis and Fran{\c c}oise Mornet and Christine Dupuy} } @article {Saint-B{\'e}at2014144, title = {How does the resuspension of the biofilm alter the functioning of the benthos-pelagos coupled food web of a bare mudflat in Marennes-Ol{\'e}ron Bay (NE Atlantic)?}, journal = {Journal of Sea Research}, volume = {92}, year = {2014}, note = {cited By 17}, pages = {144-157}, doi = {10.1016/j.seares.2014.02.003}, url = {https://www.sciencedirect.com/science/article/pii/S138511011400029X} } @article {3416, title = {Relevance of macrozoobenthic grazers to understand the dynamic behaviour of sediment erodibility and microphytobenthos resuspension in sunny summer conditions}, journal = {Journal of Sea Research}, volume = {92}, year = {2014}, month = {09/2014}, pages = {46-55}, author = {Francis Orvain and Katell Guizien and S{\'e}bastien Lefebvre and Martine Br{\'e}ret and Christine Dupuy} } @article {3419, title = {Seasonal dynamics of extracellular polymeric substances (EPS) in surface sediments of a diatom-dominated intertidal mudflat (Marennes{\textendash}Ol{\'e}ron, France)}, journal = {Journal of Sea Research}, volume = {92}, year = {2014}, month = {09/2014}, pages = {26-35}, author = {Guillaume Pierre and Jean-Michel Zhao and Francis Orvain and Christine Dupuy and G{\'e}raldine Klein and Marianne Graber and Thierry Maugard} } @article {3420, title = {Sequential resuspension of biofilm components (viruses, prokaryotes and protists) as measured by erodimetry experiments in the Brouage mudflat (French Atlantic coast)}, journal = {Journal of Sea Research}, volume = {92}, year = {2014}, month = {09/2014}, pages = {56-65}, author = {Christine Dupuy and Clarisse Mallet and Katell Guizien and H{\'e}l{\`e}ne Montani{\'e} and Martine Br{\'e}ret and Fran{\c c}oise Mornet and Camille Fontaine and Caroline N{\'e}rot and Francis Orvain} } @article {3417, title = {Structures of benthic prokaryotic communities and their hydrolytic enzyme activities resuspended from samples of intertidal mudflats: An experimental approach}, journal = {Journal of Sea Research}, volume = {92}, year = {2014}, month = {09/2014}, pages = {158-169}, author = {Clarisse Mallet and H{\'e}l{\`e}ne Agogu{\'e} and Fr{\'e}d{\'e}rique Bonnemoy and Katell Guizien and Francis Orvain and Christine Dupuy} } @article {3415, title = {Tidal and seasonal effects on the short-term temporal patterns of bacteria, microphytobenthos and exopolymers in natural intertidal biofilms (Brouage, France)}, journal = {Journal of Sea Research}, volume = {92}, year = {2014}, month = {09/2014}, pages = {6-18}, author = {Francis Orvain and Margot de Crignis and Katell Guizien and S{\'e}bastien Lefebvre and Clarisse Mallet and Takahashi, E and Christine Dupuy} }