@article {LeGuen2019, title = {Assessing the ecological status of an estuarine ecosystem: linking biodiversity and food-web indicators}, journal = {Estuarine, Coastal and Shelf Science}, volume = {228}, year = {2019}, note = {cited By 0}, publisher = {Academic Press}, abstract = {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. {\textcopyright} 2019 Elsevier Ltd}, keywords = {Biodiversity, bioindicator, community composition, ecological approach, ecological modeling, ecosystem function, ecosystem health, environmental assessment, estuarine ecosystem, food web, France, habitat management, health status, human activity, Le Havre, Normandie, Seine Estuary, Seine Maritime}, issn = {02727714}, doi = {10.1016/j.ecss.2019.106339}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0272771419300484}, author = {Le Guen, Camille and Samuele Tecchio and Jean-Claude Dauvin and De Roton, G. and Lobry, Jeremy and Lepage, Mario and Morin, Jocelyne and G{\'e}raldine Lassalle and Raoux, Aurore and Nathalie Niquil} } @article {Raoux2019728, title = {Measuring sensitivity of two OSPAR indicators for a coastal food web model under offshore wind farm construction}, journal = {Ecological Indicators}, volume = {96}, year = {2019}, note = {cited By 2}, pages = {728-738}, publisher = {Elsevier B.V.}, abstract = {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. {\textcopyright} 2018 Elsevier Ltd}, keywords = {Barium compounds, Bay of Seine, coastal zone, Ecological network analysis, Ecopath with Ecosim, ecosystem function, ecosystem structure, Ecosystems, Electric utilities, English Channel, food web, France, in situ measurement, Marine environment, Marine renewable energy, measurement method, model, Offshore wind farms, Reefs, Reserve effect, sensitivity analysis, trophic level, wind farm}, issn = {1470160X}, doi = {10.1016/j.ecolind.2018.07.014}, url = {https://www.sciencedirect.com/science/article/abs/pii/S1470160X1830534X}, author = {Raoux, Aurore and G{\'e}raldine Lassalle and Pezy, Jean-Philippe and Samuele Tecchio and Safi, Georges and Ernande, Bruno and Maz{\'e}, C. and Le Loc{\textquoteright}h, Francois and Lequesne, Justine and Girardin, Valerie and Jean-Claude Dauvin and Nathalie Niquil} } @article {5037, title = {Benthic and fish aggregation inside an offshore wind farm: Which effects on the trophic web functioning?}, journal = {Ecological indicators}, volume = {72}, year = {2017}, month = {01/2017}, pages = {33-46}, abstract = {

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, north-western 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 {\textquoteleft}{\textquoteleft}before{{\textquoteright}{\textquoteright}} 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, {\textquoteleft}{\textquoteleft}before{{\textquoteright}{\textquoteright}} and {\textquoteleft}{\textquoteleft}after{{\textquoteright}{\textquoteright}}, 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 keystone 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. (C) 2016 Elsevier Ltd. All rights reserved.

}, issn = {{1470-160X}}, doi = {10.1016/j.ecolind.2016.07.037}, author = {Raoux, Aurore and Samuele Tecchio and Pezy, Jean-Philippe and G{\'e}raldine Lassalle and Degraer, Steven and Wilhelmsson, Dan and Cachera, Marie and Ernande, Bruno and Le Guen, Camille and Haraldsson, Matilda and Karine Granger{\'e} and Le Loc{\textquoteright}h, Francois and Dauvin, Jean-Claude and Nathalie Niquil} } @article {5039, title = {Evaluating ecosystem-level anthropogenic impacts in a stressed transitional environment: The case of the Seine estuary}, journal = {ECOLOGICAL INDICATORS}, volume = {61}, year = {2016}, month = {02/2016}, pages = {833-845}, abstract = {

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. (c) 2015 Elsevier Ltd. All rights reserved.

}, issn = {{1470-160X}}, doi = {{10.1016/j.ecolind.2015.10.036}}, author = {Samuele Tecchio and Chaalali, Aur{\'e}lie and Raoux, Aurore and Rius, Armonie Tous and Lequesne, Justine and Girardin, Valerie and G{\'e}raldine Lassalle and Cachera, Marie and Riou, P and Lobry, Jeremy and Dauvin, Jean-Claude and Nathalie Niquil} } @article {5038, title = {From species distributions to ecosystem structure and function: A methodological perspective}, journal = {ECOLOGICAL MODELLING}, volume = {334}, year = {2016}, month = {08/2016}, pages = {78-90}, abstract = {

{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. (C) 2016 Elsevier B.V. All rights reserved.}

}, issn = {{0304-3800}}, doi = {{10.1016/j.ecolmodel.2016.04.022}}, author = {Chaalali, Aur{\'e}lie and Gr{\'e}gory Beaugrand and Virginie Raybaud and G{\'e}raldine Lassalle and Saint-B{\'e}at, B and Le Loc{\textquoteright}h, Francois and Bopp, Laurent and Samuele Tecchio and Safi, Georges and Chifflet, Marina and Lobry, Jeremy and Nathalie Niquil} } @article {5041, title = {Incorporating food-web parameter uncertainty into Ecopath-derived ecological network indicators}, journal = {ECOLOGICAL MODELLING}, volume = {313}, year = {2015}, month = {OCT 10}, pages = {29-40}, abstract = {

