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Auteur Draredja, M.A.; Frihi, H.; Boualleg, C.; Gofart, A.; Abadie, E.; Laabir, M. doi  openurl
  Titre Seasonal variations of phytoplankton community in relation to environmental factors in a protected meso-oligotrophic southern Mediterranean marine ecosystem (Mellah lagoon, Algeria) with an emphasis of HAB species Type Article scientifique
  Année 2019 Publication Revue Abrégée Environ. Monit. Assess.  
  Volume 191 Numéro 10 Pages 603  
  Mots-Clés coastal lagoons; Diversity; dynamics; Environmental conditions; HAB species; Mediterranean lagoon; nutrients; particulate matter; patterns; Phytoplankton monitoring; sea; temporal variations; thau lagoon; venice lagoon; water-quality  
  Résumé The spatial and temporal variation of phytoplankton communities including HAB species in relation to the environmental characteristics was investigated in the protected meso-oligotrophic Mellah lagoon located in the South Western Mediterranean. During 2016, a biweekly monitoring of phytoplankton assemblages and the main abiotic factors were realized at three representative stations. Taxonomic composition, abundance, and diversity index were determined. In total, 227 phytoplankton species (160 diatoms and 53 dinoflagellates) were inventoried. There was a clear dominance of diatoms (62.9%) compared with dinoflagellates (36.8%). Diatoms dominated in spring and dinoflagellates developed in summer and early autumn in Mellah showing a marked seasonal trend. Data showed that the dynamic of the phytoplankton taxa evolving in the lagoon was mainly driven by temperature and salinity. For the first time, a number of potentially toxic species have been identified, including 2 diatoms (Pseudo-nitzschia group delicatissima, Pseudo-nitzschia group seriata) and 5 dinoflagellates (Alexandrium minutum, Alexandrium tamarense/catenella, Dinophysis acuminata, Dinophysis sacculus, Prorocentrum lima). These harmful species could threat the functioning of the Mellah lagoon and human health and require the establishment of a monitoring network. Finally, our study suggests that the observed decrease of the phytoplankton diversity between 2001 and 2016 could result from the reduction in water exchanges between the lagoon and the adjacent coast following the gradual clogging of the channel.  
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  Langue English Langue du Résumé Titre Original  
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  Volume de collection Numéro de collection Edition  
  ISSN 0167-6369 ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000484493700001 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection (down) 2635  
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Auteur Ranchou-Peyruse, M.; Auguet, J.-C.; Maziere, C.; Restrepo-Ortiz, C.X.; Guignard, M.; Dequidt, D.; Chiquet, P.; Cezac, P.; Ranchou-Peyruse, A. doi  openurl
  Titre Geological gas-storage shapes deep life Type Article scientifique
  Année 2019 Publication Revue Abrégée Environ. Microbiol.  
  Volume Numéro Pages  
  Mots-Clés carbon; degradation; depth; desulfotomaculum; diversity; methanogenesis; microbial communities; spp.; sulfate-reducing bacteria; sulfite  
  Résumé Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H-2) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.  
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  Langue English Langue du Résumé Titre Original  
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  Volume de collection Numéro de collection Edition  
  ISSN 1462-2912 ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000480010600001 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection (down) 2627  
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Auteur Matthews, T.J.; Triantis, K.A.; Whittaker, R.J.; Guilhaumon, F. doi  openurl
  Titre sars: an R package for fitting, evaluating and comparing species-area relationship models Type Article scientifique
  Année 2019 Publication Revue Abrégée Ecography  
  Volume 42 Numéro 8 Pages 1446-1455  
  Mots-Clés accumulation; curves; diversity; diversity-area relationship; island biogeography; islands; richness; species-area relationship  
  Résumé The species-area relationship (SAR) constitutes one of the most general ecological patterns globally. A number of different SAR models have been proposed. Recent work has shown that no single model universally provides the best fit to empirical SAR datasets: multiple models may be of practical and theoretical interest. However, there are no software packages available that a) allow users to fit the full range of published SAR models, or b) provide functions to undertake a range of additional SAR-related analyses. To address these needs, we have developed the R package 'sars' that provides a wide variety of SAR-related functionality. The package provides functions to: a) fit 20 SAR models using non-linear and linear regression, b) calculate multi-model averaged curves using various information criteria, and c) generate confidence intervals using bootstrapping. Plotting functions allow users to depict and scrutinize the fits of individual models and multi-model averaged curves. The package also provides additional SAR functionality, including functions to fit, plot and evaluate the random placement model using a species-sites abundance matrix, and to fit the general dynamic model of oceanic island biogeography. The 'sars' R package will aid future SAR research by providing a comprehensive set of simple to use tools that enable in-depth exploration of SARs and SAR-related patterns. The package has been designed to allow other researchers to add new functions and models in the future and thus the package represents a resource for future SAR work that can be built on and expanded by workers in the field.  
