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Auteur Lezama-Ochoa, N.; Murua, H.; Chust, G.; Ruiz, J.; Chavance, P.; Molina, A.D. de; Caballero, A.; Sancristobal, I. url  doi
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  Titre Biodiversity in the by-catch communities of the pelagic ecosystem in the Western Indian Ocean Type Article scientifique
  Année 2015 Publication Revue Abrégée Biodivers Conserv  
  Volume 24 Numéro 11 Pages (down) 2647-2671  
  Mots-Clés By-catch; Diversity; Ecosystem Approach to Fisheries Management; Evolutionary Biology; Plant Sciences; Purse seine fishery; Tree Biology; Western Indian Ocean  
  Résumé Diversity in the by-catch communities from the pelagic ecosystem in the tropical tuna purse seine fishery has been poorly studied. This study uses different biodiversity measures to compare drifting fish aggregating devices (FADs) and Free School sets (sets made on schools of tuna) of the Western Indian Ocean. Data was collected from observer programs carried out by the European Union between 2003 and 2010 on board Spanish and French fleets. Alpha (species diversity of a particular area) and Beta diversity (difference in species composition between different areas) was analyzed to assess differences in the number of species, abundances and the species composition between areas and fishing modes. Generalized additive models were undertaken to explore which geographical/environmental variables explain the distribution of species richness index and Shannon diversity index in both fishing modes. Results showed that by-catch species in FAD communities may be used as observatories of surface pelagic biodiversity in combination with Free School communities. FAD communities were more diverse with higher number of species (74 species) and evenly distributed than Free School communities (56 species). However, environmental variables played a more important role in Free School communities. Somalia area and Mozambique Channel were the areas with highest biodiversity rates in both fishing modes. This work contributed for the future implementation of the EAFM to manage the pelagic ecosystem in a holistic and more integrated way.  
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  ISSN 0960-3115, 1572-9710 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1422  
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Auteur Escalas, A.; Bouvier, T.; Mouchet, M.A.; Leprieur, F.; Bouvier, C.; Troussellier, M.; Mouillot, D. url  doi
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  Titre A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales Type Article scientifique
  Année 2013 Publication Revue Abrégée Environmental microbiology  
  Volume 15 Numéro 10 Pages (down) 2642-2657  
  Mots-Clés Microbial communities; Rao quadratic entropy; metagenomic; microbial biodiversity; molecular fingerprint; β diversity  
  Résumé Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (alpha), regional (gamma) and the overall difference between local communities (beta). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the beta component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the alpha, beta and gamma components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (gamma = alpha + beta), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach.  
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  ISSN 1462-2920 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 430  
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Auteur Galand, P.E.; Pereira, O.; Hochart, C.; Auguet, J-C.; Debroas, D. doi  openurl
  Titre A strong link between marine microbial community composition and function challenges the idea of functional redundancy Type Article scientifique
  Année 2018 Publication Revue Abrégée Isme J.  
  Volume 12 Numéro 10 Pages (down) 2470-2478  
  Mots-Clés biosphere; cell; depth; diversity; dynamics; gene; program; sequencing data; short read alignment; waters  
  Résumé Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes.  
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  ISSN 1751-7362 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2435  
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Auteur Miloslavich, P.; Bax, N.J.; Simmons, S.E.; Klein, E.; Appeltans, W.; Aburto‐Oropeza, O.; Garcia, M.A.; Batten, S.D.; Benedetti‐Cecchi, L.; Checkley, D.M.; Chiba, S.; Duffy, J.E.; Dunn, D.C.; Fischer, A.; Gunn, J.; Kudela, R.; Marsac, F.; Muller‐Karger, F.E.; Obura, D.; Shin, Y.-J. url  doi
openurl 
  Titre Essential ocean variables for global sustained observations of biodiversity and ecosystem changes Type Article scientifique
  Année 2018 Publication Revue Abrégée Global Change Biology  
  Volume 24 Numéro 6 Pages (down) 2416-2433  
  Mots-Clés driver-pressure-state-impact-response; essential ocean variables; framework for ocean observing; global ocean observing system; marine biodiversity changes; Marine Biodiversity Observation Network; ocean change  
  Résumé Sustained observations of marine biodiversity and ecosystems focused on specific conservation and management problems are needed around the world to effectively mitigate or manage changes resulting from anthropogenic pressures. These observations, while complex and expensive, are required by the international scientific, governance and policy communities to provide baselines against which the effects of human pressures and climate change may be measured and reported, and resources allocated to implement solutions. To identify biological and ecological essential ocean variables (EOVs) for implementation within a global ocean observing system that is relevant for science, informs society, and technologically feasible, we used a driver-pressure-state-impact-response (DPSIR) model. We (1) examined relevant international agreements to identify societal drivers and pressures on marine resources and ecosystems, (2) evaluated the temporal and spatial scales of variables measured by 100+ observing programs, and (3) analysed the impact and scalability of these variables and how they contribute to address societal and scientific issues. EOVs were related to the status of ecosystem components (phytoplankton and zooplankton biomass and diversity, and abundance and distribution of fish, marine turtles, birds and mammals), and to the extent and health of ecosystems (cover and composition of hard coral, seagrass, mangrove and macroalgal canopy). Benthic invertebrate abundance and distribution and microbe diversity and biomass were identified as emerging EOVs to be developed based on emerging requirements and new technologies. The temporal scale at which any shifts in biological systems will be detected will vary across the EOVs, the properties being monitored and the length of the existing time-series. Global implementation to deliver useful products will require collaboration of the scientific and policy sectors and a significant commitment to improve human and infrastructure capacity across the globe, including the development of new, more automated observing technologies, and encouraging the application of international standards and best practices.  
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  ISSN 1365-2486 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2336  
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Auteur Arnaud-Haond, S.; Aires, T.; Candeias, R.; Teixeira, S.J.L.; Duarte, C.M.; Valero, M.; Serrao, E.A. doi  openurl
  Titre Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia Type Article scientifique
  Année 2017 Publication Revue Abrégée Mol. Ecol.  
  Volume 26 Numéro 8 Pages (down) 2379-2391  
  Mots-Clés Algae; australia; Caulerpa; Chlorophyta; clonal diversity; dna; endophytic communities; genetic diversity; holobiont; invasion paradox; marine invasion; Mediterranean Sea; microsatellite markers; parasites; plant invasions; polymorphism  
  Résumé Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of alpha and beta diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.  
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  ISSN 0962-1083 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2143  
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