Methods for Studying Microorganisms in the Environment

Fabien Joux; Jean Claude Bertrand; Rutger de Wit; Vincent Grossi; Laurent Intertaglia; Philippe Lebaron; Valérie Michotey; Philippe Normand; Pierre Peyret; Patrick Raimbault; Christian Tamburini; Laurent Urios

Methods for Studying Microorganisms in the Environment

Fabien Joux ^{1, *} 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

* Corresponding author

1 LOMIC - Laboratoire d'Océanographie Microbienne

2 MIO - Institut méditerranéen d'océanologie

3 Ecosym - Ecologie des systèmes marins côtiers

4 LGL-TPE - Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon]

5 OOB - Observatoire océanologique de Banyuls

6 LBBM - Laboratoire de Biodiversité et Biotechnologies Microbiennes

7 LEM - Laboratoire d'Ecologie Microbienne - UMR 5557

8 CIDAM - Conception, Ingénierie et Développement de l'Aliment et du Médicament

9 IPREM - Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux

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.

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

Document type :

Book sections

Domain :

Life Sciences [q-bio] / Ecology, environment

Complete list of metadatas

https://hal.sorbonne-universite.fr/hal-01235538
Contributor : Gestionnaire Hal-Upmc <>
Submitted on : Monday, November 30, 2015 - 11:47:59 AM
Last modification on : Friday, May 24, 2019 - 5:03:21 PM

Methods for Studying Microorganisms in the Environment

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Methods for Studying Microorganisms in the Environment

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