Methods for Studying Microorganisms in the Environment

  • Fabien JouxEmail author
  • Jean-Claude Bertrand
  • Rutger De Wit
  • Vincent Grossi
  • Laurent Intertaglia
  • Philippe Lebaron
  • Valérie Michotey
  • Philippe Normand
  • Pierre Peyret
  • Patrick Raimbault
  • Christian Tamburini
  • Laurent Urios


The main methods for the study of microorganisms in the environment (water, soil, sediment, biofilms), the different techniques of sampling for measuring biomass, the activities, and the diversity of the microorganisms are presented. To respond to these various issues, techniques as varied as those of flow cytometry, molecular biology, biochemistry, molecular isotopic tools, or electrochemistry are implemented. These different techniques are described with their advantages and disadvantages for different types of biotopes. The question of the isolation, culture, and conservation of microorganisms from the environment are also addressed. Without being exhaustive, this chapter emphasizes the importance of using appropriate and efficient methodological tools to properly explore the still mysterious compartment of microorganisms in the environment.


Bacterial isolation Biomarkers Cultural techniques Cytometry DNA microarray Microbial activities Microelectrodes Molecular fingerprints PCR Phospholipid fatty acid analyses Pigment analyses Sampling techniques 


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Fabien Joux
    • 1
    Email author
  • Jean-Claude Bertrand
    • 2
  • Rutger De Wit
    • 3
  • Vincent Grossi
    • 4
  • Laurent Intertaglia
    • 5
  • Philippe Lebaron
    • 6
  • Valérie Michotey
    • 2
  • Philippe Normand
    • 7
  • Pierre Peyret
    • 8
  • Patrick Raimbault
    • 2
  • Christian Tamburini
    • 2
  • Laurent Urios
    • 9
  1. 1.Laboratoire d’Océanographie Microbienne (LOMIC)UMR 7621 CNRS-UPMC, Observatoire Océanologique de BanyulsBanyuls-sur-MerFrance
  2. 2.Institut Méditerranéen d’Océanologie (MIO)UM 110, CNRS 7294 IRD 235, Université de Toulon, Aix-Marseille UniversitéMarseille Cedex 9France
  3. 3.Écologie des systèmes marins côtiers (ECOSYM, UMR5119)Universités Montpellier 2 et 1, CNRS-Ifremer-IRDMontpellier Cedex 05France
  4. 4.Laboratoire de Géologie de Lyon: Terre, Planètes, EnvironnementUMR CNRS 5276, Université Claude Bernard Lyon 1Villeurbanne CedexFrance
  5. 5.Observatoire Océanologique de Banyuls sur Mer UPMC/CNRS – UMS 2348, Plateforme BIO2MARBanyuls-sur-MerFrance
  6. 6.Observatoire Océanologique de Banyuls, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM)Sorbonne Universités, UPMC Univ Paris 06, USR CNRS 3579Banyuls-sur-MerFrance
  7. 7.Microbial Ecology CenterUMR CNRS 5557 / USC INRA 1364, Université Lyon 1VilleurbanneFrance
  8. 8.EA CIDAM 4678, CBRV, Université d’AuvergneClermont-FerrandFrance
  9. 9.Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM)UMR CNRS 5254, Université de Pau et des Pays de l’AdourPau CedexFrance

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