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1. Impacts of climate change on the Bay of Seine ecosystem: Forcing a spatio‐temporal trophic model with predictions from an ecological niche model

Author: Quentin Nogues, Samantha Grusd, Aurore Raoux, Georges Safi, Emma Araignous, Tarek Hattab, Boris Leroy, Pierre Bourdaud, Frida Ben Rais Lasram, Juliette Champagnat, Nathalie Niquil, Ghassen Halouani, Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Centre National de la Recherche Scientifique (CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut national des sciences de l'Univers (INSU - CNRS), France Energies Marines [Brest], Marine Research Institute, University of Cape Town, Rondebosch, South Africa ( MA-RE), University of Cape Town, Department of Biological Sciences, Rondebosch 7701, South Africa, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ifremer, Laboratory of Fisheries Resources, Boulogne-Sur-Mer, France, 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), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Musée National d'Histoire Naturelle de Luxembourg (MNHN), Normandie Université (NU), Morphodynamique Continentale et Côtière (M2C), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Université du Littoral Côte d'Opale (ULCO), Laboratoire Ressources halieutiques Boulogne sur mer (LRHBL), Halieutique Manche Mer du Nord (HMMN), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and 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)
Subjects: 0106 biological sciences, Ecological niche, Ecospace, 010604 marine biology & hydrobiology, Climate change, Forcing (mathematics), Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, climate change, 13. Climate action, ecological niche modelling, fisheries, Environmental science, Ecosystem, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bay, ComputingMilieux_MISCELLANEOUS, Trophic level, trophic interactions
Abstract: (IF 2.67; Q1); International audience; Climate change is already known to cause irreversible impacts on ecosystems that are difficult to accurately predict due to the multiple scales at which it will interact. Predictions at the community level are mainly focused on the future distribution of marine species biomass using ecological niche modelling, which requires extensive efforts concerning the effects that trophic interactions could have on the realized species dynamics. In this study, a set of species distribution models predictions were used to force the spatially-explicit trophic model Ecospace in order to evaluate the potentials impacts that two 2,100 climate scenarios, RCP2.6 and RCP8.5, could have on a highly exploited ecosystem, the Bay of Seine (France). Simulations demonstrated that both scenarios would influence the community of the Bay of Seine ecosystem: as expected, more intense changes were predicted with the extreme scenario RCP8.5 than with the RCP2.6 scenario. Under both scenarios, a majority of species underwent a decrease of biomass, although some increased. However, in both cases the stability of the majority of species dynamics was lowered, the sustainability of the fishery. Differences between niche modelling predictions and those obtained through the forcing in Ecospace highlighted the paramount importance of considering trophic interactions in climate change simulations. These results illustrate the requirement of multiplying novel approaches for efficiently forecasting potential impacts of climate change.
Published: 2021

2. Towards coherent GES assessments at sub-regional level: signs of fisheries expansion processes in the Bay of Biscay using an OSPAR food web indicator, the mean trophic level

Author: Georges Safi, Nina Larissa Arroyo, Tarek Hattab, François Le Loc'h, Izaskun Preciado, Lucía López-López, Nathalie Niquil, Pauline Vouriot, Instituto Español de Oceanografía (IEO), Málaga., Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Station Marine d'Endoume, Université de la Méditerranée - Aix-Marseille 2, 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 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), Institut de Recherche pour le Développement (IRD), 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), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), 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), and 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)
Subjects: 0106 biological sciences, mean trophic level, Medio Marino y Protección Ambiental, Centro Oceanográfico de Santander, [SDE.MCG]Environmental Sciences/Global Changes, OSPAR indicators, Fishing, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, Demersal zone, Ecosystem, 14. Life underwater, MSFD, Ecology, Evolution, Behavior and Systematics, Trophic level, Ecology, fisheries expansion, ACL, 010604 marine biology & hydrobiology, Pelagic zone, Bay of Biscay, fishing through, [SDE.ES]Environmental Sciences/Environmental and Society, Food web, Fishery, Geography, environmental status, food webs, Survey data collection, ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bay
Abstract: Using the Bay of Biscay (BoB) as a case study, we conducted a transnational assessment of the mean trophic level (MTL, Ospar FW4) indicator at sub-regional level, over the last three decades. Our results confirm the apparent recovery of BoB’s bentho-demersal system, as shown by trends in the MTL indicator based on survey data. However, they also point at a concomitant “fishing through” process where the apparent stability revealed by the MTL indicator based on landed catch data may be masking the expansion of demersal fisheries to deeper waters, and an over-exploitation of resources (particularly abundant pelagic species). Moreover, they show how the combined examination of independent surveys and fishery landings allows the identification of ecological trends in ecosystem studies. In addition, our results confirm that analysing MTL at various threshold levels helps discerning the causality of trends in this indicator, especially if analyses for pelagic and demersal species are run independently. Further studies, at smaller (i.e. local) spatial scales, need to be conducted to ascertain our results and suggest appropriate management strategies aimed at regulating fisheries expansions in the area., Sí
Published: 2019

3. Effets cumulés des énergies marines renouvelables et du changement climatique sur les propriétés des écosystèmes : Sensibilité de l'analyse des réseaux écologiques

Author: Nathalie Niquil, Quentin Nogues, Aurélie Chaalali, Aurore Raoux, Valérie David, François Le Loc'h, Boris Leroy, Frida Ben Rais Lasram, Tarek Hattab, Jean-Claude Dauvin, Emma Araignous, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), France Energies Marines [Brest], 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), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Centre National de la Recherche Scientifique (CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut national des sciences de l'Univers (INSU - CNRS), 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), 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), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Université du Littoral Côte d'Opale (ULCO), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), and 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)
Subjects: 0106 biological sciences, ENA food web, Ecological network analysis, General Decision Sciences, Climate change, Marine Renewable Energies, 010501 environmental sciences, 010603 evolutionary biology, 01 natural sciences, Ecosystem services, Linear inverse modeling, Ecosystem, 14. Life underwater, Sensitivity (control systems), Ecology, Evolution, Behavior and Systematics, QH540-549.5, 0105 earth and related environmental sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, business.industry, Environmental resource management, Ecological Network Analysis, Cumulative effects, 15. Life on land, Marine renewable energies, Renewable energy, Offshore wind power, Cumulative impact, 13. Climate action, Scale (social sciences), Environmental science, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, business
Abstract: (IF 6.26; Q1); International audience; In an increasingly anthropogenic world, the scientific community and managers have to take interactions between the drivers of ecosystems into consideration. Tools like ecological network analysis (ENA) indices offer the opportunity to study those interactions at the ecosystem level. However, ENA indices have never been used to test the incidence of cumulative drivers. The present study uses models combining the effects of (i) the reef caused by the future offshore wind farm of Courseulles-sur-Mer and (ii) climate change on species distribution, to test the response of multiple ENA indices. ENA indices proved sensitive to this cumulative impact, displaying a wide variety of cumulative effects. They were also very powerful to characterize the role of the cumulative impact on ecosystem functioning. These results demonstrate the capacity of ENA indices to describe and understand cumulative effects at the ecosystem scale. Using a sensitivity analysis approach, this study shows that ENA indices could be viable tools for managers. To help them in their tasks, the next step could be to link ecosystem services to ENA indices for a more practical use.
Published: 2021

4. Analysis of trophic networks: an optimisation approach

Author: Valérie Girardin, Jean-Guy Caputo, Quentin Nogues, Arnaud Knippel, Nathalie Niquil, and Minh Hieu Nguyen
Subjects: Mathematical optimization, Toy model, Computer science, Applied Mathematics, Stability (learning theory), Regular polygon, FOS: Physical sciences, Fixed point, Agricultural and Biological Sciences (miscellaneous), Nonlinear Sciences - Adaptation and Self-Organizing Systems, Ecological network, Polyhedron, Consistency (database systems), Optimization and Control (math.OC), Modeling and Simulation, Convex optimization, FOS: Mathematics, Quantitative Biology::Populations and Evolution, Biomass, Mathematics - Optimization and Control, Adaptation and Self-Organizing Systems (nlin.AO), Ecosystem
Abstract: We introduce a methodology to study the possible matter flows of an ecosystem defined by observational biomass data and realistic biological constraints. The flows belong to a polyhedron in a multi dimensional space that may make statistical exploration difficult in practice; instead, we propose to solve a convex optimization problem. Seven criteria based on ecological network indices have been selected to be used as convex goal functions. Numerical results show that the method is fast and can be used for large systems. Minimum flow solutions are analyzed using flow decomposition in paths and circuits. Their consistency is also tested by introducing a system of differential equations for the biomasses and examining the stability of the biomass fixed point. The method is illustrated and explained throughout the text on an ecosystem toy model. It is also applied to realistic food models.
Published: 2021
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5. Quantitative food web modeling unravels the importance of the microphytobenthos-meiofauna pathway for a high trophic transfer by meiofauna in soft-bottom intertidal food webs

Author: Martin Graeve, Stephen R. Pacella, Nathalie Niquil, Blanche Saint-Béat, J. Rzeznik-Orignac, Matilda Haraldsson, Ragnhild Asmus, Harald Asmus, Benoit Lebreton, L.H. van der Heijden, AWI, Wattenmeerstation Sylt, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique et Technologique (CNRST), Department of Marine Sciences [Gothenburg], University of Gothenburg (GU), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), United States Environmental Protection Agency [Cincinnati], Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), and Institut national des sciences de l'Univers (INSU - CNRS)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Inverse problems, microphytobenthos, Intertidal habitats, Meiobenthos, food web model, Ecological network analysis, soft-bottom environment, trophic level, 010603 evolutionary biology, 01 natural sciences, Ecosystems, Article, feeding ecology, Ascendency, Ecosystem, Linear inverse models, Trophic level, linear inverse model, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, deposit feeder, Carbon flow networks, biology, Markov chains, food web, quantitative analysis, Ecology, 010604 marine biology & hydrobiology, Ecological Modeling, Feeding, Detritivore, intertidal community, Monte Carlo methods, 15. Life on land, biology.organism_classification, Food web, Carbon, Ecological network, stable isotope mixing models, Markov chain Monte Carlo techniques, Sediment organic matters, Seagrass, Ecological process, meiofauna, trophic structure, Environmental science, Deposits, Trophic relationships, phytobenthos
Abstract: Publisher: Elsevier B.V.; International audience; Meiofauna are known to have an important role on many ecological processes, although, their role in food web dynamics is often poorly understood, partially as they have been an overlooked and under sampled organism group. Here, we used quantitative food web modeling to evaluate the trophic relationship between meiofauna and their food sources and how meiofauna can mediate the carbon flow to higher trophic levels in five contrasting soft-bottom intertidal habitats (including seagrass beds, mudflats and sandflats). Carbon flow networks were constructed using the linear inverse model-Markov chain Monte Carlo technique, with increased resolution of the meiofauna compartments (i.e. biomass and feeding ecology of the different trophic groups of meiofauna) compared to most previous modeling studies. These models highlighted that the flows between the highly productive microphytobenthos and the meiofauna compartments play an important role in transferring carbon to the higher trophic levels, typically more efficiently so than macrofauna. The pathway from microphytobenthos to meiofauna represented the largest flow in all habitats and resulted in high production of meiofauna independent of habitat. All trophic groups of meiofauna, except for selective deposit feeders, had a very high dependency on microphytobenthos. Selective deposit feeders relied instead on a wider range of food sources, with varying contributions of bacteria, microphytobenthos and sediment organic matter. Ecological network analyses (e.g. cycling, throughput and ascendency) of the modeled systems highlighted the close positive relationship between the food web efficiency and the assimilation of high-quality food sources by primary consumers, e.g. meiofauna and macrofauna. Large proportions of these flows can be attributed to trophic groups of meiofauna. The sensitivity of the network properties to the representation of meiofauna in the models leads to recommending a greater attention in ecological data monitoring and integrating meiofauna into food web models. © 2020 Elsevier B.V.
Published: 2020

6. Toward an Ecosystem Approach of Marine Renewable Energy: The Case of the Offshore Wind Farm of Courseulles-sur-Mer in the Bay of Seine

Author: T. Hattab, Camille Mazé, Matilda Haraldsson, Quentin Nogues, Jean-Claude Dauvin, Ghassen Halouani, M. Ching Villanueva, Karine Grangeré, Fabien Riera, Boris Leroy, Aurore Raoux, Frida Ben Rais Lasram, Georges Safi, Emma Araignous, Pierre Bourdaud, François Le Loc'h, Nathalie Niquil, and Juliette Champagnat
Subjects: Sustainable development, Offshore wind power, Ecosystem health, Impact assessment, business.industry, Environmental resource management, Environmental science, Ecosystem, Context (language use), Environmental impact assessment, business, Ecological network
Abstract: Environmental impact assessment (EIA) studies for offshore wind farm projects endeavour to consider the sensitivity of ecological compartments (benthos, fish, birds and marine mammals) to potential pressures/changes occurring in the ecosystem structure and functioning. EIA is expected to be conducted considering an integrated ecosystem approach, which is still a target to reach. In this context, and as a complementary approach to the traditional impact assessments, the objective of the ANR TROPHIK project is to develop an integrated ecosystem approach using several modelling tools for a holistic consideration of the food web. Here, we take into account the case of the Courseulles-sur-Mer offshore wind farm project located in the Bay of Seine. In this project, the potential impacts associated with this planned offshore wind farm are modelled. A model of the food web at the site of the construction was built to test possible reef- and reserve-effects, and to investigate the usefulness of Ecological Network Analysis (ENA) indices in the assessment of ecosystem health state. After the installation of the wind farm, our model showed that the ecosystem witnessed a change in its functioning mainly due to the important increase of the biomass of bivalves with the reef effect related to the installation of hard structures for the OWF. To go further into the integration of these results, we enlarged the description of the ecosystem functioning from a local to a larger spatial scale, where the initial zone was extended to the whole Bay of Seine using a spatial model. Different scenarios were built to test how the association of cumulative impacts, from climate change to fisheries, could affect the ecosystem. Finally, we propose a combined food-web and social network modelling approach to the Courseulles-sur-Mer model. The objectives of this latter analysis are to construct a decision-making process focusing on the network of actors involved, and to couple these social and ecological networks into a qualitative common model for a better understanding of the social-ecological system. Our approach aims to contribute to sustainable development through the analysis of interactions between the different categories of stakeholders groups, and can be applied in other offshore wind farm implementation in European waters.
Published: 2020

7. Isotopic analyses, a good tool to validate models in the context of Marine Renewable Energy development and cumulative impacts