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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 0906-7590 ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000477975800010 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection (down) 2625  
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Auteur Chao, A.; Chiu, C.-H.; Villeger, S.; Sun, I.-F.; Thorn, S.; Lin, Y.-C.; Chiang, J.-M.; Sherwin, W.B. doi  openurl
  Titre An attribute-diversity approach to functional diversity, functional beta diversity, and related (dis)similarity measures Type Article scientifique
  Année 2019 Publication Revue Abrégée Ecol. Monogr.  
  Volume 89 Numéro 2 Pages Unsp-e01343  
  Mots-Clés attribute diversity; biodiversity; biological diversity; consensus; conservation; differentiation measures; diversity decomposition; evenness; framework; functional (dis)similarity; functional beta diversity; functional diversity; Hill numbers; phylogenetic diversity; quadratic entropy; similarity; species diversity; species richness; species traits; trait diversity  
  Résumé Based on the framework of attribute diversity (a generalization of Hill numbers of order q), we develop a class of functional diversity measures sensitive not only to species abundances but also to trait-based species-pairwise functional distances. The new method refines and improves on the conventional species-equivalent approach in three areas: (1) the conventional method often gives similar values (close to unity) to assemblages with contrasting levels of functional diversity; (2) when a distance metric is unbounded, the conventional functional diversity depends on the presence/absence of other assemblages in the study; (3) in partitioning functional gamma diversity into alpha and beta components, the conventional gamma is sometimes less than alpha. To resolve these issues, we add to the attribute-diversity framework a novel concept: tau, the threshold of functional distinctiveness between any two species; here, tau can be chosen to be any positive value. Any two species with functional distance >= tau are treated as functionally equally distinct. Our functional diversity quantifies the effective number of functionally equally distinct species (or “virtual functional groups”) with all pairwise distances at least tau for different species pairs. We advocate the use of two complementary diversity profiles (tau profile and q profile), which depict functional diversity with varying levels of tau and q, respectively. Both the conventional species-equivalent method (i.e., tau is the maximum of species-pairwise distances) and classic taxonomic diversity (i.e., tau is the minimum of non-zero species-pairwise distances) are incorporated into our proposed tau profile for an assemblage. For any type of species-pairwise distance matrices, our attribute-diversity approach allows proper diversity partitioning, with the desired property gamma >= alpha and thus avoids all the restrictions that apply to the conventional diversity decomposition. Our functional alpha and gamma are interpreted as the effective numbers of functionally equally distinct species, respectively, in an assemblage and in the pooled assemblage, while beta is the effective number of equally large assemblages with no shared species and all species in the assemblages being equally distinct. The resulting beta diversity can be transformed to obtain abundance-sensitive Sorensen- and Jaccard-type functional (dis)similarity profiles. Hypothetical and real examples are used to illustrate the framework. Online software and R codes are available to facilitate computations.  
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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 0012-9615 ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000477640700001 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection (down) 2620  
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Auteur Cocquempot, L.; Delacourt, C.; Paillet, J.; Riou, P.; Aucan, J.; Castelle, B.; Charria, G.; Claudet, J.; Conan, P.; Coppola, L.; Hocdé, R.; Planes, S.; Raimbault, P.; Savoye, N.; Testut, L.; Vuillemin, R. doi  openurl
  Titre Coastal Ocean and Nearshore Observation: A French Case Study Type Article scientifique
  Année 2019 Publication Revue Abrégée Front. Mar. Sci.  
  Volume 6 Numéro Pages Unsp-324  
  Mots-Clés 2013/2014 winter; atlantic coast; coastal ocean; coastline; diversity; ecosystem; increases; interdisciplinary; national structuration; nutrient ratios; observation infrastructure; phytoplankton community; temperature; variability; wave activity  
  Résumé To understand and predict the physical, chemical, and biological processes at play in coastal and nearshore marine areas requires an integrated, interdisciplinary approach. The case study of the French structuration of coastal ocean and nearshore observing systems provides an original overview on a federative research infrastructure named ILICO. It is a notable example of national structuration and pan-institution efforts to investigate the forefront of knowledge on the processes at work within the critical coastal zone. ILICO comprises, in a pluridisciplinary approach, eight distributed network-systems of observation and data analysis that are accredited and financially supported by French research institutions and the French Ministry for Higher Education, Research, and Innovation. ILICO observation points are implemented along metropolitan and overseas French coasts, where coastline dynamics, sea level evolution, physical and biogeochemical water properties, coastal water dynamics, phytoplankton composition, and health of coral reefs are monitored in order to address a wide range of scientific questions. To give an overview of the diversity and potential of the observations carried out, this paper offers a detailed presentation of three constituting networks: Service Observation en Milieu LITtoral (SOMLIT), with homogeneous sampling strategies, DYNALIT, with heterogeneous sampling strategies adapted to different environments, and Mediterranean Ocean Observing System for the Environment (MOOSE), an integrated, pluri-disciplinary coasta/offshore regional observatory in the north-western Mediterranean Sea. ILICO was conceived using a European framework. It addresses the great challenges of the next decade in terms of sustainability, cost-efficiency, interoperability, and innovation. This paper emphasizes the added-value of federating these systems, and highlights some recommendations for the future.  
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