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Auteur Sebastian, M.; Smith, A.F.; Gonzalez, J.M.; Fredricks, H.F.; Van Mooy, B.; Koblizek, M.; Brandsma, J.; Koster, G.; Mestre, M.; Mostajir, B.; Pitta, P.; Postle, A.D.; Sanchez, P.; Gasol, J.M.; Scanlan, D.J.; Chen, Y. doi  openurl
  Titre Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency Type Article scientifique
  Année 2016 Publication Revue Abrégée Isme J.  
  Volume 10 Numéro 4 Pages (down) 968-978  
  Mots-Clés 2 enzymes; agrobacterium-tumefaciens; bacterioplankton groups; Ecology; Mediterranean Sea; mesocosm experiment; microbial food-web; north-atlantic ocean; nutrient limitation; phosphate starvation  
  Résumé Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean.  
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  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  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  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 1624  
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Auteur Poggiale, J.-C.; Dantigny, P.; De Wit, R.; Steinberg, C. url  isbn
openurl 
  Titre Modeling in Microbial Ecology Type Chapitre de livre
  Année 2015 Publication Revue Abrégée  
  Volume Numéro Pages (down) 847-882  
  Mots-Clés Biofilm models; Biotic interactions; Chemostat; Fermenter models; Metabolic models; Microbial Ecology; Population dynamics  
  Résumé The bases and the principles of modeling in microbial community ecology and biogeochemistry are presented and discussed. Several examples are given. Among them, the fermentation process is largely developed, thus demonstrating how the model allows determining the microbial population growth rate, the death rate, and the maintenance rate. More generally, these models have been used to increase the development of bioenergetic formulations which are presently used in biogeochemical models (Monod, Droop, DEB models). Different types of interactions (competition, predation, and virus–bacteria) are also developed. For each topic, a complete view of the models used in the literature cannot be presented. Consequently, the focus has been done on the demonstration how to build a model instead of providing a long list of existing models. Some recent results in sediment biogeochemistry are provided to illustrate the application of such models.  
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  Editeur Springer Netherlands Lieu de Publication Éditeur Bertrand, J.-C.; Caumette, P.; Lebaron, P.; Matheron, R.; Normand, P.; Sime-Ngando, T.  
  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé Environmental Microbiology: Fundamentals and Applications  
  Volume de collection Numéro de collection Edition  
  ISSN ISBN 978-94-017-9117-5 978-94-017-9118-2 Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 1395  
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Auteur Leprieur, F.; Colosio, S.; Descombes, P.; Parravicini, V.; Kulbicki, M.; Cowman, P.F.; Bellwood, D.R.; Mouillot, D.; Pellissier, L. doi  openurl
  Titre Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas Type Article scientifique
  Année 2016 Publication Revue Abrégée Ecography  
  Volume 39 Numéro 9 Pages (down) 825-835  
  Mots-Clés biodiversity hotspots; climate-change; community ecology; coral-reefs; damselfishes teleostei; evolutionary origins; genetic-structure; indo-pacific; latitudinal diversity gradient; species richness  
  Résumé Identifying the main determinants of tropical marine biodiversity is essential for devising appropriate conservation measures mitigating the ongoing degradation of coral reef habitats. Based on a gridded distribution database and phylogenetic information, we compared the phylogenetic structure of assemblages for three tropical reef fish families (Labridae: wrasses, Pomacentridae: damselfishes and Chaetodontidae: butterflyfishes) using the net relatedness (NRI) and nearest taxon (NTI) indices. We then related these indices to contemporary and historical environmental conditions of coral reefs using spatial regression analyses. Higher levels of phylogenetic clustering were found for fish assemblages in the Indo-Australian Archipelago (IAA), and more particularly when considering the NTI index. The phylogenetic structure of the Pomacentridae, and to a lower extent of the Chaeotodontidae and Labridae, was primarily associated with the location of refugia during the Quaternary period. Phylogenetic clustering in the IAA may partly result from vicariance events associated with coral reef fragmentation during the glacial periods of the Quaternary. Variation in the patterns among fish families further suggest that dispersal abilities may have interacted with past habitat availability in shaping the phylogenetic structure of tropical reef fish assemblages.  
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  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  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 Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 1633  
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Auteur Mouquet, N.; Devictor, V.; Meynard, C.N.; Munoz, F.; Bersier, L.-F.; Chave, J.; Couteron, P.; Dalecky, A.; Fontaine, C.; Gravel, D.; Hardy, O.J.; Jabot, F.; Lavergne, S.; Leibold, M.; Mouillot, D.; Münkemüller, T.; Pavoine, S.; Prinzing, A.; Rodrigues, A.S.L.; Rohr, R.P.; Thébault, E.; Thuiller, W. url  doi
openurl 
  Titre Ecophylogenetics: advances and perspectives Type Article scientifique
  Année 2012 Publication Revue Abrégée Biological Reviews  
  Volume 87 Numéro 4 Pages (down) 769-785  
  Mots-Clés community ecology; conservation biology; ecological networks; ecophylogenetics; Ecosystem functioning; evolution; phylogenetics  
  Résumé Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast-growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.  
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  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1469-185x ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 556  
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Auteur Joux, F.; Bertrand, J.-C.; De Wit, R.; Grossi, V.; Intertaglia, L.; Lebaron, P.; Michotey, V.; Normand, P.; Peyret, P.; Raimbault, P.; Tamburini, C.; Urios, L. url  isbn
openurl 
  Titre Methods for Studying Microorganisms in the Environment Type Chapitre de livre
  Année 2015 Publication Revue Abrégée  
  Volume Numéro Pages (down) 757-829  
  Mots-Clés Bacterial isolation; Biomarkers; Cultural techniques; Cytometry; DNA microarray; Microbial activities; Microbial Ecology; Microelectrodes; Molecular fingerprints; Pcr; Phospholipid fatty acid analyses; Pigment analyses; Sampling techniques  
  Résumé The main methods for the study of microorganisms in the environment (water, soil, sediment, biofilms), the different techniques of sampling for measuring biomass, the activities, and the diversity of the microorganisms are presented. To respond to these various issues, techniques as varied as those of flow cytometry, molecular biology, biochemistry, molecular isotopic tools, or electrochemistry are implemented. These different techniques are described with their advantages and disadvantages for different types of biotopes. The question of the isolation, culture, and conservation of microorganisms from the environment are also addressed. Without being exhaustive, this chapter emphasizes the importance of using appropriate and efficient methodological tools to properly explore the still mysterious compartment of microorganisms in the environment.  
  Adresse  
  Auteur institutionnel Thèse  
  Editeur Springer Netherlands Lieu de Publication Éditeur Bertrand, J.-C.; Caumette, P.; Lebaron, P.; Matheron, R.; Normand, P.; Sime-Ngando, T.  
  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé Environmental Microbiology: Fundamentals and Applications  
  Volume de collection Numéro de collection Edition  
  ISSN ISBN 978-94-017-9117-5 978-94-017-9118-2 Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 1393  
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