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1. Biodegradation of Emiliania huxleyi aggregates by a natural Mediterranean prokaryotic community under increasing hydrostatic pressure

Author: Frédéric A. C. Le Moigne, Kazuyo Tachikawa, Virginie Riou, Christian Tamburini, Chiara Santinelli, Dominique Lefèvre, Badr Al Ali, Stephanie Jacquet, Madeleine Goutx, J. Para, Catherine Guigue, Jean-Pierre Gattuso, Marc Garel, Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Istituto di Biofisica [Pisa] (IBF), Consiglio Nazionale delle Ricerche [Roma] (CNR), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), GEOMAR - Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Tishreen University, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), CE, Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Istituto di Biofisica, Area della Ricerca di Pisa, Via Moruzzi, 1, 56124 Pisa, Italy, Université du Québec, Observatoire océanologique de Villefranche-sur-mer ( OOVM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Centre européen de recherche et d'enseignement de géosciences de l'environnement ( CEREGE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Collège de France ( CdF ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national des sciences de l'Univers ( INSU - CNRS ), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Hydrostatic pressure, Alkalinity, Aquatic Science, Biology, 01 natural sciences, chemistry.chemical_compound, Water column, Total inorganic carbon, Organic matter, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Emiliania huxleyi, chemistry.chemical_classification, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Atmospheric pressure, 010604 marine biology & hydrobiology, fungi, Geology, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, [ SDE.MCG ] Environmental Sciences/Global Changes, Calcium carbonate, Oceanography, chemistry, 13. Climate action, Biological carbon pump, Mesopelagic, Mineral ballast, Coccolithophorid, Prokaryotes, Biodegradation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: In the deep ocean, fluxes of particulate organic carbon (POC) and calcium carbonate are positively correlated, suggesting that CaCO3 could increase sinking particle densities and/or protect the organic matter from degradation by prokaryotes, the so called "ballast effect". Here, we used the PArticle Sinking Simulator (PASS) system to investigate the effect of increasing pressure on the biodegradation of calcifying Emiliania huxleyi aggregates. Incubations were carried out over a period of 10 days, simulating the changes in temperature and pressure in the water column of the NW Mediterranean Sea. Aggregates sinking from a depth of 200 m to 1700 m (assuming an average sinking velocity of 150 m d(-1)) were exposed to a natural mesopelagic prokaryotic community collected from 200 m. In contrast to previous studies, where silicifying diatom aggregates were used, the calcifying E. huxleyi aggregates were found to be more sensitive to degradation with increasing hydrostatic pressure (relative to constant atmospheric pressure). This was confirmed by changes in lipid composition which suggested increased cell lysis. Changes in particulate inorganic carbon and total alkalinity indicated that CaCO3 dissolution might have been faster under pressure. Increased hydrostatic pressure also had a positive effect on particle aggregation, which may compensate for the effect of increased cell lysis. Our results imply that in coccolithophorid-dominated sinking aggregates, the ballasting and protection effects of coccoliths may collapse throughout the water column. The increased aggregation potential with pressure observed in these controlled conditions, may balance the loss of mineral ballast to a certain extent, although this needs to be confirmed in situ.
Published: 2018
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2. Cartographie et typologie des communautés benthiques : outils indispensables pour la préservation et la gestion des habitats marins de la baie de Seine

Author: Baffreau, A., Pezy, Jean-Philippe, Dancie, C., Chouquet, B., Hacquebart, P., Poisson, E., Joncourt, Y., Duhamel, S., Dauvin, Jean-Claude, Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Cellule de Suivi du Littoral Normand (CSLN), Centre de recherches en environnement côtier (CREC), Normandie Université (NU)-Normandie Université (NU), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Morphodynamique Continentale et Côtière ( M2C ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ), Cellule de Suivi du Littoral Normand, Cellule de Suivi du Littoral Normand, 53 rue de Prony, 76600 Le Havre, France, Centre de recherches en environnement côtier ( CREC ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU]Sciences of the Universe [physics], [ SDU ] Sciences of the Universe [physics]
Published: 2017

3. Molecular microbiology methods for environmental diagnosis

Author: Samuel Dequiedt, Pierre Peyret, Cécile Grand, Jennifer Hellal, Lionel Ranjard, Stéphanie Ferreira, P. Schmitt-Koplin, A. L. Blieux, Pierre-Alain Maron, Achim Quaiser, Isabelle Déportes, E. d'Oiron, Antonio Bispo, Catherine Joulian, Alexis Dufresne, Olivier Sibourg, Isabelle Domaizon, Aourell Mauffret, Fabrice Martin-Laurent, Philippe Cuny, Jean-Jacques Godon, Jean-Michel Monier, Théodore Bouchez, Hydrosystèmes et bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Welience Agroenvironnement, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), GenoScreen, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), ENOVEO, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Helmholtz-Zentrum München (HZM), Observatoire Français des Sols Vivants, Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, ADEME (French National Agency for Energy and Environment), Hydrosystèmes et bioprocédés ( UR HBAN ), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture ( IRSTEA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques ( CARRTEL ), Institut National de la Recherche Agronomique ( INRA ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ), Ecosystèmes, biodiversité, évolution [Rennes] ( ECOBIO ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -INEE-Observatoire des Sciences de l'Univers de Rennes ( OSUR ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biotechnologie de l'Environnement [Narbonne] ( LBE ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Bureau de Recherches Géologiques et Minières (BRGM) ( BRGM ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Conception, Ingénierie et Développement de l'Aliment et du Médicament ( CIDAM ), Université d'Auvergne - Clermont-Ferrand I ( UdA ), Helmholtz-Zentrum München ( HZM ), Agence de l'Environnement et de la Maîtrise de l'Energie - ADEME, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Hydrosystèmes et Bioprocédés (UR HBAN), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum München = German Research Center for Environmental Health, Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur les Macromolécules Végétales (CERMAV ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire de tectonique (LT), Centre National de la Recherche Scientifique (CNRS)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Département Recherche Déchets et Sols, Agence de l'Environnement et de la Maitrise de l'Energie, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre de Recherches sur les Macromolécules Végétales (CERMAV), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)
Subjects: 0301 basic medicine, Operability, sea, [SDE.MCG]Environmental Sciences/Global Changes, 030106 microbiology, Genomics, Technology readiness level, Biology, dna, diversity, 03 medical and health sciences, Environmental Chemistry, bacterial, microorganisms, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Ecological footprint, metatranscriptomics, business.industry, Scale (chemistry), Environmental resource management, rhizosphere microbiome, Environmental engineering, gene-expression, 030104 developmental biology, 13. Climate action, Agriculture, Metaproteomics, community, metaproteomics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Bioindicator
Abstract: [Departement_IRSTEA]Ecotechnologies [TR1_IRSTEA]TED; International audience; To reduce the environmental footprint of human activities, the quality of environmental media such as water, soil and the atmosphere should be first assessed. Microorganisms are well suited for a such assessment because they respond fast to environmental changes, they have a huge taxonomic and genetic diversity, and they are actively involved in biogeochemical cycles. Here, we review microbiological methods that provide sensitive and robust indicators for environmental diagnosis. Methods include genomics, transcriptomics, proteomics and metabolomics to study the abundance, diversity, activity and functional potentials of indigenous microbial communities in various environmental matrices such as water, soil, air and waste. We describe the advancement, technical limits and sensitivity of each method. Examples of method application to farming, industrial and urban impact are presented. We rank the most advanced indicators according to their level of operability in the different environmental matrices based on a technology readiness level scale.
Published: 2016
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4. Functional analysis and classification of phytoplankton based on data from an automated flow cytometer

Author: Anthony Malkassian, Marc van Dijk, Gérald Grégori, David Nerini, Claude Manté, Melilotus Thyssen, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, MoNOS, Huygens Laboratory, Universiteit Leiden [Leiden], Microbial Ecology (ME), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Universiteit Leiden, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), and Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 0106 biological sciences, Multivariate statistics, Histology, multivariate statistics, Fresh Water, Cell Separation, Biology, 01 natural sciences, Pathology and Forensic Medicine, 03 medical and health sciences, Histogram, Animals, Seawater, 14. Life underwater, Cluster analysis, ComputingMilieux_MISCELLANEOUS, Phylogeny, functional data analysis, 030304 developmental biology, Automation, Laboratory, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Ecology, business.industry, 010604 marine biology & hydrobiology, Sampling (statistics), Functional data analysis, Pattern recognition, Cell Biology, Flow Cytometry, automated flow cytometry, Flow (mathematics), Phytoplankton, A priori and a posteriori, Artificial intelligence, Scale (map), business, clustering
Abstract: International audience; Analytical flow cytometry (FCM) is well suited for the analysis of phytoplankton communities in fresh and sea waters. The measurement of light scatter and autofluorescence properties of particles by FCM provides optical fingerprints, which enables different phytoplankton groups to be separated. A submersible version of the CytoSense flow cy-tometer (the CytoSub) has been designed for in situ autonomous sampling and analysis , making it possible to monitor phytoplankton at a short temporal scale and obtain accurate information about its dynamics. For data analysis, a manual clustering is usually performed a posteriori: data are displayed on histograms and scatterplots, and group discrimination is made by drawing and combining regions (gating). The purpose of this study is to provide greater objectivity in the data analysis by applying a nonman-ual and consistent method to automatically discriminate clusters of particles. In other words, we seek for partitioning methods based on the optical fingerprints of each particle. As the CytoSense is able to record the full pulse shape for each variable, it quickly generates a large and complex dataset to analyze. The shape, length, and area of each curve were chosen as descriptors for the analysis. To test the developed method, numerical experiments were performed on simulated curves. Then, the method was applied and validated on phytoplankton cultures data. Promising results have been obtained with a mixture of various species whose optical fingerprints overlapped considerably and could not be accurately separated using manual gating. ' 2011 International Society for Advancement of Cytometry
Published: 2011
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5. Caldinitratiruptor microaerophilus, gen. nov., sp. nov. isolated from a French hot spring (Chaudes-Aigues, Massif Central): a novel cultivated facultative microaerophilic anaerobic thermophile pertaining to the Symbiobacterium branch within the Firmicutes

Author: Valérie Michotey, Vanessa Barsotti, Bernard Ollivier, Manon Joseph, Jean-Luc Cayol, Marie-Laure Fardeau, Patricia Bonin, Sophie Guasco, Laboratoire de Microbiologie IRD ( ESIL GMBA ), Université de Provence - Aix-Marseille 1, Extremophiles - IFR BAIM ( UR 101 ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire de Microbiologie IRD (ESIL GMBA), Extremophiles - IFR BAIM (UR 101), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Geologic Sediments, Hot Temperature, Firmicutes, Biology, Polymerase Chain Reaction, Microbiology, Hot Springs, Evolution, Molecular, Bacteria, Anaerobic, 03 medical and health sciences, Caldinitratiruptor microaerophilus, Thermophilic, Hot spring, Microaerophile, Nitrate-reduction, Ecosystem, Phylogeny, ComputingMilieux_MISCELLANEOUS, Microaerophilic, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Base Composition, 0303 health sciences, Strain (chemistry), 030306 microbiology, Thermophile, Temperature, Hot Spring, Sequence Analysis, DNA, General Medicine, Symbiobacterium thermophilum, Hydrogen-Ion Concentration, Ribosomal RNA, biology.organism_classification, Microscopy, Electron, Phenotype, Biochemistry, Molecular Medicine, Fermentation, France, Bacteria
Abstract: A novel facultative microaerophilic nitrate-reducing bacterium designated CA62N(T) was isolated from a thermal spring in France. Cells were non-motile rods (2-3 x 0.2 mum) and showed low cytoplasmic density when observed under a phase-contrast microscope. Strain CA62N(T) grew at temperatures between 50 and 75 degrees C (optimum 65 degrees C) and at a pH between 6.3 and 7.9 (optimum 7.0). NaCl was not required for growth but was tolerated up to 10 gl(-1). Sulfate, thiosulfate, elemental sulfur, sulfite, and nitrite were not used as electron acceptors. Nitrate was reduced to nitrite. Strain CA62N(T) used lactate, pyruvate, glucose, mannose, fructose, and casamino acids and some amino acids as electron donors only in the presence of nitrate as electron acceptor. None of these substrates was fermented. The main end-products of glucose oxidation were acetate, CO(2), and traces of H(2). The G + C content of the genomic DNA was 70.3 mol% (HPLC techniques). Phylogenetic analysis of the small-subunit (SSU) ribosomal RNA (rRNA) gene sequence indicated that strain CA62N(T) was affiliated to the Symbiobacterium branch within the Firmicutes and had Symbiobacterium thermophilum and "S. toebii" as its closest phylogenetic relatives. On the basis of phylogenetical and physiological characteristics, strain CA62N(T) is proposed to be the type strain for the novel species in the novel genus, Caldinitratiruptor microaerophilus gen. nov., sp. nov. (DSM 22660, JCM 16183).
Published: 2010
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6. Study of a virus–bacteria interaction model in a chemostat: application of geometrical singular perturbation theory

Author: Pierre Auger, Flora Cordoleani, Jean-Christophe Poggiale, Tri Nguyen-Huu, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 (Cameroun)-University Cadi Ayyad ( UCA ), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Singular perturbation, General Mathematics, General Physics and Astronomy, Boundary (topology), reduction, Context (language use), Models, Biological, 01 natural sciences, Domain (mathematical analysis), 03 medical and health sciences, Bioreactors, Intersection, Quantitative Biology::Populations and Evolution, invariant manifold, Bacteriophages, 14. Life underwater, 0101 mathematics, Invariant (mathematics), singular perturbation, Ecosystem, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Mathematics, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Bacteria, 010102 general mathematics, Mathematical analysis, General Engineering, Interaction model, Phase space, virus-bacteria interaction, Virus Physiological Phenomena
Abstract: This paper provides a mathematical analysis of a virus–marine bacteria interaction model. The model is a simplified case of the model published and used by Middelboe (Middelboe, M. 2000 Microb. Ecol . 40 , 114–124). It takes account of the virus, the susceptible bacteria, the infected bacteria and the substrate in a chemostat. We show that the numerical values of the parameters given by Middelboe allow two different time scales to be considered. We then use the geometrical singular perturbation theory to study the model. We show that there are two invariant submanifolds of dimension two in the four-dimensional phase space and that these manifolds cross themselves on the boundary of the domain of biological relevance. We then perform a rescaling to understand the dynamics in the vicinity of the intersection of the manifolds. Our results are discussed in the marine ecological context.
Published: 2009
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7. Consumption and release of dissolved organic %%CONV_ERR%%carbon by marine bacteria in a pulsed-substrate environment: from experiments to modelling