Author: Bruno Ernande, Jean-Claude Dauvin, Jean-Philippe Pezy, Aurore Raoux, Nathalie Niquil, Karine Grangeré, Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire Ressources halieutiques Boulogne sur mer (LRHBL), Halieutique Manche Mer du Nord (HMMN), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), International Institute for Applied Systems Analysis [Laxenburg] (IIASA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire Ressources halieutiques Manche Mer du nord, IFREMER Centre Manche Mer du Nord, (HMMN), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: 0106 biological sciences, model validation, 010504 meteorology & atmospheric sciences, wind farm, Context (language use), Aquatic Science, Energy transition, Oceanography, trophic level, 01 natural sciences, Offshore wind farm, Trophic level, alternative energy, Dieppe, policy making, English channel, Marine ecosystem, Ecosystem, 14. Life underwater, Isotopic nitrogen analysis, 0105 earth and related environmental sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Seine Maritime, English Channel, food web, business.industry, 010604 marine biology & hydrobiology, detection method, Environmental resource management, Ecosystem-based management, Food web, Normandie, Offshore wind power, marine ecosystem, 13. Climate action, Environmental science, Ecopath with ecosim, France, ecosystem approach, business
Abstract: (IF 2.93; Q1); International audience; As part of the energy transition, the French government is planning Offshore Wind Farm (OWF) constructions in the next decades. An integrated ecosystem approach of two future OWF sites of the Eastern English Channel (Courseulles-sur-mer and Dieppe-Le Tréport) was developed to model the marine ecosystems before the OWF implementation. Such ecosystem models allow simulating the possible reef and reserve effects associated to the presence of the farm, and to character the overall changes in the food-web functioning. This holistic view of OWF effects could be replicated on other sites and form the basis of an ecosystem based management of marine renewable energies. However, to use these models for management purpose, they need to be validated. In order to do so, stable isotope ratios of nitrogen were used for determining the accuracy of the effective trophic levels computed in these two models. Results showed that trophic levels estimated by the two models were consistent with the trophic levels estimated by the independent isotopic data. In the context of OWF development and cumulative impacts analysis, this step of validation of the models is essential for developing their use by management actors and policy makers. © 2020 Elsevier Ltd
Published: 2020

8. Shifting levels of ecological network’s analysis reveals different system properties

Author: Matilda Haraldsson, Stuart R. Borrett, Télesphore Sime-Ngando, Philippe Huneman, Nathalie Niquil, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Marine Sciences [Gothenburg], University of Gothenburg (GU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: 0106 biological sciences, Food Chain, Computer science, Complex system, algal bloom, Cyanobacteria, 010603 evolutionary biology, 01 natural sciences, Algal bloom, Models, Biological, General Biochemistry, Genetics and Molecular Biology, Carbon Cycle, interdisciplinary approach, Interdisciplinary, cyanobacterium, hierarchical system, Hierarchy, Levels, Hierarchical control system, Time series, network analysis, Ecosystem, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, food web, business.industry, 010604 marine biology & hydrobiology, organic carbon, Environmental resource management, plankton, Articles, organizational framework, Eutrophication, Food web, Ecological network, Lakes, time series analysis, Networks, General Agricultural and Biological Sciences, business, complexity, Network analysis
Abstract: Publisher: Royal Society Publishing; International audience; Network analyses applied to models of complex systems generally contain at least three levels of analyses. Whole-network metrics summarize general organizational features (properties or relationships) of the entire network, while node-level metrics summarize similar organization features but consider individual nodes. The network- and node-level metrics build upon the primary pairwise relationships in the model. As with many analyses, sometimes there are interesting differences at one level that disappear in the summary at another level of analysis. We illustrate this phenomenon with ecosystem network models, where nodes are trophic compartments and pairwise relationships are flows of organic carbon, such as when a predator eats a prey. For this demonstration, we analysed a time-series of 16 models of a lake planktonic food web that describes carbon exchanges within an autumn cyanobacteria bloom and compared the ecological conclusions drawn from the three levels of analysis based on inter-time-step comparisons. A general pattern in our analyses was that the closer the levels are in hierarchy (node versus network, or flow versus node level), the more they tend to align in their conclusions. Our analyses suggest that selecting the appropriate level of analysis, and above all regularly using multiple levels, may be a critical analytical decision. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations’. © 2020 The Author(s) Published by the Royal Society. All rights reserved.
Published: 2020

9. The Bay of Seine: A Resilient Socio-Eco-System Under Cumulative Pressures

Author: Aurore Raoux, Nathalie Niquil, Jean-Philippe Pezy, Jean-Claude Dauvin, and Noémie Baux
Subjects: Fishery, geography, Ecosystem health, Ecological indicator, geography.geographical_feature_category, Environmental science, Estuary, Ecosystem, Natura 2000, Bay, Channel (geography), Trophic level
Abstract: The Bay of Seine (Normandy coast of the English Channel) is a highly impacted ecosystem concerned by numerous human activities. It is subjected to heavy historic anthropogenic pressures and the emergence of new human activities: fishing, harbour extension, aggregate extraction, deposition of dredged sediment, and offshore wind farms. By contrast, this area shows a high level of protection of its natural heritage, mainly owing to the Natural Reserve and Natura 2000 sites. Moreover, an accumulation of research projects has ensured the acquisition of a high level of scientific knowledge and high-quality ecological data in this area. However, there is a lack of a systematic approach taking into account the available data. By building maps of benthic habitats, food-web modelling and calculating ecological indicators, we are able to take the first steps towards an ecosystem-based management. These integrative approaches allow us to assess the ecological quality status of the Bay of Seine and the Seine estuary. Trophic models based on the quantification of energy and matter fluxes in ecosystems, as well as indices derived from ecological network analysis, are used to describe the interaction between species across all trophic levels. When applied to spatial models, ecological functioning and ecosystem health can be assessed in different areas of the ecosystem. In the Bay of Seine, benthic habitats display high resilience while pelagic, fish and bird compartments have been shown to be highly modified, due to hydrological and climatic changes. The North Channel and the Navigation Channel of the Seine estuary appear to be far more intensely stressed, while the South Channel and marine areas of the Bay show a more mature functioning. Our conclusions reveal the need to consider the influence of human pressures on the functioning of complex ecosystems, thus providing an integrated approach that can be used to study a social-ecological system affected by global changes and investigate the cumulative impacts of human activities.
Published: 2020

10. Assessing the ecological status of an estuarine ecosystem: linking biodiversity and food-web indicators

Author: Gwenola de Roton, Aurore Raoux, Jean-Claude Dauvin, Nathalie Niquil, Mario Lepage, Géraldine Lassalle, Jérémy Lobry, Jocelyne Morin, Samuele Tecchio, Camille Le Guen, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Normandie Université (NU), Morphodynamique Continentale et Côtière (M2C), Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Caen Normandie (UNICAEN), Agence Française pour la Biodiversité (AFB), Écologie et Modèles pour l'halieutique (EMH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Ecosystèmes estuariens et poissons migrateurs amphihalins (UR EPBX), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER), Ecosystèmes aquatiques et changements globaux (UR EABX), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Biodiversity, Aquatic Science, Oceanography, 01 natural sciences, Ecosystem, 14. Life underwater, 0105 earth and related environmental sciences, computer.programming_language, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, Estuary, Food web, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Geography, Habitat, 13. Climate action, Ecosystem health indicators, Guild, Harbour, Ecosystem functioning, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer
Abstract: [Departement_IRSTEA]Eaux [ADD1_IRSTEA]Systèmes aquatiques soumis à des pressions multiples(IF 2.61 [2018]; Q1]; International audience; During the last decades, the highly-anthropized Seine estuary has been impacted by modification of its habitats (building of a major extension of Le Havre harbour, i.e. Port2000) and a significant natural decrease in freshwater discharge. A Before/After analysis, using a toolbox of indicators, was applied to characterize the effects of both events on the estuarine ecosystem status. We selected from existing tool boxes several indicators derived from food web modelling or community composition data, such as biodiversity indicators, a guild-based index (i.e. Estuarine and Lagoon Fish Index ELFI) and ecological network analysis (ENA) indices. ENA and biodiversity indicators were applied on six spatial boxes describing the Seine estuary and its outlet. Results showed an increase in taxonomic and functional richness over time, mainly due to marinisation, and significant changes in food-web properties in relation to Port2000. ENA indices appeared as a promising method in ecological status assessment, especially for estuaries considered as inherently disturbed.
Published: 2019

11. Vitamine ENA: A framework for the development of ecosystem-based indicators for decision makers

Author: Diana Giebels, Ulrike Schückel, Izaskun Preciado, Nathalie Niquil, Nina Larissa Arroyo, Aurore Raoux, Georges Safi, Samuele Tecchio, Johanna J. Heymans, Victor N. de Jonge, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Instituto Español de Oceanografía (IEO), Málaga., Scottish Association for Marine Science (SAMS), Morphodynamique Continentale et Côtière (M2C), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), The Schleswig-Holstein Agency for Coastal Defence [Tönning, Allemagne], SINAY - Maritime Data Solutions, and Department of Public Administration and Sociology
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Good Environmental Status, [SDE.MCG]Environmental Sciences/Global Changes, Management, Monitoring, Policy and Law, Aquatic Science, Oceanography, 01 natural sciences, Marine Strategy Framework Directive, Marine ecosystem, Ecosystem, 14. Life underwater, 0105 earth and related environmental sciences, Trophic level, business.industry, 010604 marine biology & hydrobiology, Environmental resource management, 15. Life on land, Ecosystem-based management, [SDE.ES]Environmental Sciences/Environmental and Society, Food web, Water Framework Directive, 13. Climate action, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: (IF 2.60 [2018]; Q1); International audience; The Water Framework Directive (article 2, paragraph 21) as well as the Marine Strategy Framework Directive (MSFD, Descriptor 4) stress the need for assessing the quality of the structure and the functioning of ecosystems. The MSFD also underlines the urgent need for development, testing, and validation of ecosystem state indicators. Holistic function-based criteria and indicators as provided by Ecological Network Analysis (ENA) could be used to define and assess the ‘Good Environmental Status’ of marine ecosystems. This approach also feeds Ecosystem Based Management (EBM). ENA generally analyses the fluxes' quality of a single medium such as here the carbon fluxes in a food web and produces a number of useful metrics that indicate, inter alia, the total carbon flow through the system, the quality of the functioning of the system or the trophic efficiency of system. A short list of indices [i.e. Detritivory over Herbivory ratio (D/H), Connectance Index (CI), Transfer Efficiency (TE) over trophic levels, System Omnivory Index (SOI), Finn's Cycling Index (FCI), relative Redundancy (R/DC), Average Mutual Information (AMI) and Interaction Strength (IS)] is proposed for practical use. This paper presents a first framework for OSPAR Regional Sea Convention food web indicators based on ENA. These are presented here focusing on their applicability and what is needed for implementation, illustrating their potential use by case studies.
Published: 2019

12. Global Changes Jeopardize the Trophic Carrying Capacity and Functioning of Estuarine Ecosystems

Author: Valérie David, Benoît Sautour, Xavier Chevillot, Gérard Castelnaud, Jérémy Lobry, Guy Bachelet, Nathalie Niquil, Jonathan Selleslagh, Aurélie Chaalali, Samuele Tecchio, Géraldine Lassalle, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Normandie Université (NU), Centre National de la Recherche Scientifique (CNRS), 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), Université de Bordeaux (UB), Laboratoire d'Océanologie Biologique d'Arcachon (LOB ARCACHON), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS), UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), 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), Écologie et Modèles pour l'halieutique (EMH), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Biome, Biodiversity, 010603 evolutionary biology, 01 natural sciences, Environmental Chemistry, Ecosystem, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Trophic level, Ecosystem health, Ecology, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Food web, Productivity (ecology), 13. Climate action, Sustainability, [SDE]Environmental Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; At the interface between terrestrial and marine biomes, estuaries display high ecological productivity and provide goods and services to humans. Associated with many ecological functions, they are nursery, refuge, and growing areas for many species fish. These ecological functions and services depend on both their ecological production and trophic carrying capacity and the durability of food web functioning. These transitional key habitats undergo both strong anthropogenic pressures and climatic influences that impact the structure and dynamics of estuarine biodiversity. In this context, we explore, here, three decades of the Gironde estuary ecosystem history to detect the food web's response to global changes-induced effect on biodiversity. At least two Ecological Abrupt Shifts associated with deep modifications in the biodiversity at most trophic levels have been documented for this particular ecosystem. Three food web models were thus calibrated, one for each of the three periods discriminated by the two shifts that occurred at the end of the 1980s and the beginning of the 2000s. Results highlighted that the ecotrophic efficiency estimate for subtidal macrofauna and shrimps reached the maximum possible values during the last period. This could mean that the Gironde estuary fully reached its trophic carrying capacity due to a food limitation especially for benthos demersal fish. We also observed a significant decrease in some food web indicators (such as Average Mutual Information, System Omnivory Index, and Average Path Length) usually associated with ecosystem stress, suggesting a significant impact of global change on the Gironde estuary ecosystem health and questioning the sustainability of the ecological functions associated with this ecosystem.
Published: 2019

13. Trophic importance of microphytobenthos and bacteria to meiofauna in soft-bottom intertidal habitats: A combined trophic marker approach

Author: Ragnhild Asmus, Jadwiga Rzeznik-Orignac, Benoit Lebreton, Q. Bernier, Nathalie Niquil, Gaël Guillou, Martin Graeve, Harald Asmus, L.H. van der Heijden, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), and Normandie Université (NU)
Subjects: 0106 biological sciences, Aquatic Organisms, Geologic Sediments, Nematoda, Meiofauna, Marennes-Oléron Bay, Oceanography, 01 natural sciences, Germany, Microalgae, Sandflats, Stable isotopes, Trophic level, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Carbon Isotopes, biology, Ecology, Stable isotope ratio, Fatty Acids, Food webs, Microphytobenthos, General Medicine, Pollution, Seagrass, Habitat, Bays, Benthic zone, France, Seasons, Bare mudflats, Food Chain, Meiobenthos, Intertidal zone, Aquatic Science, 010603 evolutionary biology, Copepoda, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Animals, Sylt-Rømø Bight, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Ecosystem, Diatoms, Bacteria, Nitrogen Isotopes, 010604 marine biology & hydrobiology, fungi, Seagrass beds, Feeding Behavior, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, Tracheophyta, Compound specific isotope analysis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bay
Abstract: International audience; Meiofauna can play an important role in the carbon fluxes of soft-bottom coastal habitats. Investigation of their feeding behavior and trophic position remains challenging due to their small size. In this study, we determine and compare the food sources used by nematodes and benthic copepods by using stable isotope compositions, fatty acid profiles and compound specific isotope analyses of fatty acids in the mudflats, seagrass beds and a sandflat of the Marennes-Oléron Bay, France, and the Sylt-Rømø Bight, Germany. Suspended particulate organic matter was much more 13C-depleted than other food sources and meiofauna, highlighting its poor role in the different studied habitats. The very low proportions of vascular plant fatty acid markers in meiofauna demonstrated that these consumers did not rely on this food source, either fresh or detrital, even in seagrass beds. The combined use of stable isotopes and fatty acids emphasized microphytobenthos and benthic bacteria as the major food sources of nematodes and benthic copepods. Compound specific analyses of a bacteria marker confirmed that bacteria mostly used microphytobenthos as a substrate.
Published: 2019

