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Environmental microbiology as a mosaic of explored ecosystems and issues

Environmental Science and Pollution Research volume 22, pages 13577–13598 (2015)Cite this article

Abstract

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium’s efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

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the Microbial Ecology EC2CO consortium:

Pierre Amato Institut de Chimie de Clermont-Ferrand, UMR6296 CNRS, Université Blaise Pascal-Ecole Nationale Supérieure de Chimie de Clermont-Ferrand, 63171 Aubière, France

Florence Arsène-Ploetze Ecophysiologie Moléculaire des Microorganismes, UMR7156, CNRS, Université de Strasbourg, 28 rue Goethe, 67000 Strasbourg, France

Jean-Christophe Auguet UMR CNRS 5254 IPREM, Equipe Environnement et Microbiologie IBEAS - BP1155, 64013 Pau Cedex, France

Laetitia Bernard Institut de Recherche pour le Développement (IRD), UMR 210 Eco&sols, Laboratoire des Radio-Isotopes (LRI), BP 3383, Antananarivo 101, Madagascar

Philippe N. Bertin Ecophysiologie Moléculaire des Microorganismes, UMR7156, CNRS, Université de Strasbourg, 28 rue Goethe, 67000 Strasbourg, France

Yvan Bettarel ECOSYM UMR 5119, IRD, CNRS, Université Montpellier 1 et 2, Université Montpellier 2, 34095 Montpellier cedex 5, France

Aurélie Bigot-Clivot Université Reims Champagne Ardenne, UMR-I 02, Stress Environnementaux et biosurveillance des milieux aquatiques (SEBIO), UFR Sciences Exactes et Naturelles, Moulin de la Housse BP 1039, 51687 Reims Cedex, France

Nicolas Blot Laboratoire Microorganismes, Génome et Environnement, UMR6023 CNRS-UBP-UdA, Université Blaise Pascal, 63171 Aubière Cedex, France

Manuel Blouin Institut d’Ecologie et des Sciences de l’Environnement de Paris (IEES-Paris), UMR 7618, Sorbonne Universities, UPMC Univ. Paris 06, Université Paris-Est Créteil, AgroParisTech, 4 place Jussieu 75252 Paris cedex 05, France

Myriam Bormans UMR 6553 ECOBIO, Université de Rennes 1 - CNRS, Campus de Beaulieu, 35042 Rennes Cedex, France

Marc Bouvy ECOSYM UMR 5519, IRD, CNRS, Université Montpellier 1 et 2, Université Montpellier 2, 34095 Montpellier cedex 5, France

Odile Bruneel, Laboratoire HydroSciences Montpellier, UMR HSM 5569, (IRD, CNRS, UM) Université Montpellier, Bâtiment 40, CCMSE, 34095 Montpellier cedex 05, France

Aurélie Cébron Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR7360 CNRS-Université de Lorraine, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-les-Nancy, France

Urania Christaki UMR LOG 8187, Univ. Lille Nord - Univ. Du Littoral, Wimereux, France

Ivan Couée UMR 6553 ECOBIO, Université de Rennes 1 - CNRS, Campus de Beaulieu, 35042 Rennes Cedex, France

Cristiana Cravo-Laureau Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l’Adour, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France

Michael Danger Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360, Université de Lorraine-CNRS, Campus Bridoux, rue Claude Bernard, 57070 Metz, France

Julien de Lorgeril ECOSYM (Ecologie des Sytèmes Marins Côtiers), CNRS, Ifremer, IRD, Universités de Montpellier 1 et 2, UMR 5119, 34095 Montpellier Cedex 5, France

Yves Desdevises UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls (OOB), Université Pierre et Marie Curie, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France

Yves Dessaux Institut de Biologie Intégrative de la cellule, CNRS, CEA, Université Paris-Sud, Saclay Plant sciences, 91 198 Gif-sur-Yvette, France

Delphine Destoumieux-Garzón ECOSYM (Ecologie des Sytèmes Marins Côtiers), CNRS, Ifremer, IRD, Universités de Montpellier 1 et 2, UMR 5119, 34095 Montpellier Cedex 5, France

Elodie Duprat Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC) Sorbonne Universités - UPMC Univ. Paris 06, UMR CNRS 7590, Muséum National d’Histoire Naturelle, UR 206, 4 Place Jussieu, 75005 Paris, France