Author: Marie Eichinger, Dominique Lefèvre, Sebastiaan A.L.M. Kooijman, Bruno Charrière, Richard Sempéré, Jean-Christophe Poggiale, Gérald Grégori, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Department of Theoretical Biology [Amsterdam], Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Vrije Universiteit, Faculty of Earth and Life Science, and Theoretical Life Sciences
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 0106 biological sciences, 010504 meteorology & atmospheric sciences, Dynamic energy budget, Biomass, Mineralogy, Aquatic Science, Bacterial growth, 01 natural sciences, Carbon cycle, Bacterial dynamics, DEB theory, Marine bacteriophage, Dissolved organic carbon, SDG 14 - Life Below Water, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, DOC degradation, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Chemistry, 010604 marine biology & hydrobiology, Substrate (marine biology), Environmental chemistry, Mechanistic model, Degradation (geology), DOC release
Abstract: To investigate the effects of episodic occurrence of dissolved organic carbon(DOC) in the natural environment, bacterial degradation of labile DOC was studied under laboratory-controlled conditions followed by modelling. A single labile DOC compound was periodically added to the experimental culture and its degradation by a monospecific marine bacterial strain was followed. The measured variables were DOC and bacterial biomass determined from the particulate organic carbon values. Experimental dynamics showed a repetition of 2 successive patterns after each DOC pulse:(1) substrate consumption and bacterial growth in the first few hours after substrate addition, followed by(2) bacterial reduction(organic carbon-related) and associated non-labile DOC release within the next few hours. Based on these experimental results, the Dynamic Energy Budget theory was applied for the first time to such conditions to develop a mechanistic model that comprised 7 parameters and 4 state variables in which bacterial biomass was fractionated into reserve and structure compartments. The model was constructed by accounting for a constant specific maintenance rate and comprised 2 different cell maintenance fluxes, one fuelled from cell reserves when substrate was abundant and one from reserves and cell structures when starvation occurred. This new model of bacterial degradation adequately matched experimental measurements and accurately reproduced the accumulation of non-labile DOC in the culture during the experiment. This model can easily be implemented in an aquatic biogeochemical model and could provide better understanding of the role of bacteria in carbon cycling in fluctuating environments. © Inter-Research 2009.
Published: 2009
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8. Short-term variation of phytoplankton assemblages in Mediterranean coastal waters recorded with an automated submerged flow cytometer

Author: Delphine Mathieu, Nicole Garcia, Michel Denis, Melilotus Thyssen, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de Technologie - Aix-Marseille (IUT AMU), Aix Marseille Université (AMU), Beaussier, Catherine, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire d'océanographie et de biogéochimie ( LOB ), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 0106 biological sciences, Mediterranean climate, 010504 meteorology & atmospheric sciences, Aquatic Science, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, 01 natural sciences, Wind speed, [SDU] Sciences of the Universe [physics], Phytoplankton, 14. Life underwater, Diel vertical migration, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Ecology, 010604 marine biology & hydrobiology, Sampling (statistics), Plankton, Salinity, Oceanography, [SDU]Sciences of the Universe [physics], Environmental science, Bay
Abstract: Short-term variations of phytoplankton communities are poorly documented. To overcome these limitations and make observations on a short-time (hours) scale, we moored a submersible flow cytometer (CytoBuoy b.v.) in the Bay of Marseille. The CytoSub monitored phytoplankton every 30 min at a fixed site (2 m depth) during summer 2005. The data treatment, conducted on the basis of pulse-shape analysis, resolved seven clusters. Daily sampling of nutrients and continuous information on salinity, temperature and wind speed allowed distinction between diel cycles and the impact of environmental factors on phytoplankton communities. Autocorrelation of the time series showed a significant periodicity of ∼24 h for most of the clusters during undisturbed meteorological conditions. Two clusters had regular daily abundance variations in the range 0->10 3 cells cm −3 . Two strong wind events revealed similar cluster succession patterns occurring over several days after the wind events. These results provided by the high frequency in situ analysis suggest that the flow cytometry resolved clusters, showing independent behaviour and distinct environment-correlated variations, which may be considered as functional groups. We point out its potential for global oceanic observing systems for which such systems could provide real biological information.
Published: 2008
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9. Enrichment Paradox Induced by Spatial Heterogeneity in a Phytoplankton - Zooplankton System

Author: Mathias Gauduchon, Pierre Auger, Jean-Christophe Poggiale, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Modélisation mathématique et informatique de systèmes complexes naturels, biologiques ou sociaux (GEODES), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Modélisation mathématique et informatique de systèmes complexes naturels, biologiques ou sociaux ( GEODES ), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 0106 biological sciences, Mixed layer, Biology, 010603 evolutionary biology, 01 natural sciences, Zooplankton, 03 medical and health sciences, symbols.namesake, Phytoplankton, Surface layer, enrichment paraox, Dispersion (water waves), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Hopf bifurcation, 0303 health sciences, Ecology, Applied Mathematics, spatial heterogeneity, Spatial heterogeneity, Modeling and Simulation, symbols, Biological dispersal, singular perturbations, AMS 92D25, 58F35, 34A47, 92D40, Biological system, bifurcations
Abstract: This paper is devoted to the study of a predator-prey model in a patchy environment. The model represents the interactions between phytoplankton and zooplankton in the water col- umn. Two patches are considered with respect to light availability: one patch is associated to the surface layer, the second patch describes the bottom layer. We show that this spatial heterogeneity may destabilize the predator-prey system, even in oligotrophic system where the nutrient is low enough to avoid "paradox-enrichment" phenomenon. Indeed, in this case, an heterogeneity index can be used as a bifurcation parameter, leading to a Hopf bifurcation. Moreover, we assume that in- dividuals can be dispersed in both patches via hydrodynamism processes, like in a mixed layer. The effect of mixing intensity is analysed as well as interactio ns between dispersion and enrichment. We also show that, in some cases, spatial heterogeneity has a stabilizing effect. These contrasted results are examined by considering the non linear interaction between heterogeneity, dispersal and enrichment and some mechanisms leading to stabilization/destabilization are exhibited.
Published: 2008
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10. Stochastic activation of the response regulator PhoB by noncognate histidine kinases

Author: Jennifer Masella Blackman, J. Paul Robinson, Barry L. Wanner, Gérald Grégori, Lu Zhou, Department of Biological Sciences [Lafayette IN], Purdue University [West Lafayette], Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Vanda Pharmaceuticals, Cytometry Laboratories and School of Veterinary Medicine, Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Poirot, Dominique, Department of Biological Sciences, Purdue University, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), and Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, cell populations, Data processing, computer science, computer systems, two-component regulatory system, Biology, qsec, Green fluorescent protein, 03 medical and health sciences, kdpd, phoa, crec, promoter reporter fusion, Gene, Histidine, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Genetics, 0303 health sciences, phor, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, 030306 microbiology, Kinase, flow cytometry, fungi, arcb, Histidine kinase, Autophosphorylation, General Medicine, single-cell, gfp, cross regulation, protein phosphorylation, Response regulator, cross talk, baes, envz, gene expression, Phosphorylation, escherichia coli, signal transduction, TP248.13-248.65, Biotechnology
Abstract: Two-component systems (TCS) are the most prevalent gene regulatory mechanism in bacteria. A typical TCS is comprised of a histidine kinase (HK) and a partner response regulator (RR). Specific environment signals lead to autophosphorylation of different HKs, which in turn act as phosphoryl donors for autophosphorylation of their partner RRs. Nonpartner HKs and RRs also interact, giving rise to cross regulation among TCSs in response to diverse signals.PhoR (HK) and PhoB (RR) constitute the TCS for detection of environmental (extracellular) inorganic phosphate (Pi). The PhoR/PhoB TCS controls the expression of a large number of genes for acquisition of alternative phosphorus sources, including phoA, which encodes the non-specific phosphohydrolase bacterial alkaline phosphatase (Bap). Cross activation of PhoB by the nonpartner HK CreC is now a classic example of cross regulation among TCSs. A systematic search for other cross talking HKs revealed five additional HKs that activate (phosphorylate) PhoB (J. M. B. and B. L. W., unpublished data).Examination of cross activation of PhoB by these non-partner HKs by flow cytometry at the single-cell level revealed a bimodal, “all-or-none,” distribution pattern for expression of a phoAp-gfp (green fluorescent protein) reporter fusion. Although the basis of the observed stochastic behavior is unclear, it seems to reflect an inherent property of TCSs. We propose that cells exploit the stochastic character of TCSs to achieve nongenetic (epigenetic) diversity within genetically homogeneous cell populations in order to facilitate adaptation to environmental changes.
Published: 2005
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11. Benthic biogeochemistry: state of the art technologies and guidelines for the future of in situ survey

Author: Christophe Rabouille, Steve G. Roberts, Anders Tengberg, Se Apitz, Martial Taillefert, Gwénaëlle Chaillou, Jl Morford, Eric Viollier, Per O. J. Hall, Christian Grenz, Ursula Witte, Felix Janssen, T Shimmield, E. Breuer, Frank Wenzhöfer, Karine Dedieu, Jean-Christophe Poggiale, Yoko Furukawa, Laboratoire d'Océanographie Physique et Biologique ( LOPB ), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Océan et Interfaces (OCEANIS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Océanographie Physique et Biogéochimique (LOPB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: 0106 biological sciences, Biogeochemical cycle, 010504 meteorology & atmospheric sciences, gel peepers, [SDE.MCG]Environmental Sciences/Global Changes, Earth science, microelectrodes, Aquatic Science, Biology, 01 natural sciences, Lead (geology), biogeochemistry, Sediment–water interface, optodes, Environmental monitoring, Ecology, Evolution, Behavior and Systematics, Seabed, 0105 earth and related environmental sciences, benthic chambers, Ecology, 010604 marine biology & hydrobiology, Biogeochemistry, Sediment, [ SDE.MCG ] Environmental Sciences/Global Changes, sediment, 13. Climate action, Benthic zone, in situ technologies
Abstract: Sediment and water can potentially be altered, chemically, physically and biologically as they are sampled at the seafloor, brought to the surface, processed and analysed. As a result, in situ observations of relatively undisturbed systems have become the goal of a growing body of scientists. Our understanding of sediment biogeochemistry and exchange fluxes was revolutionized by the introduction of benthic chambers and in situ micro-electrode profilers that allow for the direct measurement of chemical fluxes between sediment and water at the sea floor and for porewater composition. Since then, rapid progress in the technology of in situ sensors and benthic chambers (such as the introduction of gel probes, voltammetric electrodes or one- and two-dimensional optodes) have yielded major breakthroughs in the scientific understanding of benthic biogeochemistry. This paper is a synthesis of discussions held during the workshop on sediment biogeochemistry at the "Benthic Dynamics: in situ surveillance of the sediment-water interface" international conference (Aberdeen, UK--March 25-29, 2002). We present a review of existing in situ technologies for the study of benthic biogeochemistry dynamics and related scientific applications. Limitations and possible improvement (e.g., technology coupling) of these technologies and future development of new sensors are discussed. There are countless important scientific and technical issues that lend themselves to investigation using in situ benthic biogeochemical assessment. While the increasing availability of these tools will lead research in yet unanticipated directions, a few emerging issues include greater insight into the controls on organic matter (OM) mineralization, better models for the understanding of benthic fluxes to reconcile microelectrode and larger-scale chamber measurements, insight into the impacts of redox changes on trace metal behavior, new insights into geochemical reaction pathways in surface sediments, and a better understanding of contaminant fate in nearshore sediments.
Published: 2003
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12. Monitoring and expansion of Posidonia Monitoring networks along Corsican coastline

Author: Pascal, Oberti, Pergent, Gerard, Bein, Aymeric, BLANFUNÉ, Aurelie, Orsini, Antoine, DEDEKEN, M., Pergent Martini, C., Ruitton, Sandrine, Short, F., Lieux, Identités, eSpaces, Activités (LISA), Université Pascal Paoli (UPP)-Centre National de la Recherche Scientifique (CNRS), Sciences pour l'environnement (SPE), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pascal Paoli (UPP), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Lieux, Identités, eSpaces, Activités ( LISA ), Université Pascal Paoli ( UPP ) -Centre National de la Recherche Scientifique ( CNRS ), Sciences pour l'environnement ( SPE ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), and Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2
Subjects: Monitoring networks, [ SHS ] Humanities and Social Sciences, [ SHS.ECO ] Humanities and Social Sciences/Economies and finances, Expansion of Posidonia, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract: International audience
Published: 2014