14. Measuring sensitivity of two OSPAR indicators for a coastal food web model under offshore wind farm construction

Author: Aurore Raoux, Jean-Philippe Pezy, Bruno Ernande, Nathalie Niquil, Géraldine Lassalle, François Le Loc'h, Georges Safi, Jean-Claude Dauvin, Justine Lequesne, Camille Mazé, Samuele Tecchio, Valérie Girardin, Morphodynamique Continentale et Côtière (M2C), Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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 - Brest (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Laboratoire de Mathématiques Nicolas Oresme (LMNO), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Normandy Regional Council'Eoliennes Offshore du Calvados' (EOC) company, Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes aquatiques et changements globaux (UR EABX), Laboratoire Ressources halieutiques Boulogne sur mer (LRHBL), Halieutique Manche Mer du Nord (HMMN), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-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 (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), Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire Ressources halieutiques Manche Mer du nord, IFREMER Centre Manche Mer du Nord, (HMMN), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, Reef effect, Mean Trophic Level, Reserve effect, Fishing, General Decision Sciences, 010501 environmental sciences, Ecopath, 010603 evolutionary biology, 01 natural sciences, EcoSim, Ecosystem, 14. Life underwater, Marine renewable energy, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Trophic level, geography, geography.geographical_feature_category, Ecology, business.industry, ACL, Environmental resource management, Ecological Network Analysis, Food web, Offshore wind power, Ecosim, 13. Climate action, Ecopath with Ecosim, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Bay, Channel (geography)
Abstract: [Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE [ADD1_IRSTEA]Dynamique et fonctionnement des écosystèmes(IF 4.49 [2018]; Q1); International audience; A combination of modelling tools was applied to simulate the impacts of the future Courseulles-sur-mer offshore wind farm (OWF) construction (Bay of Seine, English Channel) on the ecosystem structure and functioning. To do so, food-web models of the ecosystem under three scenarios were constructed to investigate the effect caused by the OWF of added substrate (reef effect), fishing restriction (reserve effect), and their combined effect. Further, Ecological Network Analysis indices and Mean Trophic Level were derived to investigate their suitability for detecting changes in the ecosystem state. Our analysis suggests changes in the ecosystem structure and functioning after the OWF construction, the ecosystem maturity was predicted to increase, but no alterations in its overall resilience capacity.
Published: 2019

15. A new type of plankton food web functioning in coastal waters revealed by coupling Monte Carlo Markov Chain Linear Inverse method and Ecological Network Analysis

Author: Asma Sakka Hlaili, Matilda Haraldsson, Kaouther Mejri, Aurélie Chaalali, Marouan Meddeb, Olivier Pringault, Nathalie Niquil, Boutheina Grami, Université de Carthage - University of Carthage, Université Tunis El Manar (UTM), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Université de Caen Normandie (UNICAEN), Université de Monastir - University of Monastir (UM), 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 (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), Université de Tunis El Manar (UTM), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), IRD through the JEAI-ECOBIZ, LIM COSYS-Med, IRD fellowship (ARTS program), European Project: 308392,EC:FP7:ENV,FP7-ENV-2012-two-stage,DEVOTES(2012), 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), and 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)
Subjects: 0106 biological sciences, Food web modeling, General Decision Sciences, Seasonal variations, 010501 environmental sciences, 010603 evolutionary biology, 01 natural sciences, Zooplankton, Bacterial multivorous food web, Phytoplankton, Ecosystem, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Trophic level, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, Primary production, 15. Life on land, Plankton, Trophic structure, Food web, Ecological network, 13. Climate action, Coastal waters, Environmental science, Network analysis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Plankton food webs (PFW) typology is based on different categories of functioning, according to the dominant processes and the role played by heterotrophic bacteria, small vs large phytoplankton, and small vs large zooplankton. Investigating the structure and the function of planktonic foodn webs in two SW Mediterranean waters (inshore and marine sites) at four seasons, using inverse (LIM-MCMC) and ecological network (ENA) analyses, we identified a new type of food web, called the “bacterial multivorous food web”. This food web adds to the conventional trophic continuum as previously reported. The “bacterial multivorous food web” present in winter showed the lowest primary production among seasons, but highest bacterial production. Several food web ratios characterized this new typology e.g. picophytoplankton net primary production to total primary production varied from 0.20 to 0.28; bacterial to primary production ratio is higher than values reported in global scale (≅1); bacterial net production to the potential protozoan prey net production was high (> 0.2). In this special food web, carbon was mostly recycled, with a moderate fraction channeled to deep waters, which lead to a higher retention of carbon inside the ecosystem. This winter PFW also seemed to be the most organized, specialized, stable and mature, as related to common interpretations of ENA. The spring was characterized by herbivorous food web, with highest activity coinciding with low stability. Although less usual, the herbivorous pathway was also observed during summer, in inshore waters. The autumn food webs, which functioned as multivorous or microbial food webs, appeared to be stable and mature. Finally, our study demonstrates the usefulness of food web models derived ratios combined with ecological network analysis indices to conduct evaluation of the structure and functioning of ecosystems and potentially to support management decisions in marine environment.
Published: 2019

16. Towards an Ecosystem Approach to Assess the Impacts of Marine Renewable Energy

Author: Aurore Raoux, Nathalie Niquil, Jean-Philippe Pezy, Jean-Claude Dauvin, Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Normandie Université (NU), Centre National de la Recherche Scientifique (CNRS), Bispo, R., Bernardino, J., Coelho, H., Lino Costa, J., Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)
Subjects: 0106 biological sciences, Monitoring, 010603 evolutionary biology, 01 natural sciences, Ecopath, Demersal ﬁsh, Offshore wind farm, Benthos, EcoSim, Marine ecosystem, Ecosystem, 14. Life underwater, Demersal fish, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Call for bids, geography, geography.geographical_feature_category, business.industry, 010604 marine biology & hydrobiology, Environmental resource management, Ecological Network Analysis, Key-words: Offshore wind farm, Renewable energy, Offshore wind power, Suprabenthos, 13. Climate action, Ecopath with Ecosim, Environmental science, Electricity, Ecosystemic approach, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Channel (geography)
Abstract: International audience; Since the beginning of the 2000’, the French government ambition was to have an offshore wind production formed 40% of the renewable electricity in 2030. Three calls tenders of Offshore Wind Farms (OWFs) construction have been pronounced since 2011. However, no offshore wind farm (OWF) had been constructed at the end of 2017 due to long administrative procedures and numerous appeals in justice, at French and European levels. Nevertheless, several studies have been enterprised to identify the environmental conditions and ecosystem functioning in selected sites before OWF implantations. However, these studies are generally focused on the conservation of some species or groups of species, and there is no holistic study on the effects of the construction and operation of OWF on an ecosystem taken as a whole. In 2017, a complete and integrated view of the ecosystem of two future OWF sites of the eastern English Channel (Courseulles-sur-Mer and Dieppe-Le Tréport) was developed to model the marine ecosystems before OWF implementation and to simulate reef effects due to new spatial occupation of maritime territory. Results contribute to a better knowledge of the impacts of the OWFs on the functioning of marine ecosystems. They also allow to deﬁne recommendations for environmental managers and industry in terms of monitoring the effects of marine renewable energy (MRE), not only locally but also on other sites, at national and European levels.
Published: 2019

17. Modeling Strategies for Ecosystems

Author: Cédric Bacher and Nathalie Niquil
Subjects: business.industry, Ecosystem model, Environmental resource management, Environmental science, Ecosystem, business
Published: 2016

18. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive

Author: O. Kryvenko, Ibon Galparsoro, Chiara Piroddi, Marina Chifflet, Caleb Smith, Ana Carla Garcia, Krysia Mazik, Géraldine Lassalle, Guillem Chust, Eider Andonegi, Heliana Teixeira, Nathalie Niquil, Maria Kämäri, Suzanna Neville, María C. Uyarra, Vjacheslav Suslin, Tanya Churilova, María del Carmen Alvarez, Axel G. Rossberg, Christopher P. Lynam, Nadia Papadopoulou, Letizia Tedesco, Water Resources Unit [Ispra], JRC Institute for Environment and Sustainability (IES), European Commission - Joint Research Centre [Ispra] (JRC)-European Commission - Joint Research Centre [Ispra] (JRC), European Commission - Joint Research Centre [Ispra] (JRC), Centre for Environment, Fisheries and Aquaculture Science [Lowestoft] (CEFAS), Hellenic Center for Marine Research (HCMR), Universidad de la República [Montevideo] (UDELAR), University of Hull [United Kingdom], AZTI - Tecnalia, Finnish Environment Institute (SYKE), Marine and environmental research centre - IMAR-CMA (Coimbra, Portugal), University of Coimbra [Portugal] (UC), Marine Hydrophysical Institute (MHI), National Academy of Sciences of Ukraine (NASU), 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), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), European Commission, Universidad de la República [Montevideo] (UCUR), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Hellenic Centre for Marine Research (HCMR), Environnements et Paléoenvironnements OCéaniques (EPOC), and Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Good Environmental Status, [SDE.MCG]Environmental Sciences/Global Changes, Biodiversity descriptors, Biodiversity, General Decision Sciences, 01 natural sciences, Ecosystem services, [SHS]Humanities and Social Sciences, Marine Strategy Framework Directive, media_common.cataloged_instance, Ecosystem, Marine ecosystem, 14. Life underwater, European union, MSFD, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, media_common, Decision Sciences(all), Biomass (ecology), Ecology, business.industry, Model-derived indicators, 010604 marine biology & hydrobiology, Environmental resource management, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Habitats, 13. Climate action, [SDE]Environmental Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecological models, business, Marine ecosystems, Pressures
Abstract: Piroddi, Chiara ... et. al.-- 17 pages, 4 figures, 5 tables, 1 appendix supplementary data http://dx.doi.org/10.1016/j.ecolind.2015.05.037, The European Union's Marine Strategy Framework Directive (MSFD) seeks to achieve, for all European seas, “Good Environmental Status” (GEnS), by 2020. Ecological models are currently one of the strongest approaches used to predicting and understanding the consequences of anthropogenic and climate-driven changes in the natural environment. We assess the most commonly used capabilities of the modelling community to provide information about indicators outlined in the MSFD, particularly on biodiversity, food webs, non-indigenous species and seafloor integrity descriptors. We built a catalogue of models and their derived indicators to assess which models were able to demonstrate: (1) the linkages between indicators and ecosystem structure and function and (2) the impact of pressures on ecosystem state through indicators. Our survey identified 44 ecological models being implemented in Europe, with a high prevalence of those that focus on links between hydrodynamics and biogeochemistry, followed by end-to-end, species distribution/habitat suitability, bio-optical (remote sensing) and multispecies models. Approximately 200 indicators could be derived from these models, the majority of which were biomass and physical/hydrological/chemical indicators. Biodiversity and food webs descriptors, with ∼49% and ∼43% respectively, were better addressed in the reviewed modelling approaches than the non-indigenous species (0.3%) and sea floor integrity (∼8%) descriptors. Out of 12 criteria and 21 MSFD indicators relevant to the abovementioned descriptors, currently only three indicators were not addressed by the 44 models reviewed. Modelling approaches showed also the potential to inform on the complex, integrative ecosystem dimensions while addressing ecosystem fundamental properties, such as interactions between structural components and ecosystems services provided, despite the fact that they are not part of the MSFD indicators set. The cataloguing of models and their derived indicators presented in this study, aim at helping the planning and integration of policies like the MSFD which require the assessment of all European Seas in relation to their ecosystem status and pressures associated and the establishment of environmental targets (through the use of indicators) to achieve GEnS by 2020, This manuscript has resulted from the DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status) project funded by the European Union under the 7th Framework Programme, ‘The Ocean of Tomorrow’ Theme (Grant Agreement No. 308392), http://www.devotes-project.eu
Published: 2015
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19. Plankton food-web functioning in anthropogenically impacted coastal waters (SW Mediterranean Sea): An ecological network analysis

Author: Boutheina Grami, Aurélie Chaalali, Matilda Haraldsson, Asma Sakka Hlaili, Olivier Pringault, Marouan Meddeb, Nathalie Niquil, a Laboratoire de phytoplanctonologie, Faculté des Sciences de Bizerte, Université de Carthage, 7021 Zarzouna, Bizerte, Tunisia, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), 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), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), 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), Faculté des Sciences de Bizerte [Université de Carthage], Université de Carthage - University of Carthage, LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, Ecological network analysis, 010501 environmental sciences, Aquatic Science, 01 natural sciences, Mediterranean sea, Phytoplankton, Ascendency, Ecosystem, 14. Life underwater, Mediterranean coastal waters, 0105 earth and related environmental sciences, 010604 marine biology & hydrobiology, Geology, 15. Life on land, Plankton, Plankton ecology, Food web, Food-web modelling, Oceanography, 13. Climate action, [SDE]Environmental Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Eutrophication, Bay
Abstract: This work was supported by IRD through the JEAI-ECOBIZ and the LIM COSYS-Med. MM was financed by an IRD fellowship (ARTS program). The work of Nathalie Niquil on ENA derived indicators for characterizing the stress in food webs is supported by DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing Good Environmental Status) funded by the European Union under the 7th Framework Programme, 'The Ocean for Tomorrow' Theme (grant agreement no. 308392); International audience; The study is the first attempt to (i) model spring food webs in three SW Mediterranean ecosystems which are under different anthropogenic pressures and (ii) to project the consequence of this stress on their function. Linear inverse models were built using the Monte Carlo method coupled with Markov Chains to characterize the foodweb status of the Lagoon, the Channel (inshore waters under high eutrophication and chemical contamination) and the Bay of Bizerte (offshore waters under less anthropogenic pressure). Ecological network analysis was used for the description of structural and functional properties of each food web and for inter-ecosystem comparisons. Our results showed that more carbon was produced by phytoplankton in the inshore waters (966–1234 mg C m−2 d−1) compared to the Bay (727 mg C m−2 d−1). The total ecosystem carbon inputs into the three food webs was supported by high primary production, which was mainly due to > 10 µm algae. However, the three carbon pathways were characterized by low detritivory and a high herbivory which was mainly assigned to protozooplankton. This latter was efficient in channelling biogenic carbon. In the Lagoon and the Channel, foods webs acted almost as a multivorous structure with a tendency towards herbivorous one, whereas in the Bay the herbivorous pathway was more dominant. Ecological indices revealed that the Lagoon and the Channel food webs/systems had high total system throughput and thus were more active than the Bay. The Bay food web, which had a high relative ascendency value, was more organized and specialized. This inter–ecosystem difference could be due to the varying levels of anthropogenic impact among sites. Indeed, the low value of Finn’s cycling index indicated that the three systems are disturbed, but the Lagoon and the Channel, with low average path lengths, appeared to be more stressed, as both sites have undergone higher chemical pollution and nutrient loading. This study shows that ecosystem models combined with ecological indices provide a powerful approach to detect change in environmental status and anthropogenic impacts.
Published: 2018

20. Assessing cumulative socio-ecological impacts of offshore wind farm development in the Bay of Seine (English Channel)

