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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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  ISSN 1462-2912 ISBN Médium  
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  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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  ISSN 0906-7590 ISBN Médium  
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  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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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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Auteur Boavida, J.; Becheler, R.; Choquet, M.; Frank, N.; Taviani, M.; Bourillet, J.-F.; Meistertzheim, A.-L.; Grehan, A.; Savini, A.; Arnaud-Haond, S. doi  openurl
  Titre Out of the Mediterranean? Post-glacial colonization pathways varied among cold-water coral species Type Article scientifique
  Année 2019 Publication Revue Abrégée J. Biogeogr.  
  Volume 46 Numéro 5 Pages 915-931  
  Mots-Clés biodiversity; cold-water corals; computer-program; deep-sea; deep-sea corals; genetic-structure; glacial marine refugia; glacial refugia; growth; in-situ; Last Glacial Maximum; Lophelia pertusa; lophelia-pertusa; Madrepora oculata; marine phylogeography; north-atlantic ocean; software  
  Résumé Aim: To infer cold-water corals' (CWC) post-glacial phylogeography and assess the role of Mediterranean Sea glacial refugia as origins for the recolonization of the northeastern Atlantic Ocean. Location: Northeastern Atlantic Ocean and Mediterranean Sea. Taxon: Lophelia pertusa, Madrepora oculata. Methods: We sampled CWC using remotely operated vehicles and one sediment core for coral and sediment dating. We characterized spatial genetic patterns (microsatellites and a nuclear gene fragment) using networks, clustering and measures of genetic differentiation. Results: Inferences from microsatellite and sequence data were congruent, and showed a contrast between the two CWC species. Populations of L. pertusa present a dominant pioneer haplotype, local haplotype radiations and a majority of endemic variation in lower latitudes. Madrepora oculata populations are differentiated across the northeastern Atlantic and genetic lineages are poorly admixed even among neighbouring sites. Conclusions: Our study shows contrasting post-glacial colonization pathways for two key habitat-forming species in the deep sea. The CWC L. pertusa has likely undertaken a long-range (post-glacial) recolonization of the northeastern Atlantic directly from refugia located along southern Europe (Mediterranean Sea or Gulf of Cadiz). In contrast, the stronger genetic differentiation of M. oculata populations mirrors the effects of long-term isolation in multiple refugia. We suggest that the distinct and genetically divergent, refugial populations initiated the post-glacial recolonization of the northeastern Atlantic margins, leading to a secondary contact in the northern range and reaching higher latitudes much later, in the late Holocene. This study highlights the need to disentangle the influences of present-day dispersal and evolutionary processes on the distribution of genetic polymorphisms, to unravel the influence of past and future environmental changes on the connectivity of cosmopolitan deep-sea ecosystems associated with CWC.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection (down) 2602  
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