13. Spatial oxygen heterogeneity in a Hediste diversicolor irrigated burrow

Author: Jose Luis Esteves, Laura Pischedda, Jean-Christophe Poggiale, Franck Gilbert, Philippe Cuny, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratorio de Oceanografía Química y Contaminación de Aguas, Centro Nacional Patagónico ( CENPAT-CONICET ), Laboratoire Ecologie Fonctionnelle et Environnement - ECOLAB ( ECOLAB ), Institut National Polytechnique [Toulouse] ( INP ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Centro Nacional Patagónico (CENPAT), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Centro Nacional Patagonico - CENPAT (ARGENTINA), Université de la Méditerranée - Aix-Marseille II (FRANCE), and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: 0106 biological sciences, Hediste diversicolor burrow, OXYGEN HETEROGENEITY, Water circulation, [SDE.MCG]Environmental Sciences/Global Changes, chemistry.chemical_element, Soil science, Bio-irrigation, 010501 environmental sciences, Aquatic Science, 01 natural sciences, Oxygen, Ciencias de la Tierra y relacionadas con el Medio Ambiente, Marine sediments, parasitic diseases, Ecosystem, 14. Life underwater, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Hydrologie, 0105 earth and related environmental sciences, biology, Ecology, 010604 marine biology & hydrobiology, Oceanografía, Hidrología, Recursos Hídricos, fungi, 15. Life on land, biology.organism_classification, Burrow, Anoxic waters, [ SDE.MCG ] Environmental Sciences/Global Changes, chemistry, 13. Climate action, Hediste diversicolor, Laboratory experiment, Bioturbation, Heterogeneity, [ SDU.STU.HY ] Sciences of the Universe [physics]/Earth Sciences/Hydrology, CIENCIAS NATURALES Y EXACTAS
Abstract: The heterogeneity of oxygen distribution in a Hediste diversicolor burrow environment was investigated in a laboratory experiment using a 6-mm thick tank equipped with oxygen planar optodes. The two-dimensional oxygen distribution in a complete burrow was monitored every 2 min for 4 h. Oxygen concentrations fluctuated over a scale of minutes in the burrow lumen and wall (up to 2 mm) reflecting the balance between worm ventilation activity and oxygen consumption. The magnitude of the three surrounding micro-horizons (oxic, oscillating and anoxic) induced by the intermittent worm ventilation was spatially and temporally variable within the structure. Oxygen variations appeared to be controlled by distance from the sediment-water interface and the direction of water circulation. Moreover, there was an apparent 'buffer effect', induced by the proximity to the overlying water, which reduced the variations of lumen and wall oxygen in the upper part of the structure. These results highlight the heterogeneous distribution and dynamics of oxygen associated with H. diversicolor burrows and ventilation activity. They also highlight the necessity of integrating this complexity into the current burrow-base models in order to estimate the ecological importance of burrowing species in coastal ecosystems. Fil: Pischedda, Laura. Université de la Méditerranée. Centre d’Océanologie de Marseill. Laboratoire de Microbiologie, Géochimie et Ecologie Marines; Francia Fil: Cuny, Philippe. Université de la Méditerranée. Centre d’Océanologie de Marseill. Laboratoire de Microbiologie, Géochimie et Ecologie Marines; Francia Fil: Esteves, Jose Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Poggiale, Jean Christophe. Université de la Méditerranée. Centre d’Océanologie de Marseill. Laboratoire de Microbiologie, Géochimie et Ecologie Marines; Francia Fil: Gilbert, Franck. Centre National de la Recherche Scientifique. Laboratoire d’Ecologie Fonctionnelle et Environnement; Francia. Université de Toulouse. Laboratoire d’Ecologie Fonctionnelle et Environnement; Francia
Published: 2012
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14. Characterization of specificity of bacterial community structure within the burrow environment of the marine polychaete Hediste (Nereis) diversicolor

Author: Laura Pischedda, Cécile Militon, Franck Gilbert, Philippe Cuny, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Université de la Méditerranée - Aix-Marseille II (FRANCE), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire Ecologie Fonctionnelle et Environnement - ECOLAB ( ECOLAB ), Institut National Polytechnique [Toulouse] ( INP ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 0106 biological sciences, DIOPATRA-CUPREA, Geologic Sediments, PLANAR OPTODES, Biodiversité et Ecologie, Biodiversity, 01 natural sciences, Océan, Atmosphère, RNA, Ribosomal, 16S, INORGANIC NITROGEN EXCHANGE, REACTION-RATES, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, biology, Ecology, Community structure, General Medicine, musculoskeletal system, Anoxic waters, Bacterial communities, ORGANIC-MATTER, Hediste diversicolor, ARENICOLA-MARINA, Bioturbation, Hediste diversicolor burrow, Molecular Sequence Data, Callianassa subterranea, Bacterial Physiological Phenomena, Microbiology, CALLIANASSA-SUBTERRANEA, Sediments, 03 medical and health sciences, parasitic diseases, Mediterranean Sea, Animals, 14. Life underwater, Molecular Biology, Ecosystem, 030304 developmental biology, Gene Library, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Polychaete, Bacteria, 010604 marine biology & hydrobiology, fungi, Computational Biology, Polychaeta, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, Burrow, OXYGEN-UPTAKE, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, OXIDIZING BACTERIA, MICROBIAL DIVERSITY
Abstract: Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. Surface, burrow wall and anoxic sediments were collected at the Carteau beach (Gulf of Fos, Mediterranean Sea). Bacterial diversity was determined by analyzing small subunit ribosomal RNA (16S rRNA) sequences from three clone libraries (168, 179 and 129 sequences for the surface, burrow wall and anoxic sediments, respectively). Libraries revealed 306 different operational taxonomic units (OTUs) belonging to at least 15 bacterial phyla. Bioinformatic analyses and comparisons between the three clone libraries showed that the burrow walls harbored a specific bacterial community structure which differed from the surface and anoxic environments. More similarities were nevertheless found with the surface assemblage. Inside the burrow walls, the bacterial community was characterized by high biodiversity, which probably results from the biogeochemical heterogeneity of the burrow system. (C) 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
Published: 2011
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15. Desulfovibrio piezophilus sp. nov., a piezophilic, sulfate-reducing bacterium isolated from wood falls in the Mediterranean Sea

Author: Jean Luc Cayol, Françoise Gaill, Marc Garel, Bernard Ollivier, Marie Laure Fardeau, Saber Khelaifia, Clement Aussignargues, Christian Tamburini, Nathalie Pradel, Sylvie M. Gaudron, Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Systématique, adaptation, évolution ( SAE ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Oxidation-Reduction, 0106 biological sciences, Geologic Sediments, MESH : Molecular Sequence Data, Sodium Chloride, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, 7. Clean energy, chemistry.chemical_compound, MESH : Mediterranean Sea, Lactate oxidation, MESH : Seawater: microbiology, Nitrite, MESH: Phylogeny, Phylogeny, Thiosulfate, 0303 health sciences, Base Composition, Strain (chemistry), biology, Sulfates, Fatty Acids, MESH : Sulfates: metabolism, General Medicine, MESH: Seawater: microbiology, Biochemistry, GROWTH, Desulfovibrio, FATTY-ACIDS, Energy source, Oxidation-Reduction, MESH: Geologic Sediments: microbiology, MESH: Mediterranean Sea, Stereochemistry, MESH: Sulfates: metabolism, Molecular Sequence Data, chemistry.chemical_element, PRESSURE, 010603 evolutionary biology, Microbiology, MESH : Sodium Chloride: metabolism, MESH: Sodium Chloride: metabolism, MESH : Base Composition, 03 medical and health sciences, MESH: Base Composition, Sulfite, MESH : Geologic Sediments: microbiology, Mediterranean Sea, Seawater, 14. Life underwater, MESH : Fatty Acids: metabolism, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH : Oxidation-Reduction, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Fatty Acids: metabolism, MESH: Desulfovibrio: chemistry,classification,genetics,isolation & purification, MESH : Phylogeny, biology.organism_classification, Sulfur, chemistry, MESH : Desulfovibrio: chemistry,classification,genetics,isolation & purification, Bacteria, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: A novel sulfate-reducing bacterium, designated C1TLV30T, was isolated from wood falls at a depth of 1693 m in the Mediterranean Sea. Cells were motile vibrios (2–4×0.5 µm). Strain C1TLV30T grew at temperatures between 15 and 45 °C (optimum 30 °C) and at pH 5.4–8.6 (optimum 7.3). It required NaCl for growth (optimum at 25 g NaCl l−1) and tolerated up to 80 g NaCl l−1. Strain C1TLV30T used as energy sources: lactate, fumarate, formate, malate, pyruvate and ethanol. The end products from lactate oxidation were acetate, H2S and CO2 in the presence of sulfate as terminal electron acceptor. Besides sulfate, thiosulfate and sulfite were also used as terminal electron acceptors, but not elemental sulfur, fumarate, nitrate or nitrite. Strain C1TLV30T possessed desulfoviridin and was piezophilic, growing optimally at 10 MPa (range 0–30 MPa). The membrane lipid composition of this strain was examined to reveal an increase in fatty acid chain lengths at high hydrostatic pressures. The G+C content of the genomic DNA was 49.6 % and the genome size was estimated at 3.5±0.5 Mb. Phylogenetic analysis of the SSU rRNA gene sequence indicated that strain C1TLV30T was affiliated to the genus Desulfovibrio with Desulfovibrio profundus being its closest phylogenetic relative (similarity of 96.4 %). On the basis of SSU rRNA gene sequence comparisons and physiological characteristics, strain C1TLV30T ( = DSM 21447T = JCM 1548T) is proposed to be assigned to a novel species of the genus Desulfovibrio, Desulfovibrio piezophilus sp. nov.
Published: 2011
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16. Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis

Author: Hana Trigui, Sam Dukan, Michel Denis, Gérald Grégori, Sami Maalej, Aude Barani, Céline Brochier-Armanet, Salma Masmoudi, Laboratoire de Microbiologie, Faculté des sciences de Sfax, Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Centre d'océanologie de Marseille ( COM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Faculté des Sciences de Sfax, Université de Sfax - University of Sfax-Université de Sfax - University of Sfax, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d'océanologie de Marseille (COM), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, DNA, Bacterial, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Salinity, Tunisia, Halophiles, Microbiology, Ribotyping, 03 medical and health sciences, Sphingobacteria, RNA, Ribosomal, 16S, Botany, Sphingobacterium, Flow cytometry, Halorubrum, ComputingMilieux_MISCELLANEOUS, Phylogeny, 030304 developmental biology, Alphaproteobacteria, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Original Paper, biology, Bacteria, Heterotrophic prokaryote, 030306 microbiology, Bacteroidetes, Water, Prokaryote, Heterotrophic Processes, General Medicine, Biodiversity, Solar saltern, biology.organism_classification, 16S ribosomal RNA, Archaea, Haloquadratum, DNA, Archaeal, LNA, HNA, Molecular Medicine, Molecular ecology, Water Microbiology
Abstract: Here, we combined flow cytometry (FCM) and phylogenetic analyses after cell sorting to characterize the dominant groups of the prokaryotic assemblages inhabiting two ponds of increasing salinity: a crystallizer pond (TS) with a salinity of 390 g/L, and the non-crystallizer pond (M1) with a salinity of 200 g/L retrieved from the solar saltern of Sfax in Tunisia. As expected, FCM analysis enabled the resolution of high nucleic acid content (HNA) and low nucleic acid content (LNA) prokaryotes. Next, we performed a taxonomic analysis of the bacterial and archaeal communities comprising the two most populated clusters by phylogenetic analyses of 16S rRNA gene clone library. We show for the first time that the presence of HNA and LNA content cells could also be extended to the archaeal populations. Archaea were detected in all M1 and TS samples, whereas representatives of Bacteria were detected only in LNA for M1 and HNA for TS. Although most of the archaeal sequences remained undetermined, other clones were most frequently affiliated to Haloquadratum and Halorubrum. In contrast, most bacterial clones belonged to the Alphaproteobacteria class (Phyllobacterium genus) in M1 samples and to the Bacteroidetes phylum (Sphingobacteria and Salinibacter genus) in TS samples. Electronic supplementary material The online version of this article (doi:10.1007/s00792-011-0364-5) contains supplementary material, which is available to authorized users.
Published: 2011
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17. Estimating inter-group interaction radius for point processes with nested spatial structures

Author: Vincent Bretagnolle, Pierre Couteron, Grégoire Certain, Edwige Bellier, Pascal Monestiez, Avner Bar-Hen, J. Chaduf, INRA - Mathématiques et Informatique Appliquées ( Unité MIAJ ), Institut National de la Recherche Agronomique ( INRA ), Centre d'études biologiques de Chizé ( CEBC ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Université Paris Descartes - Paris 5 ( UPD5 ), École des Hautes Études en Santé Publique [EHESP] ( EHESP ), IFP Energies nouvelles ( IFPEN ), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), École des Hautes Études en Santé Publique [EHESP] (EHESP), IFP Energies nouvelles (IFPEN), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Institut Français de Pondichéry (IFP), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Centre d'Études Biologiques de Chizé (CEBC), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Statistics and Probability, Applied Mathematics, Neighbourhood (graph theory), Process (computing), Radius, Function (mathematics), Spatial distribution, 010603 evolutionary biology, 01 natural sciences, Point process, [ SDE ] Environmental Sciences, 010104 statistics & probability, Computational Mathematics, Interaction radius, Computational Theory and Mathematics, Statistics, [SDE]Environmental Sciences, Cluster (physics), Local statistics, Point (geometry), Statistical physics, 0101 mathematics, Mathematics
Abstract: International audience; A statistical procedure is proposed in order to estimate the interaction radius between points of a non-stationary point process when the process can present local aggregated and regular patterns. The model under consideration is a hierarchical process with two levels, points and clusters of points. Points will represent individuals, clusters will represent groups of individuals. Points or clusters do not interact as soon as they are located beyond a given interaction radius, and are assumed to interact if their distance is less than this interaction radius. Interaction radius estimation is performed in the following way. For a given distance, observations are split into several clusters whose in-between distances are larger than this distance. For each cluster, a neighbourhood and an area in which this cluster is randomly located is defined under the assumption that the distance between the cluster and its neighbourhood is larger than the interaction radius. The p-value of a test of this assumption is then computed for each cluster. Modelling the expectation of this p-value as a function of the distance leads to an estimate of the interaction radius by a least-square method. This approach is shown to be robust against non-stationarity. Unlike most classical approaches, this method makes no assumption on the point spatial distribution inside the clusters. Two applications are presented in animal and plant ecology.
Published: 2011
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18. Biodegradation of Hydrocarbons in Bioturbated Marine Sediments

Author: Philippe Cuny, Cristiana Cravo-Laureau, Vincent Grossi, Franck Gilbert, cecile militon, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Koukkou, Anna-Irini, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux ( IPREM ), Université de Pau et des Pays de l'Adour ( UPPA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] ( LGL-TPE ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Ecologie Fonctionnelle et Environnement - ECOLAB ( ECOLAB ), Institut National Polytechnique [Toulouse] ( INP ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Centre National de la Recherche Scientifique ( CNRS ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut pluridisciplinaire de recherche sur l'environnement et les matériaux (IPREM), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: POLYCYCLIC AROMATIC-HYDROCARBONS, POLYCHAETES NEREIS-DIVERSICOLOR, ORGANIC-MATTER QUALITY, NAPHTHALENE-DEGRADING BACTERIA, ALKYLSUCCINATE SYNTHASE GENES, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, [ SDU.STU ] Sciences of the Universe [physics]/Earth Sciences, SULFATE-REDUCING BACTERIUM, OBLIGATELY UTILIZES HYDROCARBONS, LONG-ISLAND SOUND, MACROFAUNAL BURROW SEDIMENTS, MEDITERRANEAN COASTAL SEDIMENTS
Abstract: ISBN: 978-1-904455-83-7; Sediments can serve as sinks for hydrocarbon contaminants in marine ecosystems. Once settled, hydrocarbons fate will be dominated by several abiotic and biotic processes that will result in either their partial or total degradation or in a selective preservation when buried within the sediment. Biodegradation of hydrocarbons in marine sediments is mainly due to the existence of prokaryotes harbouring specific catabolic genes enabling the degradation of these compounds under oxic, suboxic and anoxic conditions. The interplay of the various factors that govern hydrocarbons biodegradation in marine sediments is highly complex as illustrated by bioturbation processes carried out by macrofaunal organisms. For instance, the redox oscillation regimes generated by macrofaunal organisms, and the efficiency of metabolic coupling between functional groups associated to these specific redox regimes, are probably determinant factors controlling the biodegradation rates of hydrocarbons in marine sediments. From the understanding of how these natural occurring factors may modulate the rates of hydrocarbons biodegradation, innovative bioremediation strategies may emerge.
Published: 2011