Author: Jeffrey M. Dambacher, Nathalie Niquil, Camille Mazé, Aurore Raoux, Jean-Philippe Pezy, Jean-Claude Dauvin, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), CSIRO Marine and Atmosphere Research [Hobart], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Biologie des Organismes et Ecosystèmes Aquatiques ( BOREA ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Muséum National d'Histoire Naturelle ( MNHN ) -Institut de Recherche pour le Développement ( IRD ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université des Antilles ( UA ), Morphodynamique Continentale et Côtière ( M2C ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ), Laboratoire des Sciences de l'Environnement Marin (LEMAR) ( LEMAR ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Brest ( UBO ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -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 ) -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 ), LIttoral ENvironnement et Sociétés - UMR 7266 ( LIENSs ), and Université de La Rochelle ( ULR ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: 0106 biological sciences, Economics and Econometrics, Reef effect, Reserve effect, Management, Monitoring, Policy and Law, Aquatic Science, Energy transition, Ecosystem-based management, 010603 evolutionary biology, 01 natural sciences, Offshore wind farm, Effects of global warming, Ecosystem, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, General Environmental Science, Apex predator, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography, geography.geographical_feature_category, business.industry, 010604 marine biology & hydrobiology, ACL, Global warming, Environmental resource management, Offshore wind power, 13. Climate action, [SDU]Sciences of the Universe [physics], Environmental science, Press perturbation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Law, [ SDU ] Sciences of the Universe [physics], Channel (geography), Qualitative models
Abstract: (IF 2.87; Q1); International audience; As part of the energy transition, the French government is planning the construction of Offshore Wind Farms (OWFs) in Normandy. These OWFs will be integrated into an ecosystem already facing multiple anthropogenic disturbances. A holistic view of cumulated impacts (OWF construction, global warming and fisheries) were developed on the Courseulles-sur-Mer’ ecosystem through the use of a qualitative mathematical modelling approach. This modelling approach provides the mean to consider alternative hypotheses about how the ecosystem structure and function affects its dynamics. Alternative models were constructed to address the different hypotheses regarding the behaviour of top predator (whether the top predators will be scared away by the OWF or attracted by the reef effect), impacts of global warming and changes in fisheries activities. Key findings from these analyses are that the OWF construction could lead to an increase in benthos species and fish benthos feeders whatever the perturbation scenario, while the predicted response of top predators was ambiguous across all perturbation scenario. Qualitative modelling results can play a vital role in decision making by improving long term planning for the marine environment but also as a tool for communication with the public and so contribute to a better acceptability of the Marine Renewable Energy (MRE) project.
Published: 2018

21. Microbial parasites make cyanobacteria blooms less of a trophic dead end than commonly assumed

Author: Jonathan Colombet, Matilda Haraldsson, Pauline Bazin, Samuele Tecchio, Nathalie Niquil, Télesphore Sime-Ngando, Mélanie Gerphagnon, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université de Rennes 1 - Faculté des sciences pharmaceutiques et biologiques (UR1 Pharmacie), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes - Faculté des sciences pharmaceutiques et biologiques (UR Pharmacie), and Université de Rennes (UR)
Subjects: 0106 biological sciences, 0301 basic medicine, Cyanobacteria, Food Chain, Ecosystem ecology, [SDE.MCG]Environmental Sciences/Global Changes, education, 01 natural sciences, Microbiology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Article, Microbial ecology, 03 medical and health sciences, Food chain, Phytoplankton, Animals, Ecosystem, Biomass, Fungal ecology, Ecology, Evolution, Behavior and Systematics, Trophic level, 2. Zero hunger, Biomass (ecology), biology, Ecology, 010604 marine biology & hydrobiology, Virus–host interactions, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Food web, 030104 developmental biology, 13. Climate action
Abstract: International audience; Parasites exist in every ecosystem and can have large influence on food web structure and function, yet, we know little about parasites’ effect on food web dynamics. Here we investigate the role of microbial parasitism (viruses of bacteria, phytoplankton and cyanobacteria, and parasitic chytrids on cyanobacteria) on the dynamics of trophic pathways and food web functioning during a cyanobacteria bloom, using linear inverse food web modeling parameterized with a 2-month long data set (biomasses, infection parameters, etc.). We show the importance of grazing on heterotrophic bacteria (the microbial pathway: DOC → bacteria → consumer) and how consumers depended on bacteria during peak-cyanobacteria bloom, which abundance was partly driven by the viral activity. As bacteria become the main energy pathway to the consumers, the system takes a more web-like structure through increased omnivory, and may thereby facilitate the system’s persistence to the cyanobacteria outbreak. We also showed how the killing of cyanobacteria host cells by chytrids had important impact on the food web dynamics by facilitating grazing on the cyanobacteria, and by offering alternative pathways to the consumers. This seemed to increase the system’s ability to return to a mix of trophic pathways, which theoretically increases the stability of the system.
Published: 2018

22. Trophic networks: How do theories link ecosystem structure and functioning to stability properties? A review

Author: Galen A. Johnson, Ragnhild Asmus, Cédric Bacher, Alain F. Vézina, Valérie David, Blanche Saint-Béat, Nathalie Niquil, Dan Baird, Harald Asmus, Stephen R. Pacella, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), NASA Johnson Space Center (JSC), NASA, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Alfred Wegener Institute [Potsdam], 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), Institut océanographique Bedford - Bedford Oceanographic Institute [Dartmouth, Canada] (IOB), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), and Normandie Université (NU)
Subjects: Electric resistance, 0106 biological sciences, ecosystem structure, media_common.quotation_subject, Ecology (disciplines), Resistance, Ecological network analysis, General Decision Sciences, Context (language use), Local and global stabilities, Biology, 010603 evolutionary biology, 01 natural sciences, Ecosystems, thermodynamics, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, ecosystem response, ecosystem function, Ecosystem, 14. Life underwater, network analysis, Stability properties, Ecology, Evolution, Behavior and Systematics, media_common, Ecological stability, Resilience, food web, Ecology, Resistance (ecology), business.industry, 010604 marine biology & hydrobiology, Environmental resource management, Food webs, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Food web, Ecological network, 13. Climate action, Maturity, Psychological resilience, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental pressures, business, Stability
Abstract: International audience; In the context of present global changes, interest in understanding how systems respond to anthropogenic environmental pressures and stress has increased. Indices that characterize ecosystem state are helpful tools for the interpretation of ecosystem responses. The central question is how to link these responses to ecosystem structure and functioning and to quantify ecosystem persistence, resistance or resilience. Quantification and characterization of trophic networks by ecological network analysis (ENA) indices is proceeding rapidly, especially in the field of coastal ecology. In this contribution, we review several theories that relate ecosystem structure and function to stability. The structure and functioning of ecosystems change during the maturation of ecosystems. In the first section, the maturation of ecosystems is described using thermodynamics. In the second and third parts of this paper, we define some concepts for analysing structure and functioning of food webs and discuss their relation to stability. In the last section, we describe three ENA indices and their link to stability. We demonstrate that ENA provides powerful tools for describing local stability, combining quantitative and qualitative concepts. However, it remains incomplete for describing real conservation cases that combine local and global stability. © 2015 Elsevier Ltd. All rights reserved.
Published: 2015

23. Before-After analysis of the trophic network of an experimental dumping site in the eastern part of the Bay of Seine (English Channel)

Author: Stella Marmin, Aurore Raoux, Jean-Philippe Pezy, Nathalie Niquil, Jean-Claude Dauvin, Pierre Balay, Morphodynamique Continentale et Côtière ( M2C ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ), Biologie des Organismes et Ecosystèmes Aquatiques ( BOREA ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Muséum National d'Histoire Naturelle ( MNHN ) -Institut de Recherche pour le Développement ( IRD ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université des Antilles ( UA ), Cellule de Suivi du Littoral Normand, Cellule de Suivi du Littoral Normand, 53 rue de Prony, 76600 Le Havre, France, LIttoral ENvironnement et Sociétés - UMR 7266 ( LIENSs ), Université de La Rochelle ( ULR ) -Centre National de la Recherche Scientifique ( CNRS ), Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Normandie Université (NU), and Cellule de Suivi du Littoral Normand (CSLN)
Subjects: dredged material disposal, 0106 biological sciences, Geologic Sediments, Food Chain, education, Aquatic Science, Oceanography, Ecopath, complex mixtures, 010603 evolutionary biology, 01 natural sciences, Bay of Seine, Ascendency, Animals, Ecosystem, 14. Life underwater, Biomass, ComputingMilieux_MISCELLANEOUS, Trophic level, Biomass (ecology), geography, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, trophic model, Ecological Network Analysis, Detritivore, Fishes, Estuary, Pollution, Invertebrates, Refuse Disposal, Fishery, Bays, [SDU]Sciences of the Universe [physics], Benthic zone, Environmental science, France, Environmental Pollution, Estuaries, Bay, [ SDU ] Sciences of the Universe [physics], Environmental Monitoring
Abstract: International audience; An experimental study was conducted to assess the physical and biological impacts of muddy fine sand 3 dredged material dumped on a medium sand site MACHU offshore the Seine Estuary. Complementary 4 trophic web modelling tools were applied to the MACHU ecosystem to analyse the effects of dumping 5 operations. Results show that, after the dumping operations, the biomass of fish increased while 6 invertebrate biomass remained relatively stable through time. Nevertheless, the biomasses of benthic 7 invertebrates, omnivores/scavengers and predators showed some increases, while non-selective 8 deposit feeders and filter feeders decreased. At the ecosystem level, results show that the total 9 ecosystem activity, the ascendency and the overall omnivorous character of the food-web structure 10 increased after dumping operations, whereas recycling subsequently decreased. Finally, the fine and 11 medium sand habitat offshore from the Seine estuary, which undergoes regular natural physical 12 perturbations, shows a high resilience after a short dumping phase. 13
Published: 2017

24. Benthic and fish aggregation inside an offshore wind farm: Which effects on the trophic web functioning?

Author: Aurore Raoux, Géraldine Lassalle, François Le Loc'h, Camille Le Guen, Nathalie Niquil, Jean-Philippe Pezy, Dan Wilhelmsson, Steven Degraer, Jean-Claude Dauvin, Karine Grangeré, Matilda Haraldsson, Bruno Ernande, Samuele Tecchio, Marie Cachera, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Morphodynamique Continentale et Côtière (M2C), Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Royal Belgian Institute of Natural Sciences (RBINS), The Royal Swedish Academy of Sciences, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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), IFREMER Laboratoire Ressources Halieutiques (IFREMER Laboratoire Ressources Halieutiques), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), 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 Ressources halieutiques Manche Mer du nord, IFREMER Centre Manche Mer du Nord, (HMMN), Institut de Recherche pour le Développement (IRD), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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 Ressources halieutiques Boulogne sur mer (LRHBL), Halieutique Manche Mer du Nord (HMMN), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Biologie des Organismes et Ecosystèmes Aquatiques ( BOREA ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Muséum National d'Histoire Naturelle ( MNHN ) -Institut de Recherche pour le Développement ( IRD ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université des Antilles ( UA ), Morphodynamique Continentale et Côtière ( M2C ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ), Ecosystèmes aquatiques et changements globaux ( UR EABX ), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture ( IRSTEA ), Royal Belgian Institute of Natural Sciences ( RBINS ), 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 ), 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 ), IFREMER Laboratoire Ressources Halieutiques ( IFREMER Laboratoire Ressources Halieutiques ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Institut Universitaire Européen de la Mer (IUEM), and 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: 0106 biological sciences, Reef effect, 010504 meteorology & atmospheric sciences, General Decision Sciences, 01 natural sciences, [ SDE.IE ] Environmental Sciences/Environmental Engineering, Wind farm, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ecosystem model, Ecosystem-based approach, EcoSim, Ecosystem, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Trophic level, Biomass (ecology), [ SDU.STU.OC ] Sciences of the Universe [physics]/Earth Sciences/Oceanography, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, 010604 marine biology & hydrobiology, ACL, 15. Life on land, Marine renewable energies, Food web, [ SDV.EE.ECO ] Life Sciences [q-bio]/Ecology, environment/Ecosystems, Fishery, Offshore wind power, 13. Climate action, Benthic zone, Ecopath with Ecosim, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; As part of the energy transition, the French government is planning the construction of three offshore wind farms in Normandy (Bay of Seine and eastern part of the English Channel, northwestern France) in the next years. These offshore wind farms will be integrated into an ecosystem already facing multiple anthropogenic disturbances such as maritime transport, fisheries, oyster and mussel farming, and sediment dredging. Currently no integrated, ecosystem-based study on the effects of the construction and exploitation of offshore wind farms exists, where biological approaches generally focused on the conservation of some valuable species or groups of species. Complementary trophic web modelling tools were applied to the Bay of Seine ecosystem (to the 50 km 2 area covered by the wind farm) to analyse the potential impacts of benthos and fish aggregation caused by the introduction of additional hard substrates from the piles and the turbine scour protections. An Ecopath ecosystem model composed of 37 compartments, from phytoplankton to seabirds, was built to describe the situation " before " the construction of the wind farm. Then, an Ecosim projection over 30 years was performed after increasing the biomass of targeted benthic and fish compartments. Ecological Network Analysis (ENA) indices were calculated for the two periods, " before " and " after " , to compare network functioning and the overall structural properties of the food web. Our main results showed (1) that the total ecosystem activity, the overall system omnivory (proportion of generalist feeders), and the recycling increased after the construction of the wind farm; (2) that higher trophic levels such as piscivorous fish species, marine mammals, and seabirds responded positively to the aggregation of biomass on piles and turbine scour protections; and (3) a change in key-stone groups after the construction towards more structuring and dominant compartments. Nonetheless, these changes could be considered as limited impacts of the wind farm installation on this coastal trophic web structure and functioning.
Published: 2017

25. Reaction of an estuarine food web to disturbance: Lindeman’s perspective

Author: Joana Patrício, João Carlos Marques, Nathalie Niquil, Alexandra Baeta, Jérémy Lobry, Aurélie Chaalali, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), IMAR, Institute of Marine Research, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), 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), UNIVERSITY OF COIMBRA IMAR COIMBRA PRT, Partenaires IRSTEA, 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), INSTITUTE FOR ENVIRONMENT AND SUSTAINABILITY ISPRA ITA, and Irstea Publications, Migration
Subjects: [SDE] Environmental Sciences, 0106 biological sciences, Ecological pyramid, Ecological network analysis, Aquatic Science, Ecological indicator, 010603 evolutionary biology, 01 natural sciences, nutrient enrichment, Food chain, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, ecosystem function, Ecosystem, 14. Life underwater, Zostera, Coimbra [Portugal], Ecology, Evolution, Behavior and Systematics, Trophic level, disturbance, Ecosystem health, Food web models, Portugal, food web, Ecology, biology, 010604 marine biology & hydrobiology, Trophic efficiency, Mondego estuary, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, Food web, 13. Climate action, [SDE]Environmental Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, numerical model, estuarine environment
Abstract: Currently, a central demand of coastal and marine food web researchers is the search for holistic and functional ecosystem health indicators. Based on concepts directly derived from R. L. Lindeman’s work (Lindeman 1942; Ecology 23:399–418), 6 estuarine food web models were analysed to assess the potential impact of multiple disturbances on the trophic state of food webs. The models described a Zostera noltii meadow and a bare sediment site in the Mondego estuary, Portugal, during 3 distinct time periods corresponding to (1) nutrient enrichment, (2) the implementation of mitigation measures, and (3) after a centenary flood. We tested 4 candidate metrics, directly derived from the trophic-dynamic concepts proposed by Lindeman (1942): food chain length, the detritivory/herbivory ratio, trophic efficiency per trophic level and mean trophic efficiency. Based on this case study, none of the metrics are yet ready to be used per se as operational metrics to quantify and interpret the impact of disturbances on the ecosystem’s trophic state. Trophic efficiency appeared to be sensitive to external pressures. However, the mean trophic efficiency of the system might not be sufficient to draw conclusions about the trophic efficiency of the ecosystem: trophic efficiency should be observed at the trophic level in order to better understand cascading effects within food webs., JRC.H.1-Water Resources
Published: 2014

26. An assessment of the trophic structure of the Bay of Biscay continental shelf food web: Comparing estimates derived from an ecosystem model and isotopic data