Gaël Erauso Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), 13288, Marseille, Cedex 9; Université du Sud Toulon-Var, 83957, CNRS-INSU/IRD UM 110, France

Feth el Zahar Haichar UMR-CNRS 5557 Ecologie microbienne, INRA USC 1364, 69100 Villeurbanne, France

Eric Fouilland UMR 5119 ECOSYM – CNRS, University Montpellier 2, University Montpellier 1, IRD, IFREMER, Station Méditerranéenne de l’environnement Littoral, 34200 Sète, France

André-Jean Francez UMR 6553 ECOBIO, Université de Rennes 1 - CNRS, Campus de Beaulieu, 35042 Rennes Cedex, France

Nathalie Fromin Centre d’Ecologie Fonctionnelle et Evolutive, UMR 5175, 1919 route de Mende, 34293 Montpellier Cedex 5, France

Alain Geffard Université Reims Champagne Ardenne, UMR-I 02, Stress Environnementaux et biosurveillance des milieux aquatiques (SEBIO), UFR Sciences Exactes et Naturelles, Moulin de la Housse BP 1039, 51687 Reims Cedex, France

Jean-François Ghiglione, CNRS, UMR 7621, Laboratoire d’Océanographie Microbienne (LOMIC), Observatoire Océanologique, 66650 Banyuls/mer, France

Vincent Grossi, Laboratoire de Géologie de Lyon (LGLTPE UMR 5276 CNRS), Université Claude Bernard Lyon 1 - Université de Lyon, campus de la Doua, 69622 Villeurbanne, France.

Katell Guizien, CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques (LECOB - UMR8222), Observatoire Océanologique de Banyuls, 66 650 Banyuls-sur-mer, France.

Cédric Hubas, Unité Biologie des Organismes et Écosystèmes Aquatiques (BOREA, UMR 7208), Sorbonne Universités, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Université de Caen Basse-Normandie, CNRS, IRD, Université des Antilles et de la Guyane ; CP53, 61 rue Buffon 75005 Paris, France.

Arnaud Huguet Sorbonne Universités, UPMC Univ Paris 06, CNRS, EPHE, UMR 7619 METIS, 4 place Jussieu, 75252 Paris cedex, France

Ludwig Jardillier Université Paris-Sud, Laboratoire d’Ecologie, Systématique et Evolution, UMR CNRS 8079, bâtiment 360, 91405 Orsay cedex, France

Pascal Jouquet, IRD, UMR CNRS 7618 iEES Paris, IFCWS, Civil engineering Department, Indian Institute of Science, 560012 Bangalore, India

Fabien Joux, Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, 66650 Banyuls-sur-mer, France

Aurore Kaisermann, Institut d’Ecologie et des Sciences de l’Environnement de Paris (IEES-Paris), UMR 7618, Sorbonne Universities, UPMC Univ. Paris 06, Université Paris-Est Créteil, AgroParisTech, 4 place Jussieu 75252 Paris cedex 05, France

Oliver Kaltz,Institut des Sciences de l'Evolution, UMR 5554, Université de Montpellier, 34095 Montpellier Cedex 05, France

Jean-Christophe Lata Institut d’Ecologie et des Sciences de l’Environnement de Paris (IEES-Paris), UMR 7618, Sorbonne Universities, UPMC Univ. Paris 06, Université Paris-Est Créteil, AgroParisTech, 4 place Jussieu 75252 Paris cedex 05, France

Antoine Lecerf EcoLab – Laboratoire d’écologie fonctionnelle et environnement UMR 5245 CNRS-INPT-Université Paul Sabatier, 31062 Toulouse cedex, France

Corinne Leyval Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR7360 CNRS-Université de Lorraine, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-les-Nancy, France

Patricia Luis Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, 69622 Villeurbanne Cedex, France

Estelle Masseret, Biodiversité Marine, Exploitation & Conservation, UMR Marbec 9190, IRD-Université de Montpellier-Ifremer-CNRS, cc93, Place Eugène Bataillon, Montpellier cedex 5, France

Audrey Niboyet Institut d’Ecologie et des Sciences de l’Environnement de Paris (IEES-Paris), UMR 7618, Sorbonne Universities, UPMC Univ. Paris 06, Université Paris-Est Créteil, AgroParisTech, 4 place Jussieu 75252 Paris cedex 05, France

Philippe Normand Ecologie Microbienne UMR CNRS5557, Université Lyon1, 69622 cedex Villeurbanne, France

