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Auteur Bettarel, Y.; Halary, S.; Auguet, J.-C.; Mai, T.C.; Bui, N.V.; Bouvier, T.; Got, P.; Bouvier, C.; Monteil-Bouchard, S.; Christelle, D. doi  openurl
  Titre Corallivory and the microbial debacle in two branching scleractinians Type Article scientifique
  Année 2018 Publication Revue Abrégée Isme J.  
  Volume 12 Numéro 4 Pages 1109-1126  
  Mots-Clés brown band disease; coral-associated bacteria; diversity; drupella-cornus; great-barrier-reef; network analysis; red-sea; search tool; viral communities; viruses  
  Résumé The grazing activity by specific marine organisms represents a growing threat to the survival of many scleractinian species. For example, the recent proliferation of the corallivorous gastropod Drupella now constitutes a critical case in all South-East Asian waters. If the damaging effects caused by this marine snail on coral polyps are relatively well known, the indirect incidence of predation on coral microbial associates is still obscure and might also potentially impair coral health. In this study, we compared the main ecological traits of coral-associated bacterial and viral communities living in the mucus layer of Acropora formosa and Acropora millepora, of healthy and predated individuals (i.e., colonized by Drupella rugosa), in the Bay of Van Phong (Vietnam). Our results show a substantial impact of the gastropod on a variety of microbiological markers. Colonized corals harbored much more abundant and active epibiotic bacteria whose community composition shifted toward more pathogenic taxa (belonging to the Vibrionales, Clostridiales, Campylobacterales, and Alteromonadales orders), together with their specific phages. Viral epibionts were also greatly influenced by Drupella corallivory with spectacular modifications in their concentrations, life strategies, genotype richness, and diversity. Novel and abundant circular Rep-encoding ssDNA viruses (CRESS-DNA viruses) were detected and characterized in grazed corals and we propose that their occurrence may serve as indicator of the coral health status. Finally, our results reveal that corallivory can cause severe dysbiosis by altering virus-bacteria interactions in the mucus layer, and ultimately favoring the development of local opportunistic infections.  
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  Langue English Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1751-7362 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2325  
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Auteur Coll, M.; Steenbeek, J. doi  openurl
  Titre Standardized ecological indicators to assess aquatic food webs: The ECOIND software plug-in for Ecopath with Ecosim models Type Article scientifique
  Année 2017 Publication Revue Abrégée Environ. Modell. Softw.  
  Volume 89 Numéro Pages 120-130  
  Mots-Clés biodiversity; Conservation; Ecological standardized indicators; Ecopath with Ecosim; ecospace; Ecosystem indicators; Environmental status; Fisheries management; Food web models; impacts; index; marine ecosystems; Mediterranean Sea; network analysis; ocean; Software plug-in  
  Résumé Ecological indicators are useful tools to analyse and communicate historical changes in ecosystems and plausible future scenarios while evaluating environmental status. Here we introduce a new plug-in to the Ecopath with Ecosim (EwE) food web modelling approach, which is widely used to quantitatively describe aquatic ecosystems. The plug-in (ECOIND) calculates standardized ecological indicators. We describe the primary functionality of ECOIND and provide an example of its application in both static and temporal-spatial dynamic modelling, while we highlight several related features including a new taxonomy input database (species traits) and the ability to analyse input uncertainty on output results. ECOIND adds new capabilities to the widely used EwE food web modelling approach and enables broadening its applications into biodiversity and conservation-based frameworks to contribute to integrated ecosystem analyses. (C) 2016 Elsevier Ltd. All rights reserved.  
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  Langue English Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1364-8152 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2088  
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Auteur Heymans, J.J.; Coll, M.; Link, J.S.; Mackinson, S.; Steenbeek, J.; Walters, C.; Christensen, V. doi  openurl
  Titre Best practice in Ecopath with Ecosim food-web models for ecosystem-based management Type Article scientifique
  Année 2016 Publication Revue Abrégée Ecol. Model.  
  Volume 331 Numéro Pages 173-184  
  Mots-Clés benguela ecosystem; dynamics; Ecological network analysis; Ecopath with Ecosim; Ecosystem-based management; Ecosystem modelling; exploited ecosystems; impacts; indicators; marine ecosystems; Monte Carlo; network analysis; nw mediterranean sea; shelf ecosystem; southern benguela; Time series fitting  
  Résumé Ecopath with Ecosim (EwE) models are easier to construct and use compared to most other ecosystem modelling techniques and are therefore more widely used by more scientists and managers. This, however, creates a problem with quality assurance; to address this we provide an overview of best practices for creating Ecopath, models. We describe the diagnostics that can be used to check for thermodynamic and ecological principles, and highlight principles that should be used for balancing a model. We then highlight the pitfalls when comparing Ecopath models using Ecological Network Analysis indices. For dynamic simulations in Ecosim we show the state of the art in calibrating the model by fitting it to time series using a formal fitting procedure and statistical goodness of fit. Finally, we show how Monte Carlo simulations can be used to address uncertainty in input parameters, and we discuss the use of models in a management context, specifically using the concept of 'key runs' for ecosystem-based management. This novel list of best practices for EwE models will enable ecosystem managers to evaluate the goodness of fit of the given EwE model to the ecosystem management question. (C) 2016 The Authors. Published by Elsevier B.V.  
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  Volume de collection Numéro de collection Edition  
  ISSN 0304-3800 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1644  
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Auteur KIVELA, M.; ARNAUD-HAOND, S.; SARAMAKI, J. url  doi
openurl 
  Titre EDENetworks: A user-friendly software to build and analyse networks in biogeography, ecology and population genetics Type Article scientifique
  Année 2015 Publication Revue Abrégée Molecular Ecology Resources  
  Volume 15 Numéro 1 Pages 117-122  
  Mots-Clés Biogeography; biological communities; graph theory; microbial ecology; network analysis; population genetics  
  Résumé The recent application of graph-based network theory analysis to biogeography, community ecology and population genetics has created a need for user-friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy-to-use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray-Curtis or Sorensen distance, or population genetic metrics such as FST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.  
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  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1755-098x ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1119  
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Auteur Meddeb, M.; Grami, B.; Chaalali, A.; Haraldsson, M.; Niquil, N.; Pringault, O.; Sakka Hlaili, A. url  doi
openurl 
  Titre Plankton food-web functioning in anthropogenically impacted coastal waters (SW Mediterranean Sea): an ecological network analysis Type Article scientifique
  Année 2018 Publication Revue Abrégée Progress in Oceanography  
  Volume Numéro Pages  
  Mots-Clés Ecological Network Analysis; Food-web modelling; Mediterranean coastal waters; plankton ecology  
  Résumé 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 food-web 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 >10µm 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.  
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  ISSN 0079-6611 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2292  
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