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Auteur Dalongeville, A.; Benestan, L.; Mouillot, D.; Lobreaux, S.; Manel, S. doi  openurl
  Titre Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus) Type Article scientifique
  Année 2018 Publication (up) Revue Abrégée BMC Genomics  
  Volume 19 Numéro Pages 217  
  Mots-Clés Adaptive genomics; Candidate genes; climate; genetics; Genome scan; landscape genomics; local adaptation; Mediterranean Sea; methionine sulfoxide reductase; Mullus surmuletus; population genomics; principal component analysis; r package; Salinity; selection; threespine sticklebacks  
  Résumé Background: Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents impacting the physiology of organisms. With one of the highest salinity level, the Mediterranean Sea provides an excellent model to investigate adaptive genomic divergence underlying salinity adaptation. In the present study, we combined six genome scan methods to detect potential genomic signal of selection in the striped red mullet (Mullus surmuletus) populations distributed across a wide salinity gradient. We then blasted these outlier sequences on published fish genomic resources in order to identify relevant potential candidate genes for salinity adaptation in this species. Results: Altogether, the six genome scan methods found 173 outliers out of 1153 SNPs. Using a blast approach, we discovered four candidate SNPs belonging to three genes potentially implicated in adaptation of M. surmuletus to salinity. The allele frequency at one of these SNPs significantly increases with salinity independently from the effect of longitude. The gene associated to this SNP, SOCS2, encodes for an inhibitor of cytokine and has previously been shown to be expressed under osmotic pressure in other marine organisms. Additionally, our results showed that genome scan methods not correcting for spatial structure can still be an efficient strategy to detect potential footprints of selection, when the spatial and environmental variation are confounded, and then, correcting for spatial structure in a second step represents a conservative method. Conclusion: The present outcomes bring evidences of potential genomic footprint of selection, which suggest an adaptive response of M. surmuletus to salinity conditions in the Mediterranean Sea. Additional genomic data such as sequencing of a full-genome and transcriptome analyses of gene expression would provide new insights regarding the possibility that some striped red mullet populations are locally adapted to their saline environment.  
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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 1471-2164 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2324  
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Auteur Coz, R.; Ouisse, V.; Artero, C.; Carpentier, A.; Crave, A.; Feunteun, E.; Olivier, J.M.; Perrin, B.; Ysnel, F. url  doi
openurl 
  Titre Development of a new standardised method for sustainable monitoring of the vulnerable pink sea fan Eunicella verrucosa Type Article scientifique
  Année 2012 Publication (up) Revue Abrégée Marine Biology  
  Volume 159 Numéro 6 Pages 1375-1388  
  Mots-Clés atlantic canada; cavolini coelenterata octocorallia; channel; gonadal development; gorgonian paramuricea-clavata; marine invertebrate; mediterranean-sea; modular growth; movement; northeast; singularis esper; water  
  Résumé The aim of this survey was to test a standardised method to follow the demographic evolution of a dense aggregative 'forest' population of the temperate gorgonian Eunicella verrucosa (Octocorallia, Gorgoniidae) using in situ photographic recordings. Distribution, density, growth and demographic evolution of the colonies was compared along two parallel transects. Computer treatment allowed the estimation of the total branch fan surface area, and the individual growth of tagged colonies was determined by measuring the increase in this surface area, using consecutive photographs taken at two-year intervals. To integrate the potential bias of branch overlapping, we proposed a correction factor between the in situ photographic surface area and the surface area of the gorgonian calculated from ex situ photographic surface area with all branches deployed. The surface-frequency distribution of colonies was converted to estimated-age-frequency distribution using an estimated growth curve based on the net growth rate. The technique used revealed significant differences in population structure and the dynamics of gorgonian colonies, as the two transects appeared to be influenced by different environmental conditions. The recruitment also seemed to vary according to year and transect, resulting in different densities. Our work showed clear results in characterising the variations of gorgonian demographic evolution at a small spatial scale; thus, it is assumed that this method could be a sustainable tool for coastal environmental managers.  
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  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0025-3162 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 539  
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Auteur Kara, M.H.; Lacroix, D.; Rey-Valette, H.; Mathe, S.; Blancheton, J.P. doi  openurl
  Titre Dynamics of Research in Aquaculture in North Africa and Support for Sustainable Development and Innovation Type Article scientifique
  Année 2018 Publication (up) Revue Abrégée Rev. Fish. Sci. Aquac..  