Frédéric Plewniak Ecophysiologie Moléculaire des Microorganismes, UMR7156, CNRS Université de Strasbourg, 28 rue Goethe, 67000 Strasbourg, France

Franck Poly UMR-CNRS 5557 Ecologie microbienne, INRA USC 1364, 69100 Villeurbanne, France

Soizic Prado, Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM, UMR 7245), Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS, CP54 ; 63 rue Buffon 75005 Paris, France

Achim Quaiser Université de Rennes 1 - CNRS, UMR 6553 ECOBIO, Campus de Beaulieu, 35042 Rennes cedex, France

Pascal Ratet, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 0rsay, France

Agnès Richaume, Ecologie Microbienne, UMR CNRS 5557, Lyon 1, Université de Lyon, 69622 Villeurbanne cedex, France

Jean-Luc Rolland IFREMER, Université Montpellier 2, Centre National de la Recherche Scientifique, IRD, UM1, UMR 5119 Ecologie des Systèmes Marins Côtiers, 34095 Montpellier cedex 5, France

Jean-Luc Rols Université Toulouse 3, UMR CNRS 5245 EcoLab, 31 062 Toulouse cedex 9, France

Jean-François Rontani Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), 13288, Marseille, Cedex 9; Université du Sud Toulon-Var, 83957, CNRS-INSU/IRD UM 110, France

Francesca Rossi UMR5119, Université de Montpellier 2 Pl. E. Bataillon Bat 24, 34075 Montpellier, France

Sophie Sablé Littoral Environnement et Sociétés (LIENSs), UMR 7266 CNRS Université de La Rochelle, UFR Sciences, Bât. Marie Curie, 17042 La Rochelle cedex 01, France

Pierre Sivadon UMR CNRS 5254 IPREM, Equipe Environnement et Microbiologie IBEAS - BP1155, 64013 Pau cedex, France

Philippe Soudant Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR6539 UBO-CNRS-IRDIFREMER, Institut Universitaire Européen de la Mer (IUEM), Technopole Brest Iroise, Rue Dumont d’Urville, 29280 Plouzané, France

Christian Tamburini Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), 13288, Marseille, Cedex 9; Université du Sud Toulon-Var, 83957, CNRS-INSU/IRD UM 110, France

Aline Tribollet UMR IPSL-LOCEAN, Centre IRD France Nord, 93143 Bondy Cedex, France

Claire Valiente Moro UMR CNRS 5557, USC INRA 1364, Ecologie Microbienne, Université de Lyon, Université Lyon 1, 69622 Villeurbanne Cedex, France

France Van Wambeke Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), 13288, Marseille, Cedex 9; Université du Sud Toulon-Var, 83957, CNRS-INSU/IRD UM 110, France

Philippe Vandenkoornhuyse UMR 6553 ECOBIO, Université de Rennes 1 - CNRS, Campus de Beaulieu, 35042 Rennes Cedex, France

Stéphane Vuilleumier UMR 7156 UdS- CNRS Génétique Moléculaire, Génomique, Microbiologie, 67083 Strasbourg cedex, France

Acknowledgments

This work is supported by the CNRS Mission pour l’Interdisciplinarité and the Incentive Action Ecosphère Continentale et Côtière (EC2CO). We thank the present and former members of Microbial Ecology EC2CO scientific committee.

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Authors and Affiliations

  1. Institut de Biologie Intégrative de la Cellule, CNRS-CEA-Université Paris-Sud, Saclay Plant Sciences, 91198, Gif-sur-Yvette cedex, France

    Denis Faure

  2. Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), 13288, Marseille, Cedex 9, France

    Patricia Bonin

  3. Université du Sud Toulon-Var, CNRS-INSU/IRD UM 110, 83957, La Garde, France

    Patricia Bonin

  4. Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l’Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France

    Robert Duran

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  1. Denis Faure
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the Microbial Ecology EC2CO consortium

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Correspondence to Denis Faure or Patricia Bonin.

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Faure, D., Bonin, P., Duran, R. et al. Environmental microbiology as a mosaic of explored ecosystems and issues. Environ Sci Pollut Res 22, 13577–13598 (2015). https://doi.org/10.1007/s11356-015-5164-5

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Keywords

  • Environmental microbiology
  • Microbial ecology
  • Critical zone
  • Microbial ecosystems