Author: Paco Bustamante, Tiphaine Chouvelon, Géraldine Lassalle, Nathalie Niquil, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), LIttoral ENvironnement et Sociétés (LIENSs), and La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Aquatic Science, Trophic levels, Demersal fish, Isotopes, North-East Atlantic, Ecosystem model, Validation, Ecosystem, 14. Life underwater, Ecosystem management, Trophic level, geography, geography.geographical_feature_category, biology, Continental shelf, Ecology, Geology, Pelagic zone, Ecopath model, Bay of Biscay, biology.organism_classification, Food web, Comparative studies, Oceanography, Environmental science, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Bay
Abstract: Comparing outputs of ecosystem models with estimates derived from experimental and observational approaches is important in creating valuable feedback for model construction, analyses and validation. Stable isotopes and mass-balanced trophic models are well-known and widely used as approximations to describe the structure of food webs, but their consistency has not been properly established as attempts to compare these methods remain scarce. Model construction is a data-consuming step, meaning independent sets for validation are rare. Trophic linkages in the French continental shelf of the Bay of Biscay food webs were recently investigated using both methodologies. Trophic levels for mono-specific compartments representing small pelagic fish and marine mammals and multi-species functional groups corresponding to demersal fish and cephalopods, derived from modelling, were compared with trophic levels calculated from independent carbon and nitrogen isotope ratios. Estimates of the trophic niche width of those species, or groups of species, were compared between these two approaches as well. A significant and close-to-one positive (, n=16,p&nbsp
Published: 2014

27. What is marine biodiversity? Towards common concepts and their implications for assessing biodiversity status

Author: Sabine Cochrane, Jesper H. Andersen, Torsten Berg, Hugues Blanchet, Angel Borja, Jacob Carstensen, Michael Elliott, Herman Hummel, Nathalie Niquil, Paul E Renaud, Akvaplan-Niva [Tromsø], Norwegian Institute for Water Research (NIVA), Institute of Food and Resource Economics [Copenhagen] (IFRO), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), MariLim Aquatic Research GmbH, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-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), AZTI - Tecnalia, Aarhus University [Aarhus], University of Hull [United Kingdom], Royal Netherlands Institute for Sea Research (NIOZ), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), 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)
Subjects: 0106 biological sciences, Conceptual models, 010504 meteorology & atmospheric sciences, Marine Biodiversity, lcsh:QH1-199.5, [SDE.MCG]Environmental Sciences/Global Changes, assessment, Biodiversity, Ocean Engineering, Aquatic Science, Space (commercial competition), lcsh:General. Including nature conservation, geographical distribution, Oceanography, 01 natural sciences, Structuring, Natural (archaeology), components, Food-webs, Aquatic biodiversity research, Measurement of biodiversity, Marine Science, Ecosystem, 14. Life underwater, lcsh:Science, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Water Science and Technology, Global and Planetary Change, business.industry, 010604 marine biology & hydrobiology, Corporate governance, Environmental resource management, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, 13. Climate action, [SDE]Environmental Sciences, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, ecosystems
Abstract: Biodiversity' is one of the most common keywords used in environmental sciences, spanning from research to management, nature conservation, and consultancy. Despite this, our understanding of the underlying concepts varies greatly, between and within disciplines as well as among the scientists themselves. Biodiversity can refer to descriptions or assessments of the status and condition of all or selected groups of organisms, from the genetic variability, to the species, populations, communities, and ecosystems. However, a concept of biodiversity also must encompass understanding the interactions and functions on all levels from individuals up to the whole ecosystem, including changes related to natural and anthropogenic environmental pressures. While biodiversity as such is an abstract and relative concept rooted in the spatial domain, it is central to most international, European, and national governance initiatives aimed at protecting the marine environment. These rely on status assessments of biodiversity which typically require numerical targets and specific reference values, to allow comparison in space and/or time, often in association with some external structuring factors such as physical and biogeochemical conditions. Given that our ability to apply and interpret such assessments requires a solid conceptual understanding of marine biodiversity, here we define this and show how the abstract concept can and needs to be interpreted and subsequently applied in biodiversity assessments.
Published: 2016

28. Large-scale regional comparisons of ecosystem processes: Methods and approaches

Author: Nathalie Niquil, Louis Legendre, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: 0106 biological sciences, Typology, 010504 meteorology & atmospheric sciences, Computer science, Biodiversity, data set, Large-scale, Aquatic Science, Oceanography, 01 natural sciences, Ecosystems, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, ecosystem function, Ecosystem, Marine ecosystem, 14. Life underwater, comparative study, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, ecosystem management, Structure (mathematical logic), business.industry, 010604 marine biology & hydrobiology, Scale (chemistry), Environmental resource management, Methodology, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Comparative studies, Regions, marine ecosystem, Ecosystem management, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, numerical model, business
Abstract: Large-scale regional marine ecosystems can be compared for various processes that include their structure and biodiversity, functioning, services, and effects on biogeochemical processes. The comparisons can proceed from data up, or from conceptual models down, or from a combination of models and data. This study proposes a typology of methods and approaches that are currently used, or could possibly be used for making large-scale ecosystem comparisons. The various methods and approaches are illustrated with examples drawn from the literature. © 2011 Elsevier B.V.
Published: 2013

29. From species distributions to ecosystem structure and function: A methodological perspective

Author: Jérémy Lobry, Géraldine Lassalle, Aurélie Chaalali, Marina Chifflet, Blanche Saint-Béat, Laurent Bopp, Georges Safi, Samuele Tecchio, Virginie Raybaud, François Le Loc'h, Grégory Beaugrand, Nathalie Niquil, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Université de Lille-Université du Littoral Côte d'Opale-Centre National de la Recherche Scientifique (CNRS), Centre Scientifique de Monaco (CSM), Musee oceanographique de Monaco, Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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), 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), AZTI - Tecnalia, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), 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), Institut de Recherche pour le Développement (IRD), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), European Project: 308392,EC:FP7:ENV,FP7-ENV-2012-two-stage,DEVOTES(2012), Centre National de la Recherche Scientifique (CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut national des sciences de l'Univers (INSU - CNRS), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Université du Littoral Côte d'Opale-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Ecological niche, Climate change, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Effects of global warming, Marine ecosystem, Ecosystem, 14. Life underwater, Small pelagics, 0105 earth and related environmental sciences, business.industry, Ecology, 010604 marine biology & hydrobiology, Ecological Modeling, ACL, Environmental resource management, Ecological Network Analysis, Cumulative effects, Pelagic zone, Food web, 15. Life on land, Linear Inverse Model, Ecological network, Ecological Modelling, 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Climate-induced changes
Abstract: [Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE; International audience; As species biology and ecology is profoundly influenced by climate, any climatic alteration may have severe consequences on marine pelagic ecosystems and their food webs. It remains challenging to estimate the influence of climate on both structural and functional properties of food webs. In this study, we proposed an innovative approach to assess the propagating effects of climate change on ecosystem food web. The approach is based on a sensitivity analysis of a food-web model, a linear inverse model using a Monte Carlo method coupled with a Markov Chain, in which changes in the values of parameters are driven by external Ecological Niche Model outputs. Our sensitivity analysis was restricted to parameters regarding a keystone functional group in marine ecosystems, i.e. small pelagic fish. At the ecosystem level, the consequences were evaluated using both structural and functional ecological network indices. The approach is innovative as it is the first time that these three methods were combined to assess ecological network indices sensitivity to future climatic pressure. This coupling method was applied on the French continental shelf of the Bay of Biscay for which a food-web model already exists and where future changes in the distribution of small pelagic fish have already been examined through model building and projections. In response to the sensitivity analysis corresponding to an increase in small pelagics production only, our results suggested a more active system with an intense plankton-small pelagics-seabirds chain and an efficient recycling to maximize detritus use in the system in relation with detritus export. All results combined together seemed to be in favor of a system adapting to sustain the tested increase in production of small pelagic planktivores. Finally, regarding the innovative combination of numerical tools presented, even if further investigations are still necessary to get a more realistic view of cumulative effects resulting from one given pressure (or more) on a food web (e.g. altering different biological compartments at the same time), the Ecological Network Analysis indices values showed a higher variability under the scenarios of change. Our study thus pointed out a promising methodology to assess propagating changes in structural and functional ecosystem properties.
Published: 2016

30. Evaluating ecosystem-level anthropogenic impacts in a stressed transitional environment: The case of the Seine estuary

Author: Marie Cachera, Nathalie Niquil, Justine Lequesne, Valérie Girardin, Jean-Claude Dauvin, Armonie Tous Rius, Aurore Raoux, Géraldine Lassalle, Samuele Tecchio, Philippe Riou, Jérémy Lobry, Aurélie Chaalali, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Morphodynamique Continentale et Côtière (M2C), Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Laboratoire de Mathématiques Nicolas Oresme (LMNO), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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), Laboratoire Environnement et Ressources de Normandie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Ecosystèmes aquatiques et changements globaux (UR EABX), 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 Environnement Ressources de Normandie (LERN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Biologie des Organismes et Ecosystèmes Aquatiques ( BOREA ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Muséum National d'Histoire Naturelle ( MNHN ) -Institut de Recherche pour le Développement ( IRD ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université des Antilles ( UA ), Morphodynamique Continentale et Côtière ( M2C ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ), Laboratoire de Mathématiques Nicolas Oresme ( LMNO ), Normandie Université ( NU ) -Normandie Université ( NU ) -Centre National de la Recherche Scientifique ( CNRS ), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture ( IRSTEA ), 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 ), 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 ), and Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER )
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Seine estuary, General Decision Sciences, Estuarine ecosystem, Ecological succession, Linear inverse model, 01 natural sciences, E3, media_common.cataloged_instance, Ecosystem, 14. Life underwater, European union, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, media_common, Trophic level, geography, Biomass (ecology), Ecosystem health, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, English Channel, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, ACL, Estuary, 15. Life on land, Food web, 13. Climate action, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: 00000; International audience; During 2002–2005, a new container terminal in the commercial harbour of Le Havre, named “Port2000”, was built on the northern flank of the Seine estuary, northern France. This extension is already known to have modified the estuary current and sediment dynamics, as well as reducing biomass of the suprabenthos assemblage, for the whole downstream part of the system. However, studies on other biotic communities were largely inconclusive, and an ecosystem-wide analysis was still lacking. Here, we performed a before/after study of ecosystem dynamics of the different habitats of the Seine estuary, using a Linear Inverse Modelling technique (LIM-MCMC) to estimate all flows occurring in the food web. Ecological Network Analysis indices were calculated, summarising ecosystem functioning traits and giving indications about the habitat health status. Results showed that the southern flank (FS, Fosse Sud) exhibits all characteristics to be considered as the least stressed habitat of the estuary: system activity and functional specialisation of flows were stable between periods, ecosystem recycling processes and detrital dynamics were also stable; an increase in trophic specialisation (decrease in system omnivory) was the only change confirming a general ecological succession. The northern flank (FN, Fosse Nord), where the actual terminal was built, showed a food web with increased importance of lower trophic levels (increased detritivory and carbon recycling), increased stability and flow efficiency, but possibly regressed to a previous step in ecological succession. In the central navigation channel (CH), patterns of network indices were overall inconclusive and the general image is one of a constantly shifting food web, a condition possibly caused by the year-round dredging activities. The functioning of the Seine estuary – especially of FN and FS – seems to have been modified by the combination of harbour construction and the related mitigation measures. Network indices partially captured this combination of changes and, although not fully operational yet, they are promising tools to comply with the European Union mandate of defining ecosystem health status.
Published: 2016

31. An ecosystem approach for the assessment of fisheries impacts on marine top predators: the Bay of Biscay case study

Author: Jérôme Spitz, Vincent Ridoux, Géraldine Lassalle, Didier Gascuel, M.B. Santos, François Le Loc'h, Graham J. Pierce, Jérémy Lobry, Nathalie Niquil, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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, Fishing, Aquatic Science, fisheries impacts, trophic level, Oceanography, Ecopath, 010603 evolutionary biology, 01 natural sciences, EcoSim, Ecosystem, 14. Life underwater, marine mammals, Ecology, Evolution, Behavior and Systematics, Apex predator, Trophic level, Ecology, 010604 marine biology & hydrobiology, ecosystem modelling, EcoTroph, Discards, Bycatch, Fishery, Overexploitation, 13. Climate action, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, Environmental science, FISHERIES
Abstract: Lassalle, G., Gascuel, D., Le Loc'h, F., Lobry, J., Pierce, G. J., Ridoux, V., Santos, M. B., Spitz, J., and Niquil, N. 2012. An ecosystem approach for the assessment of fisheries impacts on marine top predators: the Bay of Biscay case study. – ICES Journal of Marine Science, 69: 925–938. A number of marine mammal populations is currently threatened by their interactions with fisheries. The present study aimed to provide insights into the severity of potential impacts of operational and biological interactions between top predators and fisheries, in the Bay of Biscay region. Our approach was to modify an Ecopath with Ecosim (EwE) model describing the overall structure and function of the ecosystem by including landings and discards of exploited stocks and estimations of the bycatch of non-target compartments. Second, a set of ecological indices and a trophic level (TL)-based model (EcoTroph, ET) were derived from the EwE model. ET was used to simulate the effects of increasing fishing pressure on the ecosystem and, more particularly, on top predators. The Bay of Biscay was demonstrated to be not far from overexploitation at the current fishing rate, this phenomenon being particularly noticeable for the highest TLs. Within the toothed cetacean community, bottlenose dolphins appeared the most sensitive to resource depletion, whereas common dolphins and harbour porpoises were most impacted by their incidental captures in fishing gears. This study provides a methodological framework to assess the impacts of fisheries on ecosystems for which EwE, or other ecosystem models, already exist.
Published: 2012

32. Eutrophication and trophic structure in response to the presence of the eelgrass Zostera noltii

Author: Rute Pinto, Francesca Rossi, Ivan Valiela, Pierre Richard, João Carlos Marques, Nathalie Niquil, Alexandra Baeta, 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 Biotechnology and Bioengineering (IBB), Technical University of Lisbon, Service de Biochimie Métabolique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), IMAR, Institute of Marine Research, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)
Subjects: 0106 biological sciences, seagrass, anthropogenic source, Scrobicularia plana, Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Benthos, ecosystem function, Ecosystem, 14. Life underwater, Zostera, particulate organic matter, Ecology, Evolution, Behavior and Systematics, Trophic level, food web, Ecology, 010604 marine biology & hydrobiology, Detritivore, 15. Life on land, biology.organism_classification, Zostera noltii, [SDE.ES]Environmental Sciences/Environmental and Society, Food web, Fishery, eutrophication, Benthic zone, trophic structure, meadow, nutrient availability, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, diet, Eutrophication, estuarine environment, primary production
Abstract: In estuaries, eelgrass meadows contribute to fundamental ecosystem functions of estuaries, providing food to several predators and buffering the negative effects of eutrophication. We asked whether the presence of the eelgrass Zostera noltii decreased the nitrogen concentration in the overlying water, affected the sources of nitrogen sequestrated by primary producers and changed the benthic and pelagic food web structures. We also studied the importance of these food webs in providing food to fish. We compared bare sediment to sediment covered by a Z. noltii meadow, and examined nutrient concentrations in the water column and δ15N in primary producers as indicators of anthropogenic inputs of nutrients. We then measured both δ13C and δ15N in the tissues of plants and consumers to establish food web structures. There were no differences in the concentrations and sources of nitrogen between sites. Rather, δ15N values indicated anthropogenic inputs of N (e.g. sewage discharges, agriculture) in both sites. There were no major differences in the structure of the planktonic food web, which was in part sustained by particulate organic matter and supported most predator fish, and in the structure of the benthic food web. Nonetheless, there were differences in the sources of food for omnivore consumers and for the detritivore Scrobicularia plana. Overall, the benthic food web did not use food derived from the eelgrass or macroalgae deposited on the substratum. Suspension feeders used particulate and sediment organic matter, whereas the δ13C and δ15N values of the other consumers indicated a likely contribution of benthic microalgae. Furthermore, in both habitats we found large variability in the isotope signatures of benthic macrofauna consumers, which did not allow distinguishing clearly different trophic groups and indicated a high level of omnivory and a mixed diet opportunistically making use of the availability of food in the surroundings.
Published: 2009