19. Phytoplankton Distribution During Two Contrasted Summers In A Mediterranean Harbour: Combining Automated Submersible Flow Cytometry With Conventional Techniques

Author: Melilotus Thyssen, Beatriz Beker, Dilek Ediger, Michel Denis, Doruk Yilmaz, Nicole Garcia, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Centre d'océanologie de Marseille ( COM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Beaussier, Catherine, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre d'océanologie de Marseille (COM), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, In situ, Chlorophyll, Chlorophyll a, 010504 meteorology & atmospheric sciences, Management, Monitoring, Policy and Law, Biology, Atmospheric sciences, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, 01 natural sciences, Fluorescence spectroscopy, [SDU] Sciences of the Universe [physics], chemistry.chemical_compound, Phytoplankton, Mediterranean Sea, Dominance (ecology), Fluorometry, 14. Life underwater, Picoplankton, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Chromatography, High Pressure Liquid, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, General Environmental Science, Hydrology, Microscopy, [ SDU.STU.OC ] Sciences of the Universe [physics]/Earth Sciences/Oceanography, 010604 marine biology & hydrobiology, General Medicine, Plankton, Flow Cytometry, Pollution, chemistry, [SDU]Sciences of the Universe [physics], Seawater, [ SDU ] Sciences of the Universe [physics], Environmental Monitoring
Abstract: Automated in situ flow cytometry, high-pressure liquid chromatography (HPLC), optical microscopy and fluorometry were combined to monitor phytoplankton over two summer periods (2005 and 2006). In 2006, temperature was higher and nutrients lower than in 2005, generating differences in the phytoplankton assemblages (i.e., abundance and structure). Pigment-size classes based on daily HPLC analysis provided evidence for higher proportions of picoplankton and nanoplankton with higher biomass in 2005 and a dominance of microplankton with lower biomass in 2006, the latter with lower specific diversity, as evidenced by weekly microscopy analyses. Total chlorophyll a estimations from fluorometry measurements recorded every 30 min were higher in 2005 than in 2006, as for the HPLC chlorophyll a concentrations. An automated in situ flow cytometer (Thyssen et al., J Plankton Res 30(9):1027–1040, 2008a) sampled seawater every 30 min. Data analysis yielded the resolution of seven clusters based on light scatter and fluorescence. In 2006, an increase in abundance of the largest cells was observed, confirming pigment and microscopy data. The results suggest that the ecosystem was on a constant renewing process in summer 2005 due to a strong wind event and on a highly productive and recycling way in summer 2006 due to stratification of the upper water layer. Automated submersible flow cytometry confirms to be a powerful tool providing high-resolution data by monitoring phytoplankton at the single cell level. This technology gives access to the shape of the light scatter and fluorescence signals generated by each cell passing through a laser beam and that are linked to size, structure and pigment content of the target cell. When combined with conventional techniques, it further improves our understanding of phytoplankton assemblages.
Published: 2011

20. Improved methodology to measure taxon-specific phosphate uptake in live and unfiltered samples

Author: Talarmin , Agathe, VAN-WAMBEKE , France, Duhamel , Solange, Catala , Philippe, MOUTIN , Thierry, Lebaron , Philippe, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire d'océanographie et de biogéochimie ( LOB ), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, SEA, HETEROTROPHIC BACTERIA, Biogeochemistry, PHOSPHORUS DYNAMICS, FLOW-CYTOMETRIC ANALYSIS, MARINE-PHYTOPLANKTON, SW PACIFIC-OCEAN, Phosphorus cycle (Biogeochemistry), Marine microbiology, Marine microbiology--Technique, CYANOBACTERIUM SYNECHOCOCCUS, GROWTH, SUBTROPICAL GYRE, STORAGE
Abstract: Microorganisms play a major role in the marine phosphate biogeochemical cycle but the relative contribution of picoplanktonic groups is not well understood. Previous studies have shown that combining uptake measurements of radiolabeled dissolved inorganic phosphate (P-i) substrate with cell sorting by flow cytometry is a powerful tool for the assessment of P-i fluxes at the cell-specific level. Nevertheless, using P-33 to trace P-i uptake, we show that treatments involving fixation and filtration of the sorted groups (i.e., heterotrophic prokaryotes, Synechococcus and piconanophytoeukaryotes) induce leakage of radioactive P-i (up to 50% of the signal), resulting in a sizeable underestimation of the taxon-specific P-i uptake. We suggest an alternative protocol, which significantly reduces this bias. Using this optimized protocol, the samples were treated with an excess of nonradioactive P-i to stop the incubation and sorted fractions were directly collected in microtubes for radioactivity counting, avoiding signal loss due to filtration. Sorted groups were strongly and differently impacted by fixation (0.5% PFA), with the exception of Synechococcus cells, which showed once a 10% lower signal in samples treated with the previously used protocols compared with samples treated with ours. Based on the integrity of the live sorted cells, our improved protocol provides reproducible and accurate estimations of the taxon-specific P-i uptake (
Published: 2011
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21. Erratum: Optimizing the setup of a flow cytometric cell sorter for efficient quantitative sorting of long filaments

Author: Hans L. Hoogveld, Michel Denis, Anthony Makassian, Marc van Dijk, Machteld Rijkeboer, Herman J. Gons, Gérald Grégori, Microbial Ecology (ME), Microbial Wetland Ecology (MWE), Departement of Microbial Ecology, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Histology, Sorting, technology, industry, and agriculture, chemical and pharmacologic phenomena, hemic and immune systems, Cell Biology, macromolecular substances, Biology, Bioinformatics, Filamentous cyanobacteria, Pathology and Forensic Medicine, 03 medical and health sciences, Cell sorter, 0302 clinical medicine, Flow (mathematics), 030220 oncology & carcinogenesis, otorhinolaryngologic diseases, Biological system, 030304 developmental biology
Abstract: This article corrects: Optimizing the setup of a flow cytometric cell sorter for efficient quantitative sorting of long filamentous cyanobacteria Vol. 77A, Issue 10, 911–924
Published: 2011
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22. Caldilinea tarbellica sp nov., a filamentous, thermophilic, anaerobic bacterium isolated from a deep hot aquifer in the Aquitaine Basin

Author: Manon Joseph, Patrick Gregoire, Marie-Laure Fardeau, Jean Cambar, Sophie Guasco, Patricia Bonin, Bernard Ollivier, Jean Luc Cayol, Valérie Michotey, Malek Bohli, Karine Dubourg, MEB, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Institut méditerranéen d'océanologie ( MIO ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2-Centre d'océanologie de Marseille ( COM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Centre d'océanologie de Marseille ( COM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Institut méditerranéen d'océanologie (MIO), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre d'océanologie de Marseille (COM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de la Méditerranée - Aix-Marseille 2, Centre d'océanologie de Marseille (COM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de la Méditerranée - Aix-Marseille 2, Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Centre d'océanologie de Marseille (COM), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Arabinose, Hot Temperature, SPHAEROBACTER-THERMOPHILUS, EMENDED DESCRIPTION, Sodium Chloride, chemistry.chemical_compound, RNA, Ribosomal, 16S, Cluster Analysis, Anaerobiosis, Raffinose, Phylogeny, 0303 health sciences, Base Composition, biology, Sulfates, Fatty Acids, Nucleic Acid Hybridization, RENATURATION, General Medicine, THERMOMICROBIA, LINEAGE, Hydrogen-Ion Concentration, 6. Clean water, Bacterial Typing Techniques, Biochemistry, Carbohydrate Metabolism, PHYLUM CHLOROFLEXI, GEN. NOV, France, Water Microbiology, DNA, Bacterial, Stereochemistry, Molecular Sequence Data, Microbiology, DNA, Ribosomal, 03 medical and health sciences, Caldilinea aerophila, PHOTOTROPHIC BACTERIA, Thermomicrobia, Yeast extract, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Nitrates, 030306 microbiology, Thermophile, Fructose, Maltose, Chloroflexi, Sequence Analysis, DNA, DNA, biology.organism_classification, chemistry, OIL-PRODUCING WELL, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: An anaerobic, thermophilic, filamentous (0.45 × >100 µm) bacterium, designated D1-25-10-4T, was isolated from a deep hot aquifer in France. Cells were non-motile and Gram-negative. Growth was observed at 43–65 °C (optimum 55 °C), at pH 6.8–7.8 (optimum pH 7.0) and with 0–5 g NaCl l−1 (optimum 0 g NaCl l−1). Strain D1-25-10-4T was a chemo-organotroph and fermented ribose, maltose, glucose, galactose, arabinose, fructose, mannose, sucrose, raffinose, xylose, glycerol, fumarate, peptone, starch and xylan. Yeast extract was required for growth. Sulfate, thiosulfate, sulfite, elemental sulfur, nitrate, nitrite and fumarate were not used as terminal electron acceptors. The G+C content of the DNA was 61.9 mol%. The major cellular fatty acids of strain D1-25-10-4T were C17 : 0, C18 : 0, C16 : 0 and iso-C17 : 0. The closest phylogenetic relative of strain D1-25-10-4T was Caldilinea aerophila STL-6-O1T (97.9 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain D1-25-10-4T and Caldilinea aerophila DSM 14535T was 8.7±1 %. On the basis of phylogenetic, genotypic and phenotypic characteristics, strain D1-25-10-4T represents a novel species within the genus Caldilinea, class Caldilineae, phylum Chloroflexi, for which the name Caldilinea tarbellica sp. nov. is proposed. The type strain is D1-25-10-4T ( = DSM 22659T = JCM 16120T).
Published: 2011
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23. Ecology of aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

Author: Dominique Lamy, Philippe Catala, David L. Kirchman, F. Van Wambeke, Matthew T. Cottrell, Josephine Ras, Mireille Pujo-Pay, L. Bariat, Philippe Lebaron, Christian Jeanthon, Louise Oriol, Véronique Cornet-Barthaux, O. Dahan, Laboratoire d'Océanographie Microbienne ( LOMIC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), MArine Phototrophic Prokaryotes ( MAPP ), Adaptation et diversité en milieu marin ( ADMM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), School of Marine Science and Policy, University of Delaware [Newark], Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'océanographie de Villefranche ( LOV ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Observatoire océanologique de Banyuls ( OOB ), Institut méditerranéen d'océanologie ( MIO ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Toulon ( UTLN ) -Aix Marseille Université ( AMU ) -Institut de Recherche pour le Développement ( IRD ), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), MArine Phototrophic Prokaryotes (MAPP), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, PHOTOHETEROTROPHIC BACTERIA, 010504 meteorology & atmospheric sciences, PHOTOSYNTHETIC BACTERIA, lcsh:Life, Biology, 01 natural sciences, P-LIMITATION, Carbon cycle, 03 medical and health sciences, Nutrient, Mediterranean sea, lcsh:QH540-549.5, Dissolved organic carbon, 14. Life underwater, SURFACE WATERS, Ecology, Evolution, Behavior and Systematics, SEASONAL-CHANGES, 0105 earth and related environmental sciences, Earth-Surface Processes, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Phototroph, 030306 microbiology, Ecology, lcsh:QE1-996.5, SOUTH-PACIFIC OCEAN, Anoxygenic photosynthesis, WET-OXIDATION, lcsh:Geology, lcsh:QH501-531, ORGANIC NITROGEN, 13. Climate action, Aerobic anoxygenic phototrophic bacteria, Photosynthetic bacteria, lcsh:Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, BACTERIOCHLOROPHYLL-A, COMMUNITY STRUCTURE
Abstract: Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic prokaryotes able to use both light and organic substrates for energy production. They are widely distributed in coastal and oceanic environments and may contribute significantly to the carbon cycle in the upper ocean. To better understand questions regarding links between the ecology of these photoheterotrophic bacteria and the trophic status of water masses, we examined their horizontal and vertical distribution and the effects of nutrient additions on their growth along an oligotrophic gradient in the Mediterranean Sea. Concentrations of bacteriochlorophyll-a (BChl-a) and AAP bacterial abundance decreased from the western to the eastern basin of the Mediterranean Sea and were linked with concentrations of chlorophyll-a, nutrient and dissolved organic carbon. Inorganic nutrient and glucose additions to surface seawater samples along the oligotrophic gradient revealed that AAP bacteria were nitrogen- and carbon-limited in the ultraoligotrophic eastern basin. The intensity of the AAP bacterial growth response generally differed from that of the total bacterial growth response. BChl-a quota of AAP bacterial communities was significantly higher in the eastern basin than in the western basin, suggesting that reliance on phototrophy varied along the oligotrophic gradient and that nutrient and/or carbon limitation favors BChl-a synthesis.
Published: 2011
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24. How far details are important in ecosystem modelling: the case of multi-limiting nutrients in phytoplankton–zooplankton interactions

