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Auteur Misson, B.; Garnier, C.; Lauga, B.; Dang, D.H.; Ghiglione, J.-F.; Mullot, J.-U.; Duran, R.; Pringault, O. url  doi
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  Titre Chemical multi-contamination drives benthic prokaryotic diversity in the anthropized Toulon Bay Type Article scientifique
  Année 2016 Publication Revue Abrégée Science of The Total Environment  
  Volume 556 Numéro Pages 319-329  
  Mots-Clés Marine sediment; Microbial ecotoxicology; Multi-contamination; Prokaryotic diversity  
  Résumé Investigating the impact of human activities on marine coastal ecosystems remains difficult because of the co-occurrence of numerous natural and human-induced gradients. Our aims were (i) to evaluate the links between the chemical environment as a whole and microbial diversity in the benthic compartment, and (ii) to compare the contributions of anthropogenic and natural chemical gradients to microbial diversity shifts. We studied surface sediments from 54 sampling sites in the semi-enclosed Toulon Bay (NW Mediterranean) exposed to high anthropogenic pressure. Previously published chemical data were completed by new measurements, resulting in an in depth geochemical characterization by 29 representative environmental variables. Bacterial and archaeal diversity was assessed by terminal restriction fragment length polymorphism profiling on a selection of samples distributed along chemical gradients. Multivariate statistical analyses explained from 45% to 80% of the spatial variation in microbial diversity, considering only the chemical variables. A selection of trace metals of anthropogenic origin appeared to be strong structural factors for both bacterial and archaeal communities. Bacterial terminal restriction fragment (T-RF) richness correlated strongly with both anthropogenic and natural chemical gradients, whereas archaeal T-RF richness demonstrated fewer links with chemical variables. No significant decrease in diversity was evidenced in relation to chemical contamination, suggesting a high adaptive potential of benthic microbial communities in Toulon Bay.  
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  ISSN 0048-9697 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1560  
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Auteur Hillen, J.E.J.; Coscia, I.; Vandeputte, M.; Herten, K.; Hellemans, B.; Maroso, F.; Vergnet, A.; Allal, F.; Maes, G.E.; Volckaert, F.A.M. url  doi
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  Titre Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass Type Article scientifique
  Année 2017 Publication Revue Abrégée Aquaculture  
  Volume 479 Numéro Pages 742-749  
  Mots-Clés Artificial selection; ddRAD; fish; genetic diversity; Genomics; Inbreeding  
  Résumé The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.  
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  ISSN 0044-8486 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2183  
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Auteur Amossé, J.; Bettarel, Y.; Bouvier, C.; Bouvier, T.; Tran Duc, T.; Doan Thu, T.; Jouquet, P. url  doi
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  Titre The flows of nitrogen, bacteria and viruses from the soil to water compartments are influenced by earthworm activity and organic fertilization (compost vs. vermicompost) Type Article scientifique
  Année 2013 Publication Revue Abrégée Soil Biology & Biochemistry  
  Volume 66 Numéro Pages 197-203  
  Mots-Clés Bacterial and viral abundance; Bacterial diversity; Compost; Dichogaster bolaui; Earthworms; Leaching; Organic fertilization; Vermicompost  
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  ISSN 0038-0717 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 892  
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Auteur Aubé, J.; Senin, P.; Pringault, O.; Bonin, P.; Deflandre, B.; Bouchez, O.; Bru, N.; Biritxinaga-Etchart, E.; Klopp, C.; Guyoneaud, R.; Goñi-Urriza, M. url  doi
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  Titre The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats Type Article scientifique
  Année 2016 Publication Revue Abrégée Marine Pollution Bulletin  
  Volume 111 Numéro 1 Pages 115-125  
  Mots-Clés Biogeochemical functioning; diversity; Hydrocarbonoclastic bacteria; Microbial mats  
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  ISSN 0025-326x ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2155  
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Auteur Maury, O.; Poggiale, J.-C. url  openurl
  Titre From individuals to populations to communities: A dynamic energy budget model of marine ecosystem size-spectrum including life history diversity Type Article scientifique
  Année 2013 Publication Revue Abrégée Journal of Theoretical Biology  
  Volume 324 Numéro Pages 52-71  
  Mots-Clés biodiversity; Dynamic Energy Budget theory; predation; Schooling; Size spectrum  
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  ISSN 0022-5193 ISBN Médium  
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  Notes <p>\textbackslashtextlessp\textbackslashtextgreaterIndividual metabolism, predator–prey relationships, and the role of biodiversity are major factors underlying the dynamics of food webs and their response to environmental variability. Despite their crucial, complementary and interacting influences, they are usually not considered simultaneously in current marine ecosystem models. In an attempt to fill this gap and determine if these factors and their interaction are sufficient to allow realistic community structure and dynamics to emerge, we formulate a mathematical model of the size-structured dynamics of marine communities which integrates mechanistically individual, population and community levels. The model represents the transfer of energy generated in both time and size by an infinite number of interacting fish species spanning from very small to very large species. It is based on standard individual level assumptions of the Dynamic Energy Budget theory (DEB) as well as important ecological processes such as opportunistic size-based predation and competition for food. Resting on the inter-specific body-size scaling relationships of the DEB theory, the diversity of life-history traits (i.e. biodiversity) is explicitly integrated. The stationary solutions of the model as well as the transient solutions arising when environmental signals (e.g. variability of primary production and temperature) propagate through the ecosystem are studied using numerical simulations. It is shown that in the absence of density-dependent feedback processes, the model exhibits unstable oscillations. Density-dependent schooling probability and schooling-dependent predatory and disease mortalities are proposed to be important stabilizing factors allowing stationary solutions to be reached. At the community level, the shape and slope of the obtained quasi-linear stationary spectrum matches well with empirical studies. When oscillations of primary production are simulated, the model predicts that the variability propagates along the spectrum in a given frequency-dependent size range before decreasing for larger sizes. At the species level, the simulations show that small and large species dominate the community successively (small species being more abundant at small sizes and large species being more abundant at large sizes) and that the total biomass of a species decreases with its maximal size which again corroborates empirical studies. Our results indicate that the simultaneous consideration of individual growth and reproduction, size-structured trophic interactions, the diversity of life-history traits and a density-dependent stabilizing process allow realistic community structure and dynamics to emerge without any arbitrary prescription. As a logical consequence of our model construction and a basis for future studies, we define the function Φ as the relative contribution of each species to the total biomass of the ecosystem, for any given size. We argue that this function is a measure of the functional role of biodiversity characterizing the impact of the structure of the community (its species composition) on its function (the relative proportions of losses, dissipation and biological work).\textbackslashtextless/p\textbackslashtextgreater</p> Approuvé pas de  
  Numéro d'Appel LL @ pixluser @ collection 245  
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