33. The plankton food web of the Bizerte Lagoon (South-western Mediterranean): II. Carbon steady-state modelling using inverse analysis

Author: Nathalie Niquil, Boutheina Grami, Dominique Hamel, Hassine Hadj Mabrouk, Asma Sakka Hlaili, Michel Gosselin, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Ecosystèmes forestiers (UR EFNO), and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)
Subjects: zooplankton, 0106 biological sciences, Tunisia, 010504 meteorology & atmospheric sciences, coastal Mediterranean lagoon, Aquatic Science, Carbon sequestration, trophic level, Oceanography, 01 natural sciences, Carbon cycle, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, inverse method, carbon cycle, Phytoplankton, Ecosystem, 14. Life underwater, Bacillariophyta, 0105 earth and related environmental sciences, Trophic level, food web, 010604 marine biology & hydrobiology, plankton, Bizerte, modeling, Plankton, North Africa, carbon sequestration, [SDE.ES]Environmental Sciences/Environmental and Society, Food web, lagoon, Productivity (ecology), 13. Climate action, Africa, phytoplankton, inverse analysis, Environmental science, Bizerte Lagoon, detritivory, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, primary production
Abstract: International audience; A steady-state model of the planktonic food web of the Bizerte Lagoon (Tunisia, South-western Mediterranean) was developed to characterize its structure and functioning through four stations: MA under urban discharge, MB impacted by industrial input, MJ located at proximity of shellfish farming and R in the central area of the lagoon. Carbon stocks of eight chosen compartments were determined and flows were assigned for each one from field data. Missing flow values were calculated by inverse analysis for each station. Network analysis was applied to the resulting food web models to characterize their properties. These analyses mainly showed similarity among stations concerning (1) a high primary production of phytoplankton which was dominated by \textgreater10 μm cells (i.e. diatoms); (2) important herbivory against detritivory in stations MA and MJ; (3) major role of detritivory in stations MB and R; (4) efficiency of microbial link in transferring carbon for higher trophic level; (5) efficiency of microzooplankton as a trophic link between detritus, dissolved organic carbon, autotrophs and mesozooplankton; (6) important recycling of carbon leading to conclude about an immature state of the ecosystem. Differences between the functioning of microbial food webs in the lagoon are mainly due to the location of stations. The proximity of station MB to inland and industrial discharges affected its productivity and made it the least productive station. Water circulation into the lagoon made pollutant concentrate into the south and the western sections which seemed to affect the planktonic food web, since the values of productivity reported for stations MB and R were lower than those calculated for the others stations. © 2008 Elsevier Ltd. All rights reserved.
Published: 2008

34. The mosaic of habitats of the Seine estuary: Insights from food-web modelling and network analysis

Author: Samuele Tecchio, Aurélie Chaalali, Jérémy Lobry, Jean-Claude Dauvin, Nathalie Niquil, Marie Cachera, Géraldine Lassalle, Nicolas Bacq, Armonie Tous Rius, Jocelyne Morin, Maria Ching Villanueva, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Morphodynamique Continentale et Côtière (M2C), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), 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), 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 - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Groupement d’Intérêt Public Seine-Aval (GIP-Seine-Aval), Université de Bordeaux (UB), Environnements et Paléoenvironnements OCéaniques (EPOC), Centre National de la Recherche Scientifique (CNRS), and Normandie Université (NU)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Ecological network analysis, Trophic network, 01 natural sciences, EcoSim, Ecosystem, 14. Life underwater, 0105 earth and related environmental sciences, Trophic level, geography, Biomass (ecology), geography.geographical_feature_category, Primary producers, Ecology, 010604 marine biology & hydrobiology, Ecological Modeling, Estuary, Marine habitats, Food web, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, 13. Climate action, Ecopath with Ecosim, Ecosystem health indicators, [SDE]Environmental Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Ecological network analysis was applied in the Seine estuary ecosystem, northern France, integrating ecological data from the years 1996 to 2002. The Ecopath with Ecosim (EwE) approach was used to model the trophic flows in 6 spatial compartments leading to 6 distinct EwE models: the navigation channel and the two channel flanks in the estuary proper, and 3 marine habitats in the eastern Seine Bay. Each model included 12 consumer groups, 2 primary producers, and one detritus group. Ecological network analysis was performed, including a set of indices, keystoneness, and trophic spectrum analysis to describe the contribution of the 6 habitats to the Seine estuary ecosystem functioning. Results showed that the two habitats with a functioning most related to a stressed state were the northern and central navigation channels, where building works and constant maritime traffic are considered major anthropogenic stressors. The strong top-down control highlighted in the other 4 habitats was not present in the central channel, showing instead (i) a change in keystone roles in the ecosystem towards sediment-based, lower trophic levels, and (ii) a higher system omnivory. The southern channel evidenced the highest system activity (total system throughput), the higher trophic specialisation (low system omnivory), and the lowest indication of stress (low cycling and relative redundancy). Marine habitats showed higher fish biomass proportions and higher transfer efficiencies per trophic levels than the estuarine habitats, with a transition area between the two that presented intermediate ecosystem structure. The modelling of separate habitats permitted disclosing each one's response to the different pressures, based on their a priori knowledge. Network indices, although non-monotonously, responded to these differences and seem a promising operational tool to define the ecological status of transitional water ecosystems.
Published: 2015

35. A new modeling approach to define marine ecosystems food-web status with uncertainty assessment

Author: Samuele Tecchio, Géraldine Lassalle, Claude Savenkoff, François Le Loc'h, Jérémy Lobry, Blanche Saint-Béat, Georges Safi, Nathalie Niquil, Aurélie Chaalali, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), 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 de Recherche pour le Développement (IRD), Pêches et Oceans Canada, European Project: 308392,EC:FP7:ENV,FP7-ENV-2012-two-stage,DEVOTES(2012), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), 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), Pêches et Océans Canada, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), and 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)
Subjects: linear inverse model, ecosystem, Detritus, Markov chain, Primary producers, food web, Ecological Network Analysis indices, ACL, Geology, Aquatic Science, Bay of Biscay, Food web, Oceanography, 13. Climate action, Ecosystem model, [SDE]Environmental Sciences, Environmental science, Marine ecosystem, Ecosystem, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Trophic level
Abstract: [Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE; International audience; Ecosystem models are currently one of the most powerful approaches used to predict and analyse the consequences of anthropogenic and climate-driven changes in food web structure and function. The modeling community is however still lacking techniques for taking microbial processes properly into account and assessing flow uncertainty explicitly. A linear inverse model of the Bay of Biscay continental shelf was built using a Monte Carlo method coupled with a Markov Chain (LIMMCMC) to characterize the system's trophic food-web status and its associated structural and functional properties. By taking into account the natural variability of ecosystems (and their associated flows) and the lack of data on these environments, this innovative approach enabled the quantification of uncertainties for both estimated flows and derived food-web indices. This uncertainty assessment constituted a real improvement on the existing Ecopath model for the same area and both models results were compared. Our results suggested a food web characterized by main flows at the basis of the food web and a high contribution of primary producers and detritus to the entire system input flows. The developmental stage of the ecosystem was characterized using estimated Ecological Network Analysis (ENA) indices; the LIM-MCMC produced a higher estimate of flow specialization (than the estimate from Ecopath) owing to better consideration of bacterial processes. The results also pointed to a detritus-based food-web with a web-like structure and an intermediate level of internal flow complexity, confirming the results of previous studies. Other current research on ecosystem model comparability is also presented.
Published: 2015

36. Numerical analysis of the food web of an intertidal mudflat ecosystem on the Atlantic coast of France

Author: Nathalie Niquil, Olivier Le Moine, Delphine Leguerrier, Jadwiga Rzeznik, Cédric Bacher, Nicolas Boileau, Pierre-Guy Sauriau, Centre de Recherche sur les Ecosystèmes Littoraux Anthropisés (CRELA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie et Environnement Marin (LBEM), Université de La Rochelle (ULR), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Ligue Protectrice des Oiseaux (LPO), LPO, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche sur les Ecosystèmes Marins et Aquacoles (CREMA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Dynamics of Coastal Environment Department, IFREMER, Région Poitou-Charente, France, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), La Rochelle Université (ULR), LIttoral ENvironnement et Sociétés (LIENSs), and La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Meiobenthos, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Inverse analysis, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Ecosystem, 14. Life underwater, [MATH]Mathematics [math], Ecology, Evolution, Behavior and Systematics, Trophic level, Biomass (ecology), Ecology, Primary producers, 010604 marine biology & hydrobiology, Food web, Pelagic zone, 15. Life on land, Oceanography, Benthic zone, Carbon flow, [SDE]Environmental Sciences, Environmental science, Network analysis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Food web modelling is an ideal way to describe ecosystems, because it accounts for the totality of the relationships between its various components. One difficulty of such an approach, however, lies in the lack of data and information about some ecological relationships, resulting in underdefined systems. Inverse analysis can serve to complete steady-state food webs where the number of direct flow measurements is insufficient relative to the actual number of flows. We applied this method to the intertidal mudflat ecosystem of Brouage (eastern Marennes-Oléron Bay, SW France) and estimated the annual average carbon flows between the compartments of a coupled benthic and pelagic trophic food web from primary producers (microphytobenthos and phytoplankton) to top predators (fish and birds). The resulting network was very sensitive to the primary production of the microphytobenthos which was the most important flow in the system. Sensitivity analyses demonstrated the need for additional data on the nekton, pelagic protozoa, and bacterial compartments. The resulting network showed high bacterial activity, but indices resulting from network analysis showed low cycling in comparison with other ecosystems. The meiofauna had a small biomass, but constituted a very active compartment compared to the macrofauna. Bird production was limited by macrofaunal production. Macrofaunal production reached the maximum allowed by the analysis. The intertidal mudflat ecosystem at Brouage is dominated by benthic production (including benthic primary producers, secondary producers, and predators) with an input of phytoplankton primary production.
Published: 2003

37. A toolbox to evaluate data reliability for whole-ecosystem models: Application on the Bay of Biscay continental shelf food-web model

Author: Géraldine Lassalle, Pierre Bourdaud, Sébastien Rochette, Nathalie Niquil, Blanche Saint-Béat, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Thales Alenia Space, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), and Normandie Université (NU)
Subjects: 0106 biological sciences, Operations research, Computer science, Parameter uncertainty, Data reliability, Ecosystem-based management, 010603 evolutionary biology, 01 natural sciences, Ecopath, Ecosystems, Input output programs, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Food-web models, Ecosystem, 14. Life underwater, Model evaluation, geography, geography.geographical_feature_category, Continental shelf, 010604 marine biology & hydrobiology, Ecological Modeling, Quality control, Bay of Biscay, [SDE.ES]Environmental Sciences/Environmental and Society, Toolbox, Food web, Food-web model, General level, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sensitivity analysis, Bay, Forecasting
Abstract: Ecosystem models are always simplifications of reality and as such their application for ecosystem-based management requires standard validation. Here, the "DataReli" toolbox is proposed to evaluate the quality of the data used during the construction of ecosystem models, their coherence across trophic levels, and whether data limitations prevent the model long-term applications. This toolbox is the combination of three operational and complementary analyses: (i) the pedigree index to determine to what extent a model was calibrated on data of local origin; (ii) the graphical analysis known as PREBAL to assess whether a model respects some basic ecological and fisheries principles; and (iii) a sensitivity analysis to evaluate the robustness of model predictions to small variations in input data. The toolbox is delivered to potential users with main generic recommendations on how interpreting results conjointly and on which decisions to make about parameters' revisions or model uses' restrictions. (i) Corrections of parameters should be preferentially envisaged when modelling data-rich environments. (ii) For those models with an overall pedigree index above 0.4, a closer look at the pedigree routine, i.e. values by parameters and compartments, and the PREBAL analysis would help to prioritize parameters needing improvement. (ii)' For Ecopath models of no overall acceptable quality (overall pedigree index \textless0.4), we recommend stopping the DataReli procedure at this point. (iii) In terms of sensitivity analysis, marked responses of model predictions to small variations in the input values must preferentially lead to restrictions in the model applications compared to corrections of parameter estimates. A concrete application of the "DataReli" toolbox to the pre-existing Ecopath model of the Bay of Biscay continental shelf food web is presented. For the present case study, the general level of input data reliability is considered as satisfying with regard to the model applications. © 2014 Elsevier B.V.
Published: 2014

38. Combining quantitative and qualitative models to identify functional groups for monitoring changes in the Bay of Biscay continental shelf exploited foodweb

Author: Géraldine Lassalle, Verena M. Trenkel, Jean-Sébastien Nelva Pasqual, Marie-Joëlle Rochet, Philippe Boët, Nathalie Niquil, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Ecosystèmes estuariens et poissons migrateurs amphihalins (UR EPBX), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), and Normandie Université (NU)
Subjects: ecosystem structure, environmental disturbance, functional group, Northeast Atlantic continental shelf, Aquatic Science, Oceanography, foodweb, Demersal fish, demersal fish, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, pelagic fish, community response, continental shelf, bioindicator, qualitative analysis, Ecosystem, 14. Life underwater, Functional group (ecology), Atlantic Ocean, Ecology, Evolution, Behavior and Systematics, comparative study, ecosystem management, geography, geography.geographical_feature_category, Ecology, biology, food web, comparative studies, quantitative analysis, Continental shelf, Pelagic zone, Atlantic Ocean (Northeast), biology.organism_classification, Bay of Biscay, [SDE.ES]Environmental Sciences/Environmental and Society, Fishery, ecosystem dynamics, Ecosystem management, Environmental science, ecosystem approach, loop analysis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bioindicator, Bay, primary production, management practice
Abstract: Lassalle, G., Nelva Pasqual, J-S., Boët, P., Rochet, M-J., Trenkel, V. M., and Niquil, N. Combining quantitative and qualitative models to identify functional groups for monitoring changes in the Bay of Biscay continental shelf exploited foodweb. – ICES Journal of Marine Science, 71: . To develop and implement ecosystem-based management, it is critical to monitor foodweb components or functional groups which are robust to uncertainty in ecosystem structure and functioning yet sensitive to changes. To select such functional groups for the Bay of Biscay continental shelf, both quantitative and qualitative foodweb models were developed. First, functional groups for which predictions of directions of change following an increase in primary productivity, prey or predators, or in fishing activities were identical across alternative qualitative model structures were identified. Second, the robustness to model type was assessed by comparing qualitative predictions with quantitative Ecopath model results. The demersal fish community was identified as a sensitive and robust indicator for monitoring foodweb ecological status in the Bay of Biscay. The present study also suggested the potential antagonistic effects of alternative management measures on small pelagic fish and highlighted the need for the joint management of all pressures.
Published: 2014