Author: Bernard Quéguiner, Sebastiaan A.L.M. Kooijman, Melika Baklouti, Jean-Christophe Poggiale, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Department of Theoretical Biology [Amsterdam], Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Vrije Universiteit, Faculty of Earth and Life Science, and Theoretical Life Sciences
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Stability criterion, Population, Community, Biology, 01 natural sciences, Stability (probability), Zooplankton, Models, Biological, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, models, Nutrient, Bioreactors, Phytoplankton, Animals, Ecosystem, education, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, education.field_of_study, Ecology, 010604 marine biology & hydrobiology, fungi, Articles, sensitivity, Kinetics, Population model, Food, copper, General Agricultural and Biological Sciences, Biological system
Abstract: We try to answer the question of to what extent details in nutrient uptake and phytoplankton physiology matter for population and community dynamics. To this end, we study how two nutrients interact in limiting phytoplankton growth. A popular formulation uses a product-rule for nutrient uptake, which we compare with that on the basis of synthesizing units. We first fit different nutrient uptake models to a dataset and conclude that the quantitative differences between the models are small. Then we study the sensitivity of phytoplankton growth and zooplankton-phytoplankton interactions (ZPi) models to uptake formulations. Two population models are compared; they are based on different assumptions on the relation between nutrient uptake and phytoplankton growth.We find that the population and community models are sensitive to uptake formulations. According to the uptake formulation used in the ZPi models, qualitative differences can be observed. Indeed, although two models based on functions with similar shapes have close equilibria, these can differ in stability properties. Since stability involves the derivatives of formulas, even if two formulas provide close values, large numerical differences in the stability criterion may occur after derivation. We conclude that mechanistic details can be of importance for community modelling. © 2010 The Royal Society.
Published: 2010
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25. Dynamic energy budget theory restores coherence in biology

Author: Jean-Christophe Poggiale, Tânia Sousa, Tiago Domingos, Sebastiaan A.L.M. Kooijman, Environment and Energy Section ( DEM ), Instituto Superior Técnico, Universidade Técnica de Lisboa ( IST ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Vrije Universiteit, Faculty of Earth and Life Science, Environment and Energy Section (DEM), Instituto Superior Técnico, Universidade Técnica de Lisboa (IST), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Department of Theoretical Biology [Amsterdam], Faculty of Earth and Life Sciences [Amsterdam] (FALW), Vrije Universiteit Amsterdam [Amsterdam] (VU)-Vrije Universiteit Amsterdam [Amsterdam] (VU), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Dynamic energy budget, Energy metabolism, occam, Biology, 010603 evolutionary biology, 01 natural sciences, Models, Biological, General Biochemistry, Genetics and Molecular Biology, Development (topology), evolution, Animals, Homeostasis, Humans, Dynamic energy budget energy, ComputingMilieux_MISCELLANEOUS, computer.programming_language, Physics, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, energetics, Introduction, Scope (project management), Ecology, biology, 010604 marine biology & hydrobiology, Coherence (statistics), Sketch, State (computer science), ecology, General Agricultural and Biological Sciences, Energy Metabolism, Mathematical economics, computer, metabolism
Abstract: We present the state of the art of the development of dynamic energy budget theory, and its expected developments in the near future within the molecular, physiological and ecological domains. The degree of formalization in the set-up of the theory, with its roots in chemistry, physics, thermodynamics, evolution and the consistent application of Occam's razor, is discussed. We place the various contributions in the theme issue within this theoretical setting, and sketch the scope of actual and potential applications.
Published: 2010
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26. Two-time scales in spatially structured models of population dynamics : A semigroup approach

Author: Eva Sánchez, Pierre Auger, Jean-Christophe Poggiale, Departamento de Matemática Aplicada ( MA ), Universidad Politécnica de Madrid ( UPM ), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 (Cameroun)-University Cadi Ayyad ( UCA ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Departamento de Matemática Aplicada (MA), Universidad Politécnica de Madrid (UPM), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Class (set theory), Singular perturbation, Population, Banach space, Two-times scales, 01 natural sciences, Spatially structured population dynamics, Reaction–diffusion equations, Attractor, Reaction–diffusion system, population dynamics, Applied mathematics, 0101 mathematics, education, ComputingMilieux_MISCELLANEOUS, Mathematics, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, education.field_of_study, Two-time scales, Semigroup, Applied Mathematics, Space time, 010102 general mathematics, Mathematical analysis, Aggregation of variables, Spatially structured, 010101 applied mathematics, Reaction-diffusion equations, Analysis
Abstract: The aim of this work is to provide a unified approach to the treatment of a class of spatially structured population dynamics models whose evolution processes occur at two different time scales. In the setting of the C 0 -semigroup theory, we will consider a general formulation of some semilinear evolution problems defined on a Banach space in which the two-time scales are represented by a parameter e > 0 small enough, that mathematically gives rise to a singular perturbation problem. Applying the so-called aggregation of variables method, a simplified model called the aggregated model is constructed. A nontrivial mathematical task consists of comparing the asymptotic behaviour of solutions to both problems when e → 0 + , under the assumption that the aggregated model has a compact attractor. Applications of the method to a class of two-time reaction–diffusion models of spatially structured population dynamics and to models with discrete spatial structure are given.
Published: 2010
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27. Optimizing the Setup of a Flow Cytometric Cell Sorter for Efficient Quantitative Sorting of Long Filamentous Cyanobacteria

Author: Hans L. Hoogveld, Marc van Dijk, Machteld Rijkeboer, Herman J. Gons, Anthony Malkassian, Gérald Grégori, Michel Denis, Departement of Microbial Ecology, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Microbial Ecology (ME), and Microbial Wetland Ecology (MWE)
Subjects: Cyanobacteria, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Histology, Cell Survival, Cell Separation, Filamentous cyanobacteria, cyanobacteria, Pathology and Forensic Medicine, Flow cytometry, Cycle time, Protein filament, 03 medical and health sciences, Cell sorter, quantitative, Cell Movement, Cell Adhesion, medicine, sort, filaments, Cells, Cultured, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, biology, medicine.diagnostic_test, 030306 microbiology, Ecology, Cell Biology, biology.organism_classification, Biological system, Cytometry, sorting
Abstract: Heterogeneity within natural phytoplankton communities makes it very difficult to analyze parameters at the single-cell level. Flow cytometric sorting is therefore a useful tool in aquatic sciences, as it provides material for post-sort analysis and culturing. Sorting subpopulations from natural communities, however, often requires handling morphologically diverse and complex particles with various abundances. Long particles, such as filament-forming cyanobacteria (>100-μm long), prove very difficult to handle. These potentially toxic organisms are widespread in eutrophic systems and have important ecological consequences. Being able to sort filamentous cyanobacteria efficiently and as viable cells is therefore highly desirable when studying factors associated with their toxicity and occurrence. This unconventional sorting requires extensive user experience and special instrument setup. We have investigated the effect of hydrodynamic and electromechanical components of a flow cytometer, and sorting protocol on the quantitative sorting efficiency of these long particles using two filamentous cyanobacterial strains with average lengths of ∼100 and ∼300 μm. Sorting efficiency ranged from 9.4 to 96.0% and was significantly affected by filament length, sorting envelope, drop delay (dd), and for the long species also by tip size, but not by cycle time. Filaments survived sorting and were not damaged. The optimal settings found for the modular MoFlo® cell-sorter to sort the filaments were a 100-μm flow tip at 30 psi (207 kPa) with a three-droplet envelope in Enrich mode while using an extended analysis time of 17.6 μs and an intermediate plate charge and deflection percentage combination of 3,000 V/60%, combined with a dd 0 for the cultures with 100-μm filaments and dd +1 for the culture with 300-μm filaments. To the best of our knowledge, the filaments up to 1063.5 μm sorted in this study are the longest ever sorted. © 2010 International Society for Advancement of Cytometry
Published: 2010
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28. Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum 'Chloroflexi', isolated from a deep hot aquifer in the Aquitaine Basin

Author: Marie-Laure Fardeau, Sophie Guasco, Valérie Michotey, Patricia Bonin, Sandra Biasutti, Francette Hamaide, Manon Joseph, Patrick Gregoire, Bernard Ollivier, Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Centre d'océanologie de Marseille ( COM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Centre d'océanologie de Marseille (COM), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, ESPECE NOUVELLE, Hot Temperature, LEVEL, ADN, DIVERSITY, Hot aquifer, Xylose, Acetates, Applied Microbiology and Biotechnology, Hot Springs, chemistry.chemical_compound, Thermophilic, Cell Wall, RNA, Ribosomal, 16S, PHYLOGENIE, Microscopy, Phase-Contrast, Raffinose, Thermanaerothrix daxensis, Phylogeny, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Base Composition, biology, Hydrogen-Ion Concentration, Aquitaine Basin, Bacterial Typing Techniques, Phenotype, BACTERIE THERMOPHILE, TREES, Carbohydrate Metabolism, France, Water Microbiology, Anaerobic, Molecular Sequence Data, Phylum "Chloroflexi, Microbiology, 03 medical and health sciences, Botany, Lactic Acid, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Gram-Negative Anaerobic Bacteria, Base Sequence, 030306 microbiology, Thermophile, Fructose, Genes, rRNA, Chloroflexi, biology.organism_classification, Chloroflexi (class), Glucose, chemistry, Genes, Bacterial, Galactose, Phylum "Chloroflexi", OIL-PRODUCING WELL, Fermentation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MILIEU AQUATIQUE, GENRE NOUVEAU, Bacteria, Hydrogen
Abstract: A new strictly anaerobic thermophilic multicellular filamentous bacterium (0.2-0.3 mu m x > 100 mu m), designated GNS-1(T), was isolated from a deep hot aquifer in France. It was non-motile, and stained Gram-negative. Optimal growth was observed at 65 degrees C, pH 7.0, and 2 g L-1 of NaCl. Strain GNS-1(T) was chemoorganotrophic fermenting ribose, glucose, galactose, arabinose, fructose, mannose, maltose, sucrose, xylose, raffinose, pyruvate, and xylan. Yeast extract was required for growth. The end products of glucose fermentation were lactate, acetate, CO2, and H-2. The G + C content of the DNA was 57.6 mol%. Its closest phylogenetic relative was Bellilinea caldifistulae with 92.5% similarity. Based on phylogenetic, genotypic and phenotypic characteristics, strain GNS-1(T) (DSM 23592(T), JCM 169801) is proposed to be assigned to a novel species of a novel genus within the class Anaerolineae (subphylum I), phylum "Chloroflexi". Thermanaerothrix daxensis gen. nov., sp. nov. The GenBank accession number is HM596746. (C) 2011 Elsevier GmbH. All rights reserved.
Published: 2010
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29. Ultraphytoplankton basin-scale distribution in the eastern Mediterranean Sea in winter : link to hydrodynamism and nutrients

Author: Valérie Martin, Melilotus Thyssen, F. Vidussi, Michel Denis, B. Manca, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ), Istituto Nazionale di Oceanografia e Geofisica Sperimentale ( OGS ), INOGS, Laboratoire d'océanographie de Villefranche ( LOV ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Istituto Nazionale di Geofisica e di Oceanografia Sperimentale (OGS), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), The publication of this article is financed by CNRS-INSU, Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Water mass, 010504 meteorology & atmospheric sciences, Population, Temperature salinity diagrams, lcsh:Life, Biology, 01 natural sciences, Ocean gyre, lcsh:QH540-549.5, Phytoplankton, 14. Life underwater, education, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Earth-Surface Processes, education.field_of_study, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, lcsh:QE1-996.5, Synechococcus, biology.organism_classification, lcsh:Geology, lcsh:QH501-531, Oceanography, 13. Climate action, Thermohaline circulation, Prochlorococcus, lcsh:Ecology
Abstract: The basin-scale distribution of ultraphytoplankton (Synechococcus, Prochlorococcus, pico- (Synechococcus was the most abundant population (maximum abundance of about 37 000 cells cm−3) and contributed up to 67.7% to the overall ultraphytoplanktonic carbon biomass, whereas the contribution of Prochlorococcus never exceeded 6.5%. The maximum integrated carbon biomass was 1763, 453, 58 and 571 mg C m−2 for nanoeukaryotes, picoeukaryotes, Prochlorococcus and Synechococcus respectively. Water mass properties were analyzed on the basis of temperature and salinity distributions in order to account for the general circulation and locate the main hydrodynamic structures (fronts, gyres, transition between western and eastern basins). The effect of the main hydrodynamic structures and nutrients on the ultraphytoplankton distribution was investigated. No positive correlation between nutrients and phytoplankton could be established when considering large scales. However, below 50 m depth, nutrient ratios between particular stations were correlated to corresponding density ratios. In contrast, significant relationships were found between Synechococcus abundance and density, resulting from the impact of a gyre in southern Adriatic basin and a thermohaline front in the Ionian basin. A significant relationship was also found between picoeukaryotes and salinity in the comparison of western and eastern Mediterranean Sea.
Published: 2010
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30. In situ investigation of Spongia officinalis (Demospongiae) particle feeding : coupling flow cytometry and stable isotope analysis

Author: Topcu, N. E., Perez, T., Gregori, G., Harmelin-Vivien, M., Istambul University, Istanbul University, Diversité, évolution et écologie fonctionnelle marine ( DIMAR ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, LILLE - Service de Pneumologie (LILLE - Pneumo), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Department of Physics [Oxford], University of Oxford [Oxford], Diversité, évolution et écologie fonctionnelle marine (DIMAR), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Beaussier, Catherine, Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), and University of Oxford
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU] Sciences of the Universe [physics], [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU]Sciences of the Universe [physics], Retention efficiency, Suspension feeding, Demospongiae, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, Stable isotope, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 2010
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31. Isolation of hydrocarbon-degrading extremely halophilic archaea from an uncontaminated hypersaline pond (Camargue, France)

Author: Philippe Cuny, J.C. Bertrand, Yosmina Tapilatu, Vincent Grossi, Cécile Militon, Monique Acquaviva, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), PaleoEnvironnements et PaleobioSphere (PEPS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences de l'Univers (INSU), French Foreign Ministry, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Paléoenvironnement et paléobiosphère ( PP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: Salinity, Molecular Sequence Data, Fresh Water, Phenantrene, RNA, Archaeal, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, n-Alkanes, Microbial ecology, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, RNA, Ribosomal, 16S, Extreme environment, Haloferax, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Phylogeny, 030304 developmental biology, DNA Primers, 0303 health sciences, Haloarcula, biology, Base Sequence, 030306 microbiology, General Medicine, Phenanthrene, biology.organism_classification, Archaea, Halophile, Hydrocarbons, Biodegradation, Environmental, Hypersaline ponds, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Environmental chemistry, Halophilic, Biodegradation, Molecular Medicine, France, Crystallization, Bacteria, Fuel Oils, Water Pollutants, Chemical
Abstract: International audience; Little information exists about the ability of halophilic archaea present in hypersaline environments to degrade hydrocarbons. In order to identify the potential actors of hydrocarbon degradation in these environments, enrichment cultures were prepared using samples collected from a shallow crystallizer pond with no known contamination history in Camargue, France, with n-alkanes provided as source of carbon and energy. Five alkane-degrading halophilic archaeal strains were isolated: one (strain MSNC 2) was closely related to Haloarcula and three (strains MSNC 4, MSNC 14, and MSNC 16) to Haloferax. Biodegradation assays showed that depending on the strain, 32 to 95% (0.5 g/l) of heptadecane was degraded after 30 days of incubation at 40A degrees C in 225 g/l NaCl artificial medium. One of the strains (MSNC 14) was also able to degrade phenanthrene. This work clearly shows for the first time the potential role of halophilic archaea belonging to the genera Haloarcula and Haloferax in the degradation of hydrocarbons in both pristine and hydrocarbon-contaminated hypersaline environment
Published: 2010
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32. Towards methodological approaches to implement the zooplankton component in 'end to end' food-web models