Ecological network analysis (ENA) provides numerous ecosystem level indices offering a valuable approach to compare and categorize the ecological structure and function of ecosystems. The inclusion of ENA methods in Ecopath with Ecosim (EwE) has insured their continued contribution to ecosystem-based management. In EwE, ENA-derived ecological conclusions are currently based on single values of ENA indices calculated from a unique input flow matrix. Here, we document an easy-to-use routine that allows EwE users to incorporate uncertainty in EwE input data into the calculation of ENA indices. This routine, named ENAtool, is a suite of Matlab functions that performs three main steps: (1) import of an existing Ecopath model and its associated parameter uncertainty values in the form of uncertainty intervals into Matlab; (2) generation of an ensemble of Ecopath models with the same structure as the original, and with parameter values varying based on the prescribed uncertainty limits; and (3) calculation of a set of 13 ENA indices for each ensemble member (one set of flow values) and of summary statistics across the whole ensemble. This novel routine offers the opportunity to calculate ENA indices ranges and confidence intervals, and thus to perform quantitative data analyses. An application of ENAtool on a pre-existing Ecopath model of the Bay of Biscay continental shelf is presented, with a focus on the robustness of previously published ENA-based ecological traits of this ecosystem when the newly introduced uncertainty values are added. We also describe the sensitivity of the ENAtool results to both the number of ensemble members used and to the uncertainty interval set around each input parameter. Ecological conclusions derived from EwE, particularly those regarding the comparison of structural and functional elements for a range of ecosystem types or the assessment of ecosystem properties along gradients of environmental conditions or anthropogenic disturbances, will gain in statistical interpretability. (C) 2015 Elsevier B.V. All rights reserved.

}, issn = {{0304-3800}}, doi = {{10.1016/j.ecolmodel.2015.05.036}}, author = {Guesnet, Vanessa and G{\'e}raldine Lassalle and Chaalali, Aur{\'e}lie and Kearney, Kelly and Saint-B{\'e}at, B and Karimi, Battle and Grami, Boutheina and Samuele Tecchio and Nathalie Niquil and Lobry, Jeremy} } @article {5042, title = {The mosaic of habitats of the Seine estuary: Insights from food-web modelling and network analysis}, journal = {ECOLOGICAL MODELLING}, volume = {312}, year = {2015}, month = {09/2015}, pages = {91-101}, abstract = {

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{\textquoteright}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. (C) 2015 Elsevier B.V. All rights reserved.

}, issn = {{0304-3800}}, doi = {{10.1016/j.ecolmodel.2015.05.026}}, author = {Samuele Tecchio and Rius, Armonie Tous and Dauvin, Jean-Claude and Lobry, Jeremy and G{\'e}raldine Lassalle and Morin, Jocelyne and Bacq, Nicolas and Cachera, Marie and Chaalali, Aur{\'e}lie and Villanueva, Maria Ching and Nathalie Niquil} } @article {5048, title = {A new modeling approach to define marine ecosystems food-web status with uncertainty assessment}, journal = {Progress in Oceanography}, volume = {135}, year = {2015}, pages = {37{\textendash}47}, author = {Chaalali, Aur{\'e}lie and Saint-B{\'e}at, B and G{\'e}raldine Lassalle and Le Loc{\textquoteright}h, Francois and Samuele Tecchio and Safi, Georges and Savenkoff, Claude and Lobry, Jeremy and Nathalie Niquil} } @article {5040, title = {Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive}, journal = {ECOLOGICAL INDICATORS}, volume = {58}, year = {2015}, month = {NOV}, pages = {175-191}, abstract = {

The European Union{\textquoteright}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 similar to 49\% and similar to 43\% respectively, were better addressed in the reviewed modelling approaches than the non-indigenous species (0.3\%) and sea floor integrity (similar to 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. (C) 2015 The Authors. Published by Elsevier Ltd.

}, issn = {{1470-160X}}, doi = {{10.1016/j.ecolind.2015.05.037}}, author = {Piroddi, Chiara and Teixeira, Heliana and Lynam, Christopher P. and Smith, Chris and Alvarez, Maria C. and Mazik, Krysia and Andonegi, Eider and Churilova, Tanya and Tedesco, Letizia and Chifflet, Marina and Chust, Guillem and Galparsoro, Ibon and Garcia, Ana Carla and Kamari, Maria and Kryvenko, Olga and G{\'e}raldine Lassalle and Neville, Suzanna and Nathalie Niquil and Papadopoulou, Nadia and Rossberg, Axel G. and Suslin, Vjacheslav and Uyarra, Maria C.} } @article {Lassale_etal2013, title = {{Combining quantitative and qualitative models to identify functional groups for monitoring changes in the Bay of Biscay continental shelf exploited foodweb}}, journal = {ICES Journal of Marine Science}, volume = {71}, number = {1}, year = {2014}, pages = {105{\textendash}117}, abstract = {

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.

}, keywords = {comparative studies, ecosystem management, foodweb, loop analysis, Northeast Atlantic continental shelf}, doi = {10.1093/icesjms/fst107}, author = {G{\'e}raldine Lassalle and Nelva Pasqual, J-S and Bo{\"e}t, P and Rochet, M J and Trenkel, V M and Nathalie Niquil} } @article {5052, title = {A toolbox to evaluate data reliability for whole-ecosystem models: application on the Bay of Biscay continental shelf food-web model}, journal = {Ecological modelling}, volume = {285}, year = {2014}, pages = {13{\textendash}21}, author = {G{\'e}raldine Lassalle and Bourdaud, Pierre and Saint-B{\'e}at, B and Rochette, S{\'e}bastien and Nathalie Niquil} }