39. Key Features of Intertidal Food Webs That Support Migratory Shorebirds

Author: Julien Chalumeau, Johann Lavaud, Katell Guizien, Gilles Radenac, Gwenaël Quaintenne, Pierre Richard, Alain F. Vézina, Pierre-Yves Pascal, Pierrick Bocher, Christine Dupuy, Hélène Montanié, Margot De Crignis, Sébastien Lefebvre, Blanche Saint-Béat, Nathalie Niquil, Frédéric Robin, Jean-Luc Mouget, Camille La Fontaine, Francis Orvain, LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Lab-STICC_CNRS_CID_SFIIS, Département Image et Traitement Information (ITI), Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT)-Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT)-Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Observatoire océanologique de Banyuls (OOB), 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), Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Mer, molécules et santé EA 2160 (MMS), 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 Nantes (UN)-Université de Nantes (UN), Biologie des mollusques marins et des écosystèmes associés (BioMEA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie et environnement marins - LBEM (LBEML), Normandie Université (NU), Centre d'Études Biologiques de Chizé (CEBC), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Bedford Institute of Oceanography, Fisheries and Oceans Canada (DFO), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut national des sciences de l'Univers (INSU - CNRS), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), 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 Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université du Littoral Côte d'Opale-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Centre interdisciplinaire de recherche, culture, éducation, formation, travail (CIRCEFT), and Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, lcsh:Medicine, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Nest, Flyway, lcsh:Science, Atlantic Ocean, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Biomass (ecology), Multidisciplinary, geography.geographical_feature_category, Geography, Ecology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Food web, Markov Chains, Bays, [SDE]Environmental Sciences, France, Seasons, Monte Carlo Method, Research Article, Food Chain, [SDE.MCG]Environmental Sciences/Global Changes, Intertidal zone, Biology, 010603 evolutionary biology, Models, Biological, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Birds, Animals, Ecosystem, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Shore, geography, Bacteria, 010604 marine biology & hydrobiology, lcsh:R, 15. Life on land, Invertebrates, lcsh:Q, Animal Migration, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bay, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; The migratory shorebirds of the East Atlantic flyway land in huge numbers during a migratory stopover or wintering on the French Atlantic coast. The Brouage bare mudflat (Marennes-Oléron Bay, NE Atlantic) is one of the major stopover sites in France. The particular structure and function of a food web affects the efficiency of carbon transfer. The structure and functioning of the Brouage food web is crucial for the conservation of species landing within this area because it provides sufficient food, which allows shorebirds to reach the north of Europe where they nest. The aim of this study was to describe and understand which food web characteristics support nutritional needs of birds. Two food-web models were constructed, based on in situ measurements that were made in February 2008 (the presence of birds) and July 2008 (absence of birds). To complete the models, allometric relationships and additional data from the literature were used. The missing flow values of the food web models were estimated by Monte Carlo Markov Chain – Linear Inverse Modelling. The flow solutions obtained were used to calculate the ecological network analysis indices, which estimate the emergent properties of the functioning of a food-web. The total activities of the Brouage ecosystem in February and July are significantly different. The specialisation of the trophic links within the ecosystem does not appear to differ between the two models. In spite of a large export of carbon from the primary producer and detritus in winter, the higher recycling leads to a similar retention of carbon for the two seasons. It can be concluded that in February, the higher activity of the ecosystem coupled with a higher cycling and a mean internal organization, ensure the sufficient feeding of the migratory shorebirds.
Published: 2013

40. Ecosystem status and functioning: Searching for rules of thumb using an intersite comparison of food-web models of Northeast Atlantic continental shelves

Author: Géraldine Lassalle, François Le Loc'h, Maciej T. Tomczak, Steven Mackinson, Jérémy Lobry, Nathalie Niquil, Francisco Sanchez, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Laboratoire de Photonique d'Angers (LPHIA), Université d'Angers (UA), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), UMR 212 EME 'écosystèmes marins exploités' (EME), and Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, zooplankton, ecosystem structure, 010504 meteorology & atmospheric sciences, ecosystem model, Aquatic Science, Oceanography, trophic level, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, graphical analysis, Ecosystem model, ecosystem function, continental shelf, Marine ecosystem, Ecosystem, 14. Life underwater, Atlantic Ocean, Ecology, Evolution, Behavior and Systematics, comparative study, 0105 earth and related environmental sciences, Apex predator, Trophic level, geography, abundance, geography.geographical_feature_category, Ecology, food web, comparative studies, Continental shelf, 010604 marine biology & hydrobiology, graphical method, Pelagic zone, Atlantic Ocean (Northeast), stability, Bay of Biscay, [SDE.ES]Environmental Sciences/Environmental and Society, Food web, marine ecosystem, Ecopath with Ecosim, trophic structure, ecological modeling, Environmental science, benthic-pelagic coupling, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Lassalle, G., Lobry, J., Le Loc'h, F., Mackinson, S., Sanchez, F., Tomczak, M. T., and Niquil, N. 2013. Ecosystem status and functioning: searching for rules of thumb using an intersite comparison of food-web models of Northeast Atlantic continental shelves. – ICES Journal of Marine Science, 70:135–149. This work aimed to provide a better understanding of how the structure and function of marine ecosystems and trophic control mechanisms influence their response to perturbations. Comparative analysis of Ecopath models of four Northeast Atlantic ecosystems was used to search for rules of thumb defining the similarities and differences between them. Ecosystem indicators, related to the ecology of species interactions, were derived from these models and compared. Two main questions were addressed. (i) What are the main energy pathways and mechanisms of control? (ii) Do these ecosystems exhibit the widespread and potentially stabilizing food-web structure such that top predators couple distinct energy pathways? A strong bentho-pelagic coupling operated over the Bay of Biscay Shelf, while energy reached higher trophic levels mostly through pelagic compartments, in northern areas. Zooplankton was demonstrated to be trophically important in all ecosystems, acting as a regulator of the abundance of small pelagic fish. A latitudinal pattern in flow control was highlighted by this analysis, with a significant contribution of top-down effect at higher latitudes. This top-down control of the Baltic Sea, combined with the fact that this ecosystem did not exhibit the potentially stabilizing two-channel structure, suggested a non-stable environment.
Published: 2013

41. Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models: A case study from the Marennes-Oléron Estuary, France

Author: Donald L. Phillips, Pierre Richard, Stephen R. Pacella, Benoit Lebreton, Theodore H. DeWitt, Nathalie Niquil, College of Earth, Ocean and Atmospheric Sciences [Corvallis] (CEOAS), Oregon State University (OSU), Western Ecology Division, Office of Research and Development, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, biology, Stable isotope ratio, Ecology, 010604 marine biology & hydrobiology, Ecological Modeling, δ15N, Atmospheric sciences, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Food web, Seagrass, 13. Climate action, [SDE]Environmental Sciences, Social ecological model, Environmental science, Ecosystem, Marine ecosystem, 14. Life underwater, Mixing (physics)
Abstract: International audience; We investigated the use of output from Bayesian stable isotope mixing models asconstraints for a linear inverse food web model of a temperate intertidal seagrass systemin the Marennes-Oléron Bay, France. Linear inverse modeling (LIM) is a technique thatestimates a complete network of flows in an under-determined system using acombination of site-specific data and relevant literature data. This estimation of completeflow networks of food webs in marine ecosystems is becoming more recognized for itsutility in understanding ecosystem functioning. However, diets and consumption rates oforganisms are often difficult or impossible to accurately and reliably measure in the field,resulting in a large amount of uncertainty in the magnitude of consumption flows andresource partitioning in ecosystems. In order to address this issue, this study utilizedstable isotope data to help aid in estimating these unknown flows. δ13C and δ15N isotopedata of consumers and producers in the Marennes-Oléron seagrass system was used inBayesian mixing models. The output of these mixing models was then translated asinequality constraints (minimum and maximum of relative diet contributions) into aninverse analysis model of the seagrass ecosystem. We hypothesized that incorporatingthe diet information gained from the stable isotope mixing models would result in a moreconstrained food web model. In order to test this, two inverse food web models werebuilt to track the flow of carbon through the seagrass food web on an annual basis, withunits of mg C m-2 d-1. The first model (Traditional LIM) included all available data, withthe exception of the diet constraints formed from the stable isotope mixing models. Thesecond model (Isotope LIM) was identical to the Traditional LIM, but included the SIARdiet constraints. Both models were identical in structure, and intended to model the sameMarennes-Oléron intertidal seagrass bed. Each model consisted of 27 compartments (24living, 3 detrital) and 175 flows. Comparisons between the outputs of the models showedthe addition of the SIAR-derived isotopic diet constraints further constrained the solutionrange of all food web flows on average by 26%. Flows that were directly affected by anisotopic diet constraint were 45% further constrained on average. These resultsconfirmed our hypothesis that incorporation of the isotope information would result in amore constrained food web model, and demonstrated the benefit of utilizing multi-tracerstable isotope information in ecosystem models.
Published: 2013

42. The effect of physical drivers on ecosystem indices derived from ecological network analysis: Comparison across estuarine ecosystems

Author: Dan Baird, Eric Chaumillon, Ragnhild Asmus, Harald Asmus, Galen A. Johnson, Cédric Bacher, Boutheina Grami, Valérie David, Xavier Bertin, Nathalie Niquil, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Xbrane Bioscience, Xbrane Bioscience (AB), Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), NASA Johnson Space Center (JSC), and NASA
Subjects: 0106 biological sciences, ecological network analysis, Tidal range, 010504 meteorology & atmospheric sciences, media_common.quotation_subject, Context (language use), Aquatic Science, Oceanography, 01 natural sciences, semi-enclosed systems, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, physical forcing, Ecosystem, 14. Life underwater, [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, media_common, Trophic level, Detritus, Ecology, 010604 marine biology & hydrobiology, mass-balance model, Food web, estuaries, 13. Climate action, comparison, ecosystem functioning, Environmental science, Psychological resilience, Catchment area, Physical geography, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; The structure and function of estuarine food webs change in response to both natural and anthropogenic stresses. The construction of quantitative food webs and their analysis by means of Ecological Network Analysis provides outputs that have been used in many studies to assess system development, stress, robustness, resilience and maturity. Here we attempt to relate to the physical characteristics of the environment, ecosystem indices derived from Ecological Network Analysis. Ten models of food webs were gathered, across a selection of soft-bottom estuaries representative of a large morphological and hydrodynamic diversity, from wave-dominated to mixed energy tide-dominated systems. The selection allowed the comparison of their derived Ecological Network Analysis indices, because of similarities of accuracy in the representation of detritus and bacteria, and because models took into account all trophic levels up to top-predators. In order to obtain comparable physical characteristics, global models were used for a homogeneous description of tide and tidal prisms. Spearman correlations, hierarchical ascendant clustering and Redundancy Analysis were applied to examine the relationship between Ecological Network Analysis indices and physical characteristics. The set of four physical variables selected (catchment area, tidal range at neap tide, index of tide-wave domination and latitude in absolute value) explained 67% of the structure of the Ecological Network Analysis indices. This implies that the physical forcing related to climate, hydrodynamics and morphology is essential for determining the ecological emergent properties of the food web. In the European policy context of determining the ‘good ecological status’ of coastal ecosystems, it implies that the use of Ecological Network Analysis indices for basing the determination of operational indicators should be done, taking into account this context of a strong influence of physical factors.
Published: 2012

43. Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing

Author: Sébastien, Monchy, Giovanna, Sanciu, Marlène, Jobard, Serena, Rasconi, Mélanie, Gerphagnon, Magali, Chabé, Amandine, Cian, Dionigia, Meloni, Nathalie, Niquil, Urania, Christaki, Eric, Viscogliosi, and Télesphore, Sime-Ngando
Subjects: Base Sequence, Ecology, Molecular Sequence Data, Colony Count, Microbial, Fungi, Fresh Water, Biodiversity, Water Microbiology, DNA, Ribosomal, Ecosystem, Phylogeny
Abstract: Water samples were collected along transects from the shore to the centre of two French lakes: the deep, volcanic, oligomesotrophic and low allochthonic-impacted Lake Pavin, and the productive and higher allochthonic-impacted Lake Aydat. The biodiversity was analysed using two approaches: the classical approach consisting of cloning/sequencing of the 18S, ITS1, 5.8S, ITS2 and partial 28S region using primers designed for fungus sequences, and the pyrosequencing of 18S rRNA hypervariable V2, V3 and V5 regions using two primer sets (one universal for eukaryotes and one for fungi). The classical approach yielded 146 (Lake Pavin) and 143 (Lake Aydat) sequences, corresponding to 46 and 63 operational taxonomic units (OTUs) respectively. Fungi represented half of the OTUs identified in Lake Pavin and 30% in Lake Aydat, and were dominated by sequences from Chytridiomycota found throughout Lake Pavin but mostly in the central pelagic zone of Lake Aydat. The pyrosequencing approach yielded 42,064 (Pavin) and 61,371 (Aydat) reads, of which 12-15% and 9-19% reads were assigned to fungi in Lakes Pavin and Aydat respectively. Chytridiomycota members were also dominant among these reads, with OTUs displaying up to33-fold overrepresentation in the centre compared with the riparian areas of Lake Aydat. Besides fungi, both approaches revealed other major eukaryote groups, with the highest diversity in the central areas of lakes. One of the major findings of our study was that the two lakes displayed contrasting spatial distributions, homogenous for Lake Pavin and heterogeneous for Lake Aydat, which may be related to their peculiarities. This study represents the first unveiling of microbial eukaryote and fungus diversity assessed with two complementary molecular methods, and is considered a major milestone towards understanding the dynamics and ecology of fungi in freshwater lake ecosystems, which are directly link to the abundance and distribution of taxa.
Published: 2011

44. Modelling the effects of eutrophication, mitigation measures and an extreme flood event on estuarine benthic food webs