Author: Francois Carlotti, Jean-Christophe Poggiale, Laboratoire d'Océanographie Physique et Biogéochimique (LOPB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, The authors would like to thank the IGBP programs IMBER and GLOBEC as well as the Network of Excellence EUR-OCEANS of the European Union's 6th Framework Program for funding the symposium on 'Parameterisation of Trophic Interaction in Ecosystem Modelling', European Project: 511106,EUR-OCEANS NoE, Laboratoire d'Océanographie Physique et Biogéochimique ( LOPB ), Université de la Méditerranée - Aix-Marseille 2, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, European Project : 511106,EUR-OCEANS NoE, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDU.STU.OC ] Sciences of the Universe [physics]/Earth Sciences/Oceanography, 010504 meteorology & atmospheric sciences, Management science, 010604 marine biology & hydrobiology, Geology, Large range, Aquatic Science, Biology, 01 natural sciences, Zooplankton, Food web, End-to-end principle, Component (UML), Ecological organization, 14. Life underwater, Strengths and weaknesses, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Trophic level
Abstract: International audience; The modelling of marine zooplankton has made great progress over the two last decades covering a large range of representations from detailed individual processes to functional groups. A new challenge is to dynamically represent zooplankton within marine food webs coupling lower trophic levels to fish and to thereby further our understanding of the role of zooplankton in global change. In this respect, the “rhomboid strategy” (deYoung et al., 2004) has been suggested as a generic approach to model the various trophic levels of pelagic ecosystems and is deemed to be adaptable to different spatial and temporal frames of applications. The present paper identifies directions to develop zooplankton modelling by combining the skills of modellers, experimentalists, observers and theoreticians. In the first part, we present the main types of existing models, specifying the scientific issues, their characteristic time and space scales, across the ecological organization levels. In the second part, we focus on the strengths and weaknesses of parameterizations for the different processes. Finally in the last part, we make suggestions for improving these parameterizations by combining experiments and observations, using modelling techniques to transfer information across scales and testing theories which can themselves help to organize experimental and modelling research.
Published: 2010
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33. Effects of chronic uranium exposure on life history and physiology of Daphnia magna over three successive generations

Author: Frédéric Alonzo, L. Garcia-Sanchez, Jacqueline Garnier-Laplace, Sandrine Massarin, Rodolphe Gilbin, Jean-Christophe Poggiale, Laboratoire de Modélisation Environnementale ( DEI/SECRE/LME ), Institut de Radioprotection et de Sûreté Nucléaire ( IRSN ), Laboratoire de Radioécologie et d'Ecotoxicologie ( DEI/SECRE/LRE ), Service d'Etude du Comportement des Radionucléides dans les Ecosystèmes, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire de Modélisation Environnementale (IRSN/DEI/SECRE/LME), Service d'Etude du Comportement des Radionucléides dans les Ecosystèmes (IRSN/DEI/SECRE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Laboratoire de Radioécologie et d'Ecotoxicologie (IRSN/DEI/SECRE/LRE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Modélisation Environnementale (DEI/SECRE/LME), Laboratoire de Radioécologie et d'Ecotoxicologie (DEI/SECRE/LRE), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Water Pollutants, Radioactive, Health, Toxicology and Mutagenesis, Daphnia magna, 0211 other engineering and technologies, chemistry.chemical_element, Zoology, Branchiopoda, 02 engineering and technology, 010501 environmental sciences, Aquatic Science, 01 natural sciences, Daphnia, Recovery, Cohort Effect, Ecotoxicology, Animals, Life history, Toxicity Tests, Chronic, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Multigeneration, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 021110 strategic, defence & security studies, biology, Dose-Response Relationship, Drug, Ecology, Reproduction, Environmental exposure, Environmental Exposure, Feeding Behavior, Uranium, biology.organism_classification, chemistry, Cladocera, Energy budget
Abstract: Daphnia magna was exposed to waterborne uranium (U) at concentrations ranging from 10 to 75 microgL(-1) over three successive generations (F0, F1 and F2). Progeny was either exposed to the same concentration as mothers to test whether susceptibility to this radioelement might vary across generations or returned to a clean medium to examine their capacity to recover after parental exposure. Maximum body burdens of 17, 32 and 54 ng U daphnid(-1) were measured in the different exposure conditions and converted to corresponding internal alpha dose rates. Low values of 5, 12 and 20 microGy h(-1) suggested that radiotoxicity was negligible compared to chemotoxicity. An increasing sensitivity to toxicity was shown across exposed generations with significant effects observed on life history traits and physiology as low as 10 microgL(-1) and a capacity to recover partially in a clean medium after parental exposure toor=25 microgL(-1). Using a (14)C-labelled food technique, the study showed that uranium affected carbon assimilation in F0 at concentrations of 25 and 75 microgL(-1) (34 and 80% reduction respectively) and as low as 10 microgL(-1) in F1 and F2 (40 and 36% reduction respectively). Consequences were strong for both somatic growth and reproduction and increased in severity across generations. Maximum size was reduced by 12% at 75 microgL(-1) in F0 and 23% at 25 microgL(-1) in F2. Reduction in 21-day fecundity ranged from 27 to 48% respectively at 25 and 75 microgL(-1) in F0 and from 43 to 71% respectively at 10 and 25 microgL(-1) in F2. Growth retardation caused a delay in deposition of first brood of 1.3 days at 75 microgL(-1) in F0, of 1.9 days at 25 microgL(-1) in F1 and of 5 days at 25 microgL(-1) in F2. Differences in respiration rates and egg dry mass between the control and exposed daphnids were mainly an indirect result of uranium effect on body size. The observed increase in toxic effects across generations indicated the necessity of carrying out multigeneration tests to assess environmental risk of uranium in daphnids.
Published: 2010
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34. Increased bacterial growth efficiency with environmental variability : results from DOC degradation by bacteria in pure culture experiments

Author: Marie Eichinger, Dominique Lefèvre, Bruno Charrière, Jean-Christophe Poggiale, Richard Sempéré, Gérald Grégori, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Aix Marseille Université (AMU), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement ( IRD ), Aix Marseille Université ( AMU ), Centre National de la Recherche Scientifique ( CNRS ), Institut méditerranéen d'océanologie ( MIO ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Toulon ( UTLN ) -Aix Marseille Université ( AMU ) -Institut de Recherche pour le Développement ( IRD ), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ), Poirot, Dominique, Theoretical Life Sciences, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Biogeochemical cycle, 010504 meteorology & atmospheric sciences, Dynamic energy budget, lcsh:Life, Soil science, Bacterial growth, DOC, 01 natural sciences, Bacterial growth efficiency, BGE, lcsh:QH540-549.5, Statistics, Empirical formula, DEB, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Earth-Surface Processes, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Reproducibility, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, 010604 marine biology & hydrobiology, lcsh:QE1-996.5, modeling, Substrate (marine biology), lcsh:Geology, lcsh:QH501-531, Environmental science, Degradation (geology), lcsh:Ecology, Respiration rate
Abstract: International audience; This paper assesses how considering variation in DOC availability and cell maintenance in bacterial models affects Bacterial Growth Efficiency (BGE) estimations. For this purpose, we conducted two biodegradation experiments simultaneously. In experiment one, a given amount of sub-strate was added to the culture at the start of the experiment whilst in experiment two, the same amount of substrate was added, but using periodic pulses over the time course of the experiment. Three bacterial models, with different levels of complexity, (the Monod, Marr-Pirt and the dynamic energy budget – DEB – models), were used and calibrated using the above experiments. BGE has been estimated using the experimental values obtained from discrete samples and from model generated data. Cell maintenance was derived experimentally , from respiration rate measurements. The results showed that the Monod model did not reproduce the experimental data accurately, whereas the Marr-Pirt and DEB models demonstrated a good level of reproducibility, probably because cell maintenance was built into their formula. Whatever estimation method was used, the BGE value was always higher in experiment two (the periodically pulsed substrate) as compared to the initially one-pulsed-substrate experiment. Moreover, BGE values estimated without considering cell maintenance (Monod model and empirical formula) were always smaller than BGE values obtained from models taking cell maintenance into account. Since BGE is commonly estimated using constant experimental systems and ignore Correspondence to: R. Sempéré (richard.sempere@univmed.fr) maintenance, we conclude that these typical methods underestimate BGE values. On a larger scale, and for biogeochem-ical cycles, this would lead to the conclusion that, for a given DOC supply rate and a given DOC consumption rate, these BGE estimation methods overestimate the role of bacterio-plankton as CO 2 producers.
Published: 2010
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35. Analyse de l'ADN et du cycle cellulaire des bactéries marines par cytométrie en flux

Author: Grégori, Gérald, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Grunwald D., Ronot D., Mayol J.F., Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Grunwald D., Ronot D., Mayol J.F., Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), and Pin, Thierry
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere
Abstract: Analyse de l'ADN et du cycle cellulaire des bactéries marines par cytométrie en flux
Published: 2010

36. Dyed microspheres for characterization of photochemical reactor behavior

Author: Blatchley , E., Shen , Chao, Naunovic , Z., Lin , L., Lyn , D., Bergstrom , D., Fang , S., Guan , Y., Robinson , J., Ragheb , K., GREGORI , Gerald, Purdue University [West Lafayette], Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Pin, Thierry
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, technology, industry, and agriculture, equipment and supplies, complex mixtures
Abstract: Dyed microspheres for characterization of photochemical reactor behavior.
Published: 2010

37. Detection of Extracellular Phosphatase Activity of Heterotrophic Prokaryotes at the Single‐Cell Level by Flow Cytometry

Author: Solange Duhamel, Gerald Gregori, France Van Wambeke, Jiří Nedoma, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Biological Centre of the Academy of Sciences, Czech Academy of Sciences [Prague] ( ASCR ), J. Paul Robinson, Zbigniew Darzynkiewicz, et al., Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Czech Academy of Sciences [Prague] (CAS), J. Paul Robinson, Zbigniew Darzynkiewicz, et al., Pin, Thierry, Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, phosphatase activity, Histology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Microorganism, Phosphatase, Heterotroph, ectoenzyme, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 01 natural sciences, Biochemistry, Flow cytometry, 03 medical and health sciences, functional measurement, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, medicine, Extracellular, aquatic heterotrophic bacteria, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, 030304 developmental biology, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, medicine.diagnostic_test, 010604 marine biology & hydrobiology, flow cytometry, Heterotrophic bacteria, Phosphatases, Functional measurement, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, Biological activity, General Medicine, Biogeochemistry, respiratory system, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [ SDV.EE.ECO ] Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Medical Laboratory Technology, [INFO.INFO-BT] Computer Science [cs]/Biotechnology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, cell concentration, Bacteria, [ INFO.INFO-BT ] Computer Science [cs]/Biotechnology
Abstract: Monitoring cell activity using substrates, which turn fluorescent due to biological activity, allows observing the presence and dynamics of sub-populations, and provides a very valuable insight in ecological studies. The phosphatase substrate ELF97 phosphate (ELF-P) is a useful tool to detect and quantify phosphatase activity (PA) of microorganisms at the single-cell level. Most of the studies dealing with PA at the single-cell level focus on autotrophic cells and only few concern heterotrophic prokaryotes (referred as bacteria in the text). While flow cytometry is a promising tool to assess the single-cell analysis, only microscopy tools have been used until now to measure the ELF labeling associated with bacteria expressing PA. Therefore, we have developed a new protocol that enables the detection of ELF alcohol (ELFA), the product of ELF-P hydrolysis, making possible the specific identification of bacteria showing PA using flow cytometry. Curr. Protoc. Cytom. 49:11.18.1-11.18.8. © 2009 by John Wiley & Sons, Inc. Keywords: aquatic heterotrophic bacteria; phosphatase activity; ectoenzyme; flow cytometry; cell concentration; functional measurement
Published: 2009

38. Le picoplancton photosynthétique

Author: Loïc Charpy, Gérald Grégori, Martine RODIER, Charpy, Loïc (coord.), Institut de Recherche pour le Développement ( IRD ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Muséum National d'Histoire Naturelle, Poirot, Dominique, Institut de Recherche pour le Développement (IRD), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, STRUCTURE DU PEUPLEMENT, MICROORGANISME, ABONDANCE, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, LAGON, PICOPLANCTON, TAILLE, ATOLL, CYTOMETRIE DE FLUX, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Published: 2009

39. Detection of Extracellular Phosphatase Activity at the Single-Cell Level by Enzyme-Labeled Fluorescence and Flow Cytometry : the Importance of Time Kinetics in ELFA Labeling

Author: Solange Duhamel, Gerald Gregori, France Van Wambeke, Jiří Nedoma, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Biological Centre of the Academy of Sciences, Czech Academy of Sciences [Prague] (CAS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire d'océanographie et de biogéochimie ( LOB ), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Czech Academy of Sciences [Prague] ( ASCR ), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Histology, Phosphatase, Kinetics, Fresh Water, Biology, 01 natural sciences, Pathology and Forensic Medicine, Flow cytometry, 03 medical and health sciences, Organophosphorus Compounds, medicine, Extracellular, Seawater, ComputingMilieux_MISCELLANEOUS, Quinazolinones, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Bacteria, Staining and Labeling, medicine.diagnostic_test, 010604 marine biology & hydrobiology, Cell Biology, Flow Cytometry, Fluorescence, Phosphoric Monoester Hydrolases, Enzyme assay, ELF phosphate, Biochemistry, kinetics, Phytoplankton, biology.protein, Alkaline phosphatase, Cytometry, alkaline phosphatase, heterotrophic bacteria
Abstract: ELF97 phosphate (ELF-P) is a useful compound for assessing the phosphorus-related status of planktonic aquatic populations. The technique has been successfully applied to phytoplankton and more recently to heterotrophic prokaryotes in both freshwater and marine samples. We have used a recently developed protocol that enables the detection by flow cytometry of ELF alcohol (ELFA), the product of ELF-P hydrolysis. This protocol allows for identification of the fraction of cells able to express phosphatase activity (i.e., ELFA-labeled). This protocol is also very valuable in the study of time kinetics in this ELFA-labeling. The percentage of ELFA-labeled cells, the relative median ELFA fluorescence per cell, and the absolute ELFA fluorescence were determined in both freshwater (lake) and marine samples. The incubation time necessary to reach a stable percentage of active cells with maximal fluorescence intensity varied widely among samples. We highlight very subtle but important problems of discrimination between active and nonactive cells and of estimation of per-cell activity and we underline the importance of studying time kinetics of ELFA-labeling to determine the appropriate incubation time and thus making sample comparisons more relevant. Working on time kinetics of ELFA-labeling is promising for phosphomonoester hydrolysis rate determination at single cell level. © 2008 International Society for Advancement of Cytometry
Published: 2008
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40. Visual censuses around drifting fish aggregating devices (FADs) : a new approach for assessing the diversity of fish in open-ocean waters