  Volume 26 Numéro 3 Pages 309-318  
  Mots-Clés agriculture; aquaculture; development; impact; Mediterranean; North Africa; research; sustainability  
  Résumé This article examines the supporting role of research in the development of marine aquaculture in the aquaculture-producing countries of North Africa: Algeria, Egypt, Morocco, and Tunisia. Research plays a significant role not only in the support of the development of the sector, but also in the evolution toward sustainable aquaculture practices and a better integrated management of this activity. This analysis was conducted as part of the Aquamed project whose main objective was to create a multi-stakeholder platform (institutional decision makers, producers, researchers, NGOs, etc.) to strengthen cooperation and stimulate innovation for sustainable aquaculture in the Mediterranean. In particular, the Aquamed project aimed at an exploration of forms of collaboration through the identification of sub-groups of countries whose similarity of situations or challenges could help promote dialogue. The study of aquaculture and research in the countries reveals the contrasted situations between Egypt and the three western North African countries (Algeria, Morocco, and Tunisia). The analysis of research capabilities was carried out on the basis of several indicators, which were compiled from a survey among the relevant main institutes in the various countries, as well as from bibliometric research on the publications produced in the field of aquaculture. Beyond the differences identified among the countries, the analysis emphasizes the similarity of the challenges and the benefits of strengthening collaborations on a sub-regional scale.  
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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 2330-8249 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2342  
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Auteur Coll, M.; Steenbeek, J. doi  openurl
  Titre Standardized ecological indicators to assess aquatic food webs: The ECOIND software plug-in for Ecopath with Ecosim models Type Article scientifique
  Année 2017 Publication (up) Revue Abrégée Environ. Modell. Softw.  
  Volume 89 Numéro Pages 120-130  
  Mots-Clés biodiversity; Conservation; Ecological standardized indicators; Ecopath with Ecosim; ecospace; Ecosystem indicators; Environmental status; Fisheries management; Food web models; impacts; index; marine ecosystems; Mediterranean Sea; network analysis; ocean; Software plug-in  
  Résumé Ecological indicators are useful tools to analyse and communicate historical changes in ecosystems and plausible future scenarios while evaluating environmental status. Here we introduce a new plug-in to the Ecopath with Ecosim (EwE) food web modelling approach, which is widely used to quantitatively describe aquatic ecosystems. The plug-in (ECOIND) calculates standardized ecological indicators. We describe the primary functionality of ECOIND and provide an example of its application in both static and temporal-spatial dynamic modelling, while we highlight several related features including a new taxonomy input database (species traits) and the ability to analyse input uncertainty on output results. ECOIND adds new capabilities to the widely used EwE food web modelling approach and enables broadening its applications into biodiversity and conservation-based frameworks to contribute to integrated ecosystem analyses. (C) 2016 Elsevier Ltd. All rights reserved.  
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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 1364-8152 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2088  
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Auteur Blanchet, M.; Pringault, O.; Panagiotopoulos, C.; Lefevre, D.; Charriere, B.; Ghiglione, J.-F.; Fernandez, C.; Aparicio, F.L.; Marrase, C.; Catala, P.; Oriol, L.; Caparros, J.; Joux, F. doi  openurl
  Titre When riverine dissolved organic matter (DOM) meets labile DOM in coastal waters: changes in bacterial community activity and composition Type Article scientifique
  Année 2017 Publication (up) Revue Abrégée Aquat. Sci.  
  Volume 79 Numéro 1 Pages 27-43  
  Mots-Clés Bacterial community composition; bacterioplankton; biodegradation; carbon; coastal waters; Dissolved organic matter; Fluorescence; growth efficiency; lake water; marine; Mediterranean Sea; open-ocean; Priming effect; rhone river; terrestrial  
  Résumé Heterotrophic bacterial communities in marine environments are exposed to a heterogeneous mixture of dissolved organic compounds with different bioreactivity that may control both their activity and composition. The coastal environment is an example of a mixing area where recalcitrant allochthonous organic matter from rivers can encounter labile organic matter from marine phytoplanktonic blooms. The objective of this study was to explore the effects of mixed qualities of dissolved organic matter (DOM) on bacterial community activity (BCA) and bacterial community composition (BCC) and to test for a priming effect when DOM sources are added in combination. Coastal marine bacterial communities were incubated separately with a mixture of amino acids and with natural riverine DOM or with both sources together for 42 days. Addition of amino acids alone or in combination with riverine DOM led to a similar stimulation of BCA compared to control condition, whereas addition of riverine DOM alone did not modify BCA compared to the control. On the contrary, BCC analyzed by 16S rRNA gene pyrosequencing was not affected by the addition of amino acids alone, but changed dramatically with riverine DOM alone or in combination with amino acids. Our results show that changes in BCA and BCC can be driven by different types of DOM, but that these changes are not necessarily coupled. Moreover, the addition of labile DOM did not modify the microbial decomposition of riverine DOM, nor the BCC, suggesting that a priming effect did not occur under these experimental conditions.  
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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 1015-1621 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 2090  
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