Author: Alexandra Baeta, Joana Patrício, João Carlos Marques, Nathalie Niquil, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), IMAR, Institute of Marine Research, Marine and environmental research centre - IMAR-CMA (Coimbra, Portugal), and University of Coimbra [Portugal] (UC)
Subjects: 0106 biological sciences, seagrass, Physiology, ecological impact, Hydrobia ulvae, 01 natural sciences, Mondego Estuary, Hediste diversicolor, snail, Biomass, extreme event, Trophic level, ecosystem health, algae, disturbance, Biomass (ecology), abundance, biology, Primary producers, Ecology, Food web, Sedimentology, Management, eutrophication, Benthic zone, ecological modeling, detritus, Ecological models, Estuaries, primary production, Zostera, algal bloom, Scrobicularia plana, 010603 evolutionary biology, Ecopath, Ecosystems, Flood, Anoxic sediments, mitigation, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ecosystem, grazing, 14. Life underwater, Coimbra [Portugal], estuarine ecosystem, Ecological model, Detritus, Portugal, software, 010604 marine biology & hydrobiology, fungi, benthos, human activity, 15. Life on land, biology.organism_classification, omnivory, Throughput, [SDE.ES]Environmental Sciences/Environmental and Society, Floods, 13. Climate action, Environmental science, habitat fragmentation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, mass balance
Abstract: Human-mediated and natural disturbances such as nutrient enrichment, habitat modification, and flood events often result in significant shifts in species composition and abundance that translate into changes in the food web structure. Six mass-balanced models were developed using the " Ecopath with Ecosim" software package to assess changes in benthic food web properties in the Mondego estuarine ecosystem (Portugal). Field, laboratory and literature information were used to construct the models. The main study objective was to assess at 2 sites (a Zostera meadow and a bare sediment area) the effects of: (1) a period of anthropogenic enrichment, which led to excessive production of organic matter in the form of algal blooms (1993/1994); (2) the implementation of mitigation measures, following a long period of eutrophication (1999/2000); and (3) a centenary flood (winter 2000/2001). Different numbers of compartments were identified at each site and in each time period. In general, the Zostera site, due to its complex community, showed a higher number of compartments and a higher level of system activity (i.e. sum of consumptions, respiration, flow to detritus, production, total system throughput, net primary production and system omnivory index). The differences at the two sites in the three time periods in the breakdown of throughput were mainly due to differences in the biomass of the primary producers (higher primary production at the Zostera site). Consumption, respiration and flow to detritus were dominated by the grazers Hydrobia ulvae and Scrobicularia plana at the Zostera and bare sediment sites respectively. At both sites, after recovery measures were implemented there was an increase in S. plana and Hediste diversicolor biomass, consumption, respiration and flows to detritus, and a decrease in H. ulvae biomass and associated flows, which increased again after the flood event. The mass-balanced models showed that the trophic structure of the benthic communities in Mondego estuary was affected differently by each disturbance event. Interestingly, in our study a high system throughput seems to be associated with higher stress levels, which contradicts the idea that higher system activity is always a sign of healthier conditions. © 2010 Elsevier B.V.
Published: 2011

45. Lower trophic levels and detrital biomass control the Bay of Biscay continental shelf food web: Implications for ecosystem management

Author: Grégoire Certain, Christian Hily, Jérôme Spitz, Claire Labry, Claire Pusineri, Elise Marquis, F. Le Loc'h, Pierre Petitgas, Vincent Ridoux, Paco Bustamante, Géraldine Lassalle, O. Le Pape, Christine Dupuy, Jérémy Lobry, Nathalie Niquil, Daniel Delmas, LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes estuariens et poissons migrateurs amphihalins (UR EPBX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), UMR 212 EME 'écosystèmes marins exploités' (EME), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM), Dyneco - Département DYNamiques de l'Environnement CÔtier, 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 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), Département DYNamiques de l'Environnement CÔtier (Dyneco), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Écologie et Modèles pour l'halieutique (EMH), Office National de la Chasse et de Faune Sauvage, Cellule Technique Océan Indien, Centre de Recherche sur les Mammifères Marins (CRMM), Université de La Rochelle (ULR), European Project: 244966,EC:FP7:KBBE,FP7-KBBE-2009-3,FACTS(2010), Centre National de la Recherche Scientifique (CNRS), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institut National de la Recherche Agronomique (INRA), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Dynamiques des Écosystèmes Côtiers (DYNECO), 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), Écologie et Modèles pour l'Halieutique (EMH), La Rochelle Université (ULR), French program PNEC'Chantier Golfe de Gascogne', EU FP7 grant FACTS (Forage Fish Interactions), Grant Agreement No. 244966, European project REPRODUCE (EratNet-Marifish, WP7, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Dynamiques de l'Environnement Côtier (DYNECO), 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 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), Écologie et Modèles pour l'Halieutique (IFREMER EMH), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, multispecies fisheries, BISCAYE BAIE, Aquatic Science, 01 natural sciences, Ecopath, North-East Atlantic, Energy flow, continental shelf, EcoSim, Marine ecosystem, Ecosystem, 14. Life underwater, 0105 earth and related environmental sciences, ecosystem management, Primary producers, 010604 marine biology & hydrobiology, Marine habitats, aquatic communities, Geology, 15. Life on land, Bay of Biscay, Fishery, Oceanography, bottom-up control, trophic structure, [SDE]Environmental Sciences, Ecosystem management, Environmental science, Fisheries management, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology
Abstract: [Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE; International audience; The Bay of Biscay (North-East Atlantic) has long been subjected to intense direct and indirect human activities that lead to the excessive degradation and sometimes overexploitation of natural resources. Fisheries management is gradually moving away from single-species assessments to more holistic, multi-species approaches that better respond to the reality of ecosystem processes. Quantitative modelling methods such as Ecopath with Ecosim can be useful tools for planning, implementing and evaluating ecosystem-based fisheries management strategies. The aim of this study was therefore to model the energy fluxes within the food web of this highly pressured ecosystem and to extract practical information required in the diagnosis of ecosystem state/health. A well-described model comprising 30 living and two non-living compartments was successfully constructed with data of local origin, for the Bay of Biscay continental shelf. The same level of aggregation was applied to primary producers, mid-trophic-levels and top-predators boxes. The model was even more general as it encompassed the entire continuum of marine habitats, from benthic to pelagic domains. Output values for most ecosystem attributes indicated a relatively mature and stable ecosystem, with a large proportion of its energy flow originating from detritus. Ecological network analysis also provided evidence that bottom-up processes play a significant role in the population dynamics of upper-trophic-levels and in the global structuring of this marine ecosystem. Finally, a novel metric based on ecosystem production depicted an ecosystem not far from being overexploited. This finding being not entirely consistent over indicators, further analyses based on dynamic simulations are required.
Published: 2011

46. Functional effects of parasites on food web properties during the spring diatom bloom in Lake Pavin: a linear inverse modeling analysis

Author: Marlène Jobard, Télesphore Sime-Ngando, Blanche Saint-Béat, Serena Rasconi, Boutheina Grami, Nathalie Niquil, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés (LIENSs), and La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Diatom bloom, Marine and Aquatic Sciences, lcsh:Medicine, 01 natural sciences, Food chain, Food Web Structure, Chytrids, Lake Pavin, lcsh:Science, Freshwater Ecology, Multidisciplinary, biology, Ecology, Plankton, Eutrophication, Food web, Chytridiomycota, Community Ecology, France, Seasons, Bloom, Research Article, Freshwater Environments, Food Chain, Mycology, 010603 evolutionary biology, Microbiology, Ecosystems, Animals, Ecosystem, Parasites, 14. Life underwater, Biology, Diatoms, Detritus, 010604 marine biology & hydrobiology, lcsh:R, fungi, Fungi, biology.organism_classification, Carbon, Diet, Lakes, Diatom, 13. Climate action, Linear Models, Earth Sciences, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem Modeling, Ecological Environments
Abstract: International audience; This study is the first assessment of the quantitative impact of parasitic chytrids on a planktonic food web. We used a carbon-based food web model of Lake Pavin (Massif Central, France) to investigate the effects of chytrids during the spring diatom bloom by developing models with and without chytrids. Linear inverse modelling procedures were employed to estimate undetermined flows in the lake. The Monte Carlo Markov chain linear inverse modelling procedure provided estimates of the ranges of model-derived fluxes. Model results support recent theories on the probable impact of parasites on food web function. In the lake, during spring, when 'inedible' algae (unexploited by planktonic herbivores) were the dominant primary producers, the epidemic growth of chytrids significantly reduced the sedimentation loss of algal carbon to the detritus pool through the production of grazer-exploitable zoospores. We also review some theories about the potential influence of parasites on ecological network properties and argue that parasitism contributes to longer carbon path lengths, higher levels of activity and specialization, and lower recycling. Considering the "structural asymmetry" hypothesis as a stabilizing pattern, chytrids should contribute to the stability of aquatic food webs.
Published: 2011

47. Editorial: 'Disregarded' microbial diversity and ecological potentials in aquatic systems: a new paradigm shift ahead

Author: Nathalie Niquil, Télesphore Sime-Ngando, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), LIttoral ENvironnement et Sociétés (LIENSs), and La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, DYNAMICS, Aquatic systems, Microbial diversity, Rare biosphere, Ecology (disciplines), Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Microbial ecology, ECOSYSTEMS, Ecosystem, 14. Life underwater, DEEP-SEA, 030304 developmental biology, 0303 health sciences, SEQUENCES, Ecology, Aquatic ecosystem, 15. Life on land, RARE BIOSPHERE, LAKE, Microbial biodiversity, 13. Climate action, Paradigm shift, PLANKTON, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, COMMUNITIES
Abstract: International audience; The introduction of molecular methods to the study of prokaryotes in the mid-1980s (Pace et al., 1986), and their expansion to small eukaryotes in the early 2000s (Lopez-Garcia et al., 2001; Moon-van der Staay et al., 2001) have allowed investigation of uncultured microbes in natural environments, and have greatly increased our knowledge of microbial biodiversity. The resulting major methodological, conceptual and empirical advances in aquatic microbial ecology are arguably the greatest advances in environmental sciences. Recent developments in sequencing technology and the use of SSU rRNA hypervariable tag sequencing are beginning to reveal the huge dimension of the microbial diversity hidden in natural aquatic ecosystems (Sogin et al., 2006; Huse et al., 2008). A very large number of microbial species may be represented by only one single cell among an assemblage of over a million cells present in 1 ml of water. This is because (i) aquatic systems are the largest on the Earth, (ii) microbial extinction is unlikely, (iii) sexuality is not a limiting factor, (iv) microbes live in all types of environments, including the most extreme conditions and (v) the number of microbial ''species'' ranges from millions to hundreds of millions. This corroborates with the Baas- Becking hypothesis on prokaryote and protist biogeography (i.e. 'everything is everywhere, but, the environment selects'), meaning that while the whole of microbial life is distributed worldwide, in a target environment the majority of species are only latently present (cf. de Wit&Bouvier, 2006). Hence, on a small spatial scale, most microbial biodiversity is hidden for our observation, because most species are cryptic or will occur at densities below our limit of detection........
Published: 2011

48. Network analysis and inter-ecosystem comparison of two intertidal mudflat food webs (Brouage Mudflat and Aiguillon Cove, SW France)

Author: Delphine Degré, Delphine Leguerrier, Nathalie Niquil, Centre de Recherche sur les Ecosystèmes Littoraux Anthropisés (CRELA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), and Normandie Université (NU)
Subjects: 0106 biological sciences, Inverse analysis, Oceanography, 01 natural sciences, intertidal environment, Ecosystem comparison, Grazing, network analysis, geography.geographical_feature_category, biology, food web, Ecology, Food web, net ecosystem production, Europe, detritus, inverse analysis, intertidal mudflat, Network analysis, France, steady-state equilibrium, primary production, Intertidal zone, Western Europe, Aquatic Science, 010603 evolutionary biology, bivalve, Atlantic Coast [France], [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Intertidal mudflat, ecosystem function, Ecosystem, 14. Life underwater, Cove, Atlantic Coast [Europe], geography, Detritus, 010604 marine biology & hydrobiology, Estuary, Bivalvia, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, Fishery, ecosystem comparison, Atlantic coast, Environmental science, coastal zone, Eurasia, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, mudflat
Abstract: Network analysis was used to analyse steady-state models of the food webs of two intertidat mudflat ecosystems: Aiguillon Cove and Brouage Mudflat, on the South-Western Atlantic Coast of France. The aim was to highlight emergent properties of food-web functioning in these two ecosystems and to compare these properties with other coastal ecosystems. Both ecosystems imported detritus in parallel to a high benthic primary production. They were characterised by a high diversity of resources. Both also exported living material, leading to a high quality production, quantified as export of Exergy. This export was mainly composed of cultivated bivalves during the cold season for Brouage Mudflat, and of the migration of grazing fish in Aiguillon Cove during the warm season. Their internal organization was characterised by short pathways, high recycling, high redundancy and low net ecosystem production, compared to the other systems selected. These characteristics, encountered in many estuaries, presented less extreme values. (c) 2007 Elsevier Ltd. All rights reserved.
Published: 2007

49. Community structure of digenean parasites of sparid and labrid fishes of the Mediterranean sea: A new approach

Author: Pierre Sasal, Nathalie Niquil, P. Bartoli, Parasitologie fonctionnelle et évolutive [2003-2006] (PFE), Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Diversité, évolution et écologie fonctionnelle marine (DIMAR), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, fish disease, Statistics as Topic, Parasite community, phylogeny, 01 natural sciences, 030308 mycology & parasitology, Fish Diseases, Parasite hosting, Host-Parasite Relations, 0303 health sciences, teleost, biology, Ecology, Statistics, Community structure, Fishes, article, Infectious Diseases, host, priority journal, parasite, Digeneans, Specificity, community, Trematoda, Niche, Trematode Infections, 010603 evolutionary biology, Intraspecific competition, Host-Parasite Interactions, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Canonical correspondence analysis, Mediterranean Sea, Animals, 14. Life underwater, Ecosystem, nonhuman, Canonical Correspondence Analysis, Species diversity, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, Fish, Animal Science and Zoology, Parasitology, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, diet, Digestive System
Abstract: The aim of this work was to study the structure of the parasite communities of Digeneans of 2 families of Teleost fishes (Sparidae and Labridae) of the Mediterranean sea. We tried to quantify the importance of both the microhabitat requirements of the parasite species and the effect of host biological factors on the parasite communities. We applied, for the first time in parasite community studies, the Canonical Correspondence Analysis (CCA) to analyse (i) the spatial distribution of parasite species within the digestive tract of the hosts; (ii) the host's biological factors (such as diet, host length, gregariousness and abundance) that may influence this spatial distribution of parasite species. Our results showed that potential microhabitats were vacant in the 2 host families studied revealing a lack of niche saturation because either there was little inter- and/or intraspecific competition or there were enough available space and resources within the host. Our results also indicated that the position of the parasite in the digestive tract is much more important than host biological factors for the structure of parasite community. Finally, we highlight the potential use of the CCA method for controlling for phylogenetic constraints in multi-species analyses.
Published: 1999

50. Inverse model analysis of the planktonic food web of Takapoto Atoll (French Polynesia)

Author: Bruno Delesalle, George A. Jackson, Nathalie Niquil, Louis Legendre, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), École pratique des hautes études (EPHE), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), and Université Paris sciences et lettres (PSL)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Atoll, French Polynesia, carbon cycling, Aquatic Science, 01 natural sciences, Zooplankton, Carbon cycle, modelling, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Tuamotu Archipelago, Inverse model analysis, Phytoplankton, Ecosystem, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, geography, Detritus, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, organic carbon, fungi, plankton, Food web, Coral reef, Plankton, Frnech Polynesia, [SDE.ES]Environmental Sciences/Environmental and Society, Oceanography, Takapoto Atoll, Atoll lagoon, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: A steady-state model of the planktonic food web of the lagoon of Takapoto Atoll (Tuamotu Archipelago, French Polynesia) was developed to assess the characteristics of that ecosystem. The planktonic food web was divided into 7 compartments, whose carbon biomasses and rates of exchange were determined from field data combined with inverse analysis, the latter being used to estimate missing rates. Results indicate that the system was characterized by high phytoplankton production and, in agreement with previous results, low bacterial production. Due to their high metabolism, metazoan zooplankton played a dominant role in the cycling of carbon. In contrast, the contribution of protozoa was small. The non-living particulate organic carbon compartment also played a key role, qualitatively and quantitatively, because detritus was directly consumed by all heterotrophic compartments.
Published: 1998

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