Author: Jean-Claude Gaertner, David Itano, Marc Taquet, Bastien Mérigot, Laurent Dagorn, Gorka Sancho, Riaz Aumeeruddy, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, IFREMER ( CRH ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Thons tropicaux et écosystèmes pélagiques : taxies, interactions et stratégies d'exploitation ( THETIS ), Seychelles Fishing Authority, Fishing Autority, College of Charleston, Pelagic Fisheries Research Program ( JIMAR ), University of Hawaii, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Halieutique Méditerranéenne et Tropicale (CRH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Thons tropicaux et écosystèmes pélagiques : taxies, interactions et stratégies d'exploitation (THETIS), Pelagic Fisheries Research Program (JIMAR), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and IFREMER (CRH)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, Diversity index, Survey methodology, Drifting fads, 14. Life underwater, Indian Ocean, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Diversity, Drifting FADs, Ecology, 010604 marine biology & hydrobiology, Species diversity, Pelagic zone, Pelagic fishes, Fishery, Species evenness, Indian ocean, Species richness, Diversity (business), Global biodiversity
Abstract: This study provides a baseline measure of pelagic fish species diversity around fish aggregating devices (FADs) in the Western Indian Ocean. Using data from visual censuses made by SCUBA divers around drifting FADs we (1) analysed 11 diversity indices describing 4 main compo- nents of pelagic diversity: number of species, evenness, taxonomic diversity and rarity and (2) dis- cussed the viability of using visual censuses around FADs to monitor temporal and spatial changes in diversity patterns of pelagic fishes in the future. Our results not only show that a single index, such as species richness or the Shannon-Wiener index, cannot provide a complete description of pelagic fish diversity around FADs, but also that some components of diversity appear to be multifaceted themselves and require the simultaneous use of several complementary indices in order to be accu- rately described and monitored. Despite a limited sampling effort, our results suggest that using visual censuses around FADs could provide reproducible 'relative' indices of diversity for a well- delimited assemblage of species (intra- and extranatant species in the epipelagic domain). In this con- text, we propose a preliminary 'short list' of diversity indices based firstly on their complementarity and secondly on their simplicity. While visual censuses of pelagic fishes at FADs (like any other sam- pling method) cannot give an exhaustive picture of diversity, they are a fishery-independent survey method that can complement other sampling techniques and provide reproducible information to monitor the diversity of these very difficult-to-access pelagic fish communities.
Published: 2008
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41. Factors limiting heterotrophic bacterial production in the southern Pacific Ocean

Author: Cécile Guieu, S Bonnet, Patrick Raimbault, Thierry Moutin, F. Van Wambeke, Gadiel Alarcón, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ), Géoazur ( GEOAZUR ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de la Côte d'Azur, Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'océanographie et de biogéochimie ( LOB ), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Oceanography & Center for Oceanographic Research in the eastern South Pacific, Universidad de Concepción [Chile], Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Géoazur (GEOAZUR 6526), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Universidad de Concepción - University of Concepcion [Chile], Laboratoire d'océanographie de Villefranche ( LOV ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Oceanography and Center for Oceanographic Research in the eastern South Pacific, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 010504 meteorology & atmospheric sciences, PRODUCTION PRIMAIRE, Heterotroph, lcsh:Life, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, BACTERIE, Bacterial growth, Biology, [ PHYS.ASTR.CO ] Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], 01 natural sciences, ABONDANCE, FACTEUR LIMITANT, [PHYS.ASTR.CO]Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], chemistry.chemical_compound, AZOTE, Nitrate, Ocean gyre, lcsh:QH540-549.5, Phytoplankton, [ SDU.ENVI ] Sciences of the Universe [physics]/Continental interfaces, environment, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Ecology, Evolution, Behavior and Systematics, [ SDU.ASTR ] Sciences of the Universe [physics]/Astrophysics [astro-ph], 0105 earth and related environmental sciences, Earth-Surface Processes, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography, Plateau, geography.geographical_feature_category, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], 010604 marine biology & hydrobiology, lcsh:QE1-996.5, [ SDU.STU ] Sciences of the Universe [physics]/Earth Sciences, CARBONE, lcsh:Geology, lcsh:QH501-531, Oceanography, chemistry, Upwelling, Seawater, lcsh:Ecology
Abstract: The role of potential factors limiting bacterial growth was investigated along vertical and longitudinal gradients across the South Eastern Pacific Gyre. The effects of glucose, nitrate, ammonium and phosphate additions on heterotrophic bacterial production (using leucine technique) were studied in parallel in unfiltered seawater samples incubated under natural daily irradiance. The enrichments realized on the subsurface showed three types of responses. From 141° W (Marquesas plateau) to approx 125° W, bacteria were not bottom-up controlled, as confirmed by the huge potential of growth in non-enriched seawater (median of enhancement factor×39 in 24 h). Within the Gyre (125° W–95° W), nitrogen alone stimulated leucine incorporation rates (median×4.2), but rapidly labile carbon (glucose) became a second limiting factor (median×37) when the two elements were added. Finally from the border of the gyre to the Chilean upwelling (95° W–73° W), labile carbon was the only factor stimulating heterotrophic bacterial production. Interaction between phytoplankton and heterotrophic bacterial communities and the direct versus indirect effect of iron and macronutrients on bacterial production were also investigated in four selected sites: two sites on the vicinity of the Marquesas plateau, the centre of the gyre and the Eastern border of the gyre. Both phytoplankton and heterotrophic bacteria were limited by availability of nitrogen within the gyre, but not by iron. Iron limited phytoplankton at Marquesas plateau and at the eastern border of the gyre. However 48 h enrichment experiments were not sufficient to show any clear limitation of heterotrophic bacteria within Marquesas plateau and showed a limitation of these organisms by labile carbon in the eastern border of the Gyre.
Published: 2008
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42. Heterotrophic nanoflagellate and ciliate bacterivorous activity and growth in the northeast Atlantic Ocean : a seasonal mesoscale study

Author: Karayanni , Hera, Christaki , Urania, Van Wambeke , France, Thyssen , Melilotus, Denis , Michel, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Hellenic Centre for Marine Research ( HCMR ), Ecosystèmes Littoraux et Cotiers, Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Hellenic Centre for Marine Research (HCMR), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Bacterivore, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 010504 meteorology & atmospheric sciences, Aquatic Science, 01 natural sciences, Algal bloom, Heterotrophic nanoflagellates, Growth rates, Phytoplankton, 14. Life underwater, Atlantic Ocean, Ecology, Evolution, Behavior and Systematics, Ingestion rates, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Ciliate, Microbial food web, Ciliates, biology, Ecology, 010604 marine biology & hydrobiology, Plankton, biology.organism_classification, Oceanography, 13. Climate action, Tintinnids, Bloom, Tintinnid, Bacterivory
Abstract: The grazing effect of heterotrophic nanoflagellates (HNF) and ciliates on bacterial pro- duction (BP), as well as their growth rates, was studied in winter, spring and autumn 2001 during the French research project Programme Ocean Multidisciplinaire Meso-Echelle (POMME) in the north- east Atlantic Ocean (38 to 45° N, 16 to 22° W). The variability of different parameters studied appears to be largely controlled by the seasonal and latitudinal gradients of primary production rather than the strong eddy activity at the mesoscale level in the area. Heterotrophic microbial abundance, bio- mass and protistan grazing varied temporally, presenting highest values during the phytoplankton bloom, during the spring period and following the northward propagation of the bloom. HNF biomass integrated over the upper 100 m was highest in spring (270 to 850 mg C m -2 ). Ciliate integrated bio- mass was generally ≤160 mg C m -2 except in a Tintinnus sp. bloom in a northern anticyclonic eddy (A1) in spring when it reached 637 mg C m -2 . HNF and ciliate growth rates varied from 0.2 to 0.7 d -1 and 0.2 to 1.4 d -1 , respectively. The fraction of BP consumed by ciliates was generally
Published: 2008
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43. A method for analysing phosphatase activity in aquatic bacteria at the single cell level using flow cytometry

Author: Solange Duhamel, Gerald Gregori, France Van Wambeke, Romain Mauriac, Jiří Nedoma, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire d'océanographie et de biogéochimie ( LOB ), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Biological Centre of the Academy of Sciences, Czech Academy of Sciences [Prague] ( ASCR ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (CAS), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Microbiology (medical), [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Phosphatase, Centrifugation, Fresh Water, 01 natural sciences, Microbiology, Bacterial cell structure, Flow cytometry, 03 medical and health sciences, chemistry.chemical_compound, Fluorescence microscope, medicine, Seawater, Propidium iodide, DAPI, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, biology, medicine.diagnostic_test, Bacteria, 010604 marine biology & hydrobiology, Heterotrophic Processes, biology.organism_classification, Flow Cytometry, 6. Clean water, Phosphoric Monoester Hydrolases, chemistry, Biochemistry, Reagent Kits, Diagnostic, Filtration
Abstract: It has been demonstrated that ELF97-phosphate (ELF-P) is a useful tool to detect and quantify phosphatase activity of phytoplankton populations at a single cell level. Recently, it has been successfully applied to marine heterotrophic bacteria in culture samples, the cells exhibiting phosphatase activity being detected using epifluorescence microscopy. Here, we describe a new protocol that enables the detection of ELF alcohol (ELFA), the product of ELF-P hydrolysis, allowing the detection of phosphatase positive bacteria, using flow cytometry. Bacteria from natural samples must be disaggregated and, in oligotrophic waters, concentrated before they can be analyzed by flow cytometry. The best efficiency for disaggregating/separating bacterial cell clumps was obtained by incubating the sample for 30 min with Tween 80 (10 mg l(-1), final concentration). A centrifugation step (20,000 g; 30 min) was required in order to recover all the cells in the pellet (only 7+/-2% of the cells were recovered from the supernatant). The cells and the ELFA precipitates were resistant to these treatments. ELFA-labelled samples were stored in liquid nitrogen for up to four months before counting without any significant loss in total or ELFA-labelled bacterial cell abundance or in the ELFA fluorescence intensity. We describe a new flow cytometry protocol for detecting and discriminating the signals from both ELFA and different counterstains (4',6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI)) necessary to distinguish between ELFA-labelled and non ELFA-labelled heterotrophic bacteria. The method has been successfully applied in both freshwater and marine samples. This method promises to improve our understanding of the physiological response of heterotrophic bacteria to P limitation.
Published: 2008
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44. Aggregation methods in dynamical systems and applications in population and community dynamics

Author: R. Bravo de la Parra, Pierre Auger, Eva Sánchez, Jean-Christophe Poggiale, Luis Perez Sanz, Modélisation mathématique et informatique de systèmes complexes naturels, biologiques ou sociaux ( GEODES ), Departamento de Matematicas [Alcala de Henares], Universidad de Alcalá = University of Alcalá ( UAH ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Departamento de Matemática Aplicada ( MA ), Universidad Politécnica de Madrid ( UPM ), Modélisation mathématique et informatique de systèmes complexes naturels, biologiques ou sociaux (GEODES), Universidad de Alcalá - University of Alcalá (UAH), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Departamento de Matemática Aplicada (MA), Universidad Politécnica de Madrid (UPM), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Dynamical systems theory, Population dynamics, Differential equation, Matemáticas, Approximate aggregation of variables, Population, Complex system, General Physics and Astronomy, 010603 evolutionary biology, 01 natural sciences, Global variable, 03 medical and health sciences, Artificial Intelligence, Dynamical systems, Calculus, Statistical physics, Dynamical system (definition), education, ANALYSE MATHEMATIQUE, 030304 developmental biology, Mathematics, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, MODELE MATHEMATIQUE, 0303 health sciences, education.field_of_study, Time scales, Rotation formalisms in three dimensions, MODELISATION, Ordinary differential equation, DYNAMIQUE DE POPULATION, General Agricultural and Biological Sciences, ECOLOGIE
Abstract: Approximate aggregation techniques allow one to transform a complex system involving many coupled variables into a simpler reduced model with a lesser number of global variables in such a way that the dynamics of the former can be approximated by that of the latter. In ecology, as a paradigmatic example, we are faced with modelling complex systems involving many variables corresponding to various interacting organization levels. This review is devoted to approximate aggregation methods that are based on the existence of different time scales, which is the case in many real systems as ecological ones where the different organization levels (individual, population, community and ecosystem) possess a different characteristic time scale. Two main goals of variables aggregation are dealt with in this work. The first one is to reduce the dimension of the mathematical model to be handled analytically and the second one is to understand how different organization levels interact and which properties of a given level emerge at other levels. The review is organized in three sections devoted to aggregation methods associated to different mathematical formalisms: ordinary differential equations, infinite-dimensional evolution equations and difference equations.
Published: 2008
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45. Heterotrophic bacterial production in the eastern South Pacific: longitudinal trends and coupling with primary production

