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Methods for Studying Microorganisms in the Environment

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Environmental Microbiology: Fundamentals and Applications

Abstract

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.

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Notes

  1. 1.

    The use of substrates enriched in radioisotopes (such as 14C) is less often considered in molecular studies and is not considered in this chapter.

  2. 2.

    However, δ13C values of biogenic and thermogenic methane can exhibit a large range of variability.

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Authors and Affiliations

  1. Laboratoire d’Océanographie Microbienne (LOMIC), UMR 7621 CNRS-UPMC, Observatoire Océanologique de Banyuls, 66650, Banyuls-sur-Mer, France

    Fabien Joux

  2. Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Université de Toulon, Aix-Marseille Université, Campus de Luminy, 13288, Marseille Cedex 9, France

    Jean-Claude Bertrand, Valérie Michotey, Patrick Raimbault & Christian Tamburini

  3. Écologie des systèmes marins côtiers (ECOSYM, UMR5119), Universités Montpellier 2 et 1, CNRS-Ifremer-IRD, 34095, Montpellier Cedex 05, France

    Rutger De Wit

  4. Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, UMR CNRS 5276, Université Claude Bernard Lyon 1, 69622, Villeurbanne Cedex, France

    Vincent Grossi

  5. Observatoire Océanologique de Banyuls sur Mer UPMC/CNRS – UMS 2348, Plateforme BIO2MAR, 66650, Banyuls-sur-Mer, France

    Laurent Intertaglia

  6. Observatoire Océanologique de Banyuls, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Sorbonne Universités, UPMC Univ Paris 06, USR CNRS 3579, 66650, Banyuls-sur-Mer, France

    Philippe Lebaron

  7. Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364, Université Lyon 1, 69622, Villeurbanne, France

    Philippe Normand

  8. EA CIDAM 4678, CBRV, Université d’Auvergne, 63001, Clermont-Ferrand, France

    Pierre Peyret

  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’Adour, B.P. 1155, 64013, Pau Cedex, France

    Laurent Urios

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  1. Fabien Joux
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  12. Laurent Urios
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Correspondence to Fabien Joux .

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Editors and Affiliations

  1. Université de Toulon, Aix-Marseille Université, Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Cedex 9, Marseille, France

    Jean-Claude Bertrand

  2. Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM), UM 110, CNRS 5254, Pau Cedex, France

    Pierre Caumette

  3. Observatoire Océanologique de Banyuls, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Sorbonne Universités, UPMC Univ, Paris 06, USR CNRS 3579, Banyuls-sur-Mer, France

    Philippe Lebaron

  4. Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), UMR-CNRS-IRD 7263, Aix-Marseille Université, Cedex 20, Marseille, France

    Robert Matheron

  5. Microbial Ecology Center, UMR CNRS 5557/USC INRA 1364, Villeubanne, France

    Philippe Normand

  6. Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Blaise Pascal, Clermont Université, Aubère Cedex, France

    Télesphore Sime-Ngando

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Joux, F. et al. (2015). Methods for Studying Microorganisms in the Environment. In: Bertrand, JC., Caumette, P., Lebaron, P., Matheron, R., Normand, P., Sime-Ngando, T. (eds) Environmental Microbiology: Fundamentals and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9118-2_17

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