Author: Solange Duhamel, Ingrid Obernosterer, Thierry Moutin, Osvaldo Ulloa, F. Van Wambeke, Hervé Claustre, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie biologique de Banyuls (LOBB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Departmento de Oceanografía & Centro de Investigación Oceanográfica en el Pacífico Sur-Oriental, Universidad de Concepción [Chile], Géoazur (GEOAZUR 6526), Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ), Observatoire océanologique de Banyuls ( OOB ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'océanographie biologique de Banyuls ( LOBB ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'océanographie et de biogéochimie ( LOB ), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Géoazur ( GEOAZUR ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de la Côte d'Azur, Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Universidad de Concepción - University of Concepcion [Chile], Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), and Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 010504 meteorology & atmospheric sciences, lcsh:Life, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Subtropics, Biology, [ PHYS.ASTR.CO ] Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], 01 natural sciences, [PHYS.ASTR.CO]Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Ocean gyre, lcsh:QH540-549.5, TheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITY, Temperate climate, [ SDU.ENVI ] Sciences of the Universe [physics]/Continental interfaces, environment, Photic zone, 14. Life underwater, Transect, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Ecology, Evolution, Behavior and Systematics, [ SDU.ASTR ] Sciences of the Universe [physics]/Astrophysics [astro-ph], 0105 earth and related environmental sciences, Earth-Surface Processes, South Pacific Gyre, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography, geography.geographical_feature_category, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], 010604 marine biology & hydrobiology, fungi, lcsh:QE1-996.5, Biogeochemistry, [ SDU.STU ] Sciences of the Universe [physics]/Earth Sciences, lcsh:Geology, lcsh:QH501-531, Oceanography, Upwelling, lcsh:Ecology
Abstract: Spatial variation of heterotrophic bacterial production and phytoplankton primary production were investigated across the eastern South Pacific Ocean (−141° W, −8° S to −72° W, −35° S) in November–December 2004. Bacterial production (3H leucine incorporation) integrated over the euphotic zone encompassed a wide range of values, from 43 mg C m−2 d−1 in the hyper-oligotrophic South Pacific Gyre to 392 mg C m−2 d−1 in the upwelling off Chile. In the gyre (120° W, 22° S) records of low phytoplankton biomass (7 mg Total Chla m−2) were obtained and fluxes of in situ 14C-based particulate primary production were as low as 153 mg C m−2 d−1, thus equal to the value considered as a limit for primary production under strong oligotrophic conditions. Average rates of 3H leucine incorporation rates, and leucine incorporation rates per cell (5–21 pmol l−1 h−1 and 15–56×10−21 mol cell−1 h−1, respectively) determined in the South Pacific gyre, were in the same range as those reported for other oligotrophic subtropical and temperate waters. Fluxes of dark community respiration, determined at selected stations across the transect varied in a narrow range (42–97 mmol O2 m−2 d−1), except for one station in the upwelling off Chile (245 mmol O2 m−2 d−1). Bacterial growth efficiencies varied between 5 and 38%. Bacterial carbon demand largely exceeded 14C particulate primary production across the South Pacific Ocean, but was lower or equal to gross community production.
Published: 2008
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46. Using a mathematical model to simulate the influence of tubifi cid worms (Oligochaeta) on oxygen concentrations in hyporheic sediments

Author: Florian Mermillod-Blondin, M. C. Des Châtelliers, C. Tolla, W. Thuiller, Pierre Auger, Jean-Christophe Poggiale, Laboratoire d'Ecologie des Hydrosystèmes Fluviaux (EHF), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Modélisation mathématique et informatique de systèmes complexes naturels, biologiques ou sociaux (GEODES), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Laboratoire d'Ecologie des Hydrosystèmes Fluviaux ( EHF ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), and Modélisation mathématique et informatique de systèmes complexes naturels, biologiques ou sociaux ( GEODES )
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, 0106 biological sciences, Biogeochemical cycle, [SDE.MCG]Environmental Sciences/Global Changes, chemistry.chemical_element, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Aquatic Science, 01 natural sciences, Oxygen, microbial activity, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, modelling, Respiration, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, animal-microbes interactions, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Ecology, biology, 010604 marine biology & hydrobiology, Sediment, biology.organism_classification, Tubifex, O2 respiration, [SDE.ES]Environmental Sciences/Environmental and Society, [ SDE.MCG ] Environmental Sciences/Global Changes, chemistry, Oligochaeta, Environmental chemistry, Tubifex tubifex, hyporheic sediments, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [ SDE.ES ] Environmental Sciences/Environmental and Society, 010606 plant biology & botany, Hydrobiology
Abstract: International audience; The aim of the study was to present a model to simulate the infl uence of tubifi cid worms (Limnodrilus sp. and Tubifex sp.) on O2 concentrations in hyporheic sediments. A mathematical model was developed to reproduce vertical distribution of O2 in experimental columns of sediments. Vertical columns were simulated as grids with cells of 1-cm depth each. The model took into account the hydrodynamic properties, the microbial respiration and distribution, the stimulation effect of tubifi cids on microbial activity, and the vertical distribution of worms in the system. Parameters of the mathematical model were determined to fit experimental oxygen concentrations obtained during two experiments: one experiment testing the infl uence of 100 Tubifex sp. (mainly Tubifex tubifex) and one experiment testing the effect of 100 Limnodrilus sp. (80 % Limnodrilus hoffmeisteri). The spatial model gave an adequate assessment of the vertical profi les of O2 concentrations in columns with and without tubifi cid worms. The parameters used to fi t simulations with experimental data supposed that Limnodrilus burrowed deeper and produced a higher stimulation of microbial respiration than Tubifex in our experimental system. Such results are in accordance with literature data and clearly suggest that this spatial model could be easily used to characterize the effects of animals (modifi cation rate of the microbial respirations by animals and location of the animal effect) on biogeochemical processes in hyporheic sediments
Published: 2008
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47. Characterizing fish communities associated with drifting fish aggregating devices (FADs) in the Western Indian Ocean using underwater visual surveys

Author: Riaz Aumeeruddy, Christophe Peignon, Gorka Sancho, David Itano, Bertrand Wendling, Marc Taquet, Jean-Claude Gaertner, Laurent Dagorn, IFREMER ( CRH ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), College of Charleston, Thons tropicaux et écosystèmes pélagiques : taxies, interactions et stratégies d'exploitation ( THETIS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Pelagic Fisheries Research Program ( JIMAR ), University of Hawaii, Seychelles Fishing Authority, Fishing Autority, IRD, Centre de Recherche Halieutique Méditerranéenne et Tropicale (CRH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Thons tropicaux et écosystèmes pélagiques : taxies, interactions et stratégies d'exploitation (THETIS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Pelagic Fisheries Research Program (JIMAR), IFREMER (CRH), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Coral reef fish, Triggerfish, Aquatic Science, reunion Island, Seychelles, 010603 evolutionary biology, 01 natural sciences, Visual census, Common species, 14. Life underwater, Indian Ocean, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Coryphaena, biology, Ecology, 010604 marine biology & hydrobiology, Pelagic zone, Pelagic fishes, biology.organism_classification, Drifting FAD, Canthidermis, Fishery, Reunion Island, Carcharhinus, Fish aggegations, Tuna, Fish aggregations
Abstract: We adapted a visual census method, mainly used in demersal and reef fish studies, to characterize fish communities associated to drifting fish aggregating devices (FADs) in the Western Indian Ocean. Drifting FAD associated fishes from both equatorial (Seychelles) and tropical waters (Reunion Island) were examined by divers. A total of 32 species (belonging to 16 families) were observed associated with drifting FADs in equatorial waters, and 24 species (14 families) were found around FADs in tropical waters. Twenty species were found in both regions. The highest number of species observed at a single FAD was 18 (12 +/- 2, mean +/- SD) in equatorial and 13 (10 +/- 3) in tropical waters, not counting circumnatant species loosely associated with the FAD. Some species like Kyphosus vaigiensis, Canthidermis maculata, Elagatis bipinnulata, Acanthocybium solandri and Coryphaena hippurus were observed on all or most of the surveys. In this study, the contribution in biomass of the 18 common species associated with drifting FADs (but excluding circumnatant species), represents more than 98% of the biomass. The overall biomass values of closely associated species remains well below tuna biomass estimates for circumnatant tuna schools at FADs, estimated as high as 200 tons. The species that most significantly contribute to the by-catch in tuna purse-seines logically match those that showing the highest biomass values in our surveys (Carcharhinus spp., Elagatis bipinnulata, Coryphaena hippurus, Canthidermis maculata, and Acanthocybium solandri). One of the most abundant and ubiquitous species in our study was the spotted oceanic triggerfish Canthidermis maculata that sometimes formed massive schools of many thousands individuals around the drifting FADs. Future research is needed to explore the role of such non tuna species in the attraction and aggregation processes of tuna around drifting FADs.
Published: 2008
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48. New tools for isolation and identification of micro-organisms

Author: cecile militon, Corinne Biderre, Pierre Peyret, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Ashok Pandey, Christian Larroche, Carlos Ricardo Soccol and Claude-Gilles Dussap, Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Pin, Thierry, Ashok Pandey, Christian Larroche, Carlos Ricardo Soccol and Claude-Gilles Dussap, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire Microorganismes : Génome et Environnement ( LMGE ), and Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Centre National de la Recherche Scientifique ( CNRS ) -Université d'Auvergne - Clermont-Ferrand I ( UdA )
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: The microbial world contains a highly heterogeneous group of organisms sharing only one common characteristic, their small sizes. These organisms make up two (out of three) entire Domains of life on earth, the prokaryotic Bacteria and Archaea (Woese, 1987). Within the third Domain Eukarya, the majority of the phylogenetic diversity is contained within eukaryotic micro-organisms such as protozoa, algae, and fungi. Micro-organisms are estimated to make up more than a third of Earth's biomass (Whitman, et al., 1998). Because culturing provided the platform for building the depth and detail of modern microbiological knowledge, for a long time microbiologists ignored the challenge to identify and characterize uncultured organisms. One of the indicators that cultured micro-organisms did not represent much of the microbial world was the oft-observed "great plate count anomaly" (Staley and Konopka, 1985). The discrepancy between the sizes of populations estimated by dilution plating and by microscopy is particularly dramatic in some aquatic environments, in which plate counts and viable cells estimated by acridine orange staining can differ by four to six orders of magnitude, and in soil, in which 0.1 to 1% of bacteria are readily culturable on common media under standard conditions (Torsvik and Ovreas, 2002). Understanding the extend and importance of the genetic and biochemical diversity among strains of the same or very closely related species is a cornerstone issue for many microbiological disciplines such as biotechnology, taxonomy, diagnosis, diversity surveys, etc. We are only at the beginning of the history of the discovery of the amazing microbial diversity.
Published: 2008

49. Behavior of dolphinfish (Coryphaena hippurus) around drifting FADs as observed from automated acoustic receivers

Author: Gorka Sancho, Laurent Dagorn, Charlotte Girard, Marc Taquet, Jean-Claude Gaertner, Riaz Aumerruddy, David Itano, Centre de Recherche Halieutique Méditerranéenne et Tropicale (CRH), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Thons tropicaux et écosystèmes pélagiques : taxies, interactions et stratégies d'exploitation (THETIS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Seychelles Fishing Authority, Fishing Autority, College of Charleston, Pelagic Fisheries Research Program (JIMAR), University of Hawaii, IFREMER (CRH), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, IFREMER ( CRH ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Thons tropicaux et écosystèmes pélagiques : taxies, interactions et stratégies d'exploitation ( THETIS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, and Pelagic Fisheries Research Program ( JIMAR )
Subjects: 0106 biological sciences, [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Ultrasonic telemetry, Behavoir of fish, Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, Dolphinfish, Range finding, Meeting point, Utrasonic telemetry, 14. Life underwater, Ecological trap, Indian Ocean, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Coryphaena, Behavior of fish, Ecology, FAD, Acoustic tagging, 010604 marine biology & hydrobiology, Significant difference, biology.organism_classification, Fishery, Indian ocean, Coryphaenidae, Aquatic environment, %22">Fish
Abstract: To study the behavior of dolphinfish (Coryphaena hippurus) around drifting Fish Aggregating Devices (FADs), we tagged individuals with long-lived, coded sonic transmitters and attached automated sonic receivers to drifting FADs in two regions of the Western Indian Ocean. Among the three tagging methods used in this study (surgery, external hooks, underwater bait without capture), the latest resulted in residence times significantly shorter than the other ones, likely due to regurgitation. Dolphinfish tagged with the two other methods usually stayed several days associated to FADs (Kaplan-Meier survival analysis 5.09 days, mean 6.25 days, SD 4.39 days, maximum 15.26 days), drifting with them. There was no significant difference in the residence times of dolphinfish in equatorial and tropical areas. While associated to FADs, dolphinfish spent most of their time close to floating object (< 365 m). The total time spent away from FADs was low (median 8%), and likely corresponded to making feeding excursions. Dolphinfish did not form a single school while associated to a given FADs, but formed multiple small schools. FADs are likely to be sites with exchanges of individuals between schools. These results are discussed in regards to the possibility of FADs acting as ecological traps and the validity of meeting-point hypotheses as an explanation for fish aggregations under floating objects.
Published: 2008
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50. Biological Invasion: The Thau Lagoon, a Japanese biological island in the Mediterranean Sea

Author: Sandrine Ruitton, Marc Verlaque, Judith C. Klein, Charles-François Boudouresque, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, CECCALDI H.J., DEKEYSER I., GIRAULT M., STORA G., Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, CECCALDI H.J., DEKEYSER I., GIRAULT M., STORA G., and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Biomass (ecology), biology, business.industry, 010604 marine biology & hydrobiology, [SDE.MCG]Environmental Sciences/Global Changes, Species diversity, Introduced species, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Macrophyte, Fishery, [ SDE.MCG ] Environmental Sciences/Global Changes, Geography, Mediterranean sea, Aquaculture, Crassostrea, 14. Life underwater, business, Shellfish, ComputingMilieux_MISCELLANEOUS
Abstract: Shellfish aquaculture represents one of the major vectors of marine macrophyte introductions. In the 1970s through at least the 1990s, massive imports of Japanese oysters, Crassostrea gigas, from the Pacific (mainly from Japan) to Europe were carried out. As a result, a large number of exotic species have been introduced to European shores. In the Mediterranean Sea, the Thau Lagoon (south-western France) has become a hot-spot of introduction of marine macrophytes. A total of 58 species of macrophytes have been labeled as introduced. They currently represent 32% of the species diversity and 48–99% of the macrophyte biomass on hard substrates. Most of them are native to the northwestern Pacific, including Japan. These figures do not take into account cryptogenic and cryptic introduced species and could therefore prove to be underestimates. The Thau Lagoon could therefore be the harbinger of the next century globalized world ocean.
Published: 2008

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