Methods for Studying Microorganisms
in the Environment
17
Fabien Joux, Jean-Claude Bertrand, Rutger De Wit, Vincent Grossi,
Laurent Intertaglia, Philippe Lebaron, Vale ´rie Michotey, Philippe Normand,
Pierre Peyret, Patrick Raimbault, Christian Tamburini, and Laurent Urios
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
F. Joux* (*)
Laboratoire d’Oce ´anographie Microbienne (LOMIC), UMR 7621
CNRS-UPMC, Observatoire Oce ´anologique de Banyuls,
66650 Banyuls-sur-Mer, France
e-mail: fabien.joux@obs-banyuls.fr
J.-C. Bertrand V. Michotey P. Raimbault C. Tamburini
Institut Me ´diterrane ´en d’Oce ´anologie (MIO), UM 110, CNRS 7294
IRD 235, Universite ´ de Toulon, Aix-Marseille Universite ´,
Campus de Luminy, 13288 Marseille Cedex 9, France
R. De Wit
E ´ cologie des syste `mes marins co ˆtiers (ECOSYM, UMR5119),
Universite ´s Montpellier 2 et 1, CNRS-Ifremer-IRD, 34095 Montpellier
Cedex 05, France
V. Grossi
Laboratoire de Ge ´ologie de Lyon: Terre, Plane `tes, Environnement,
UMR CNRS 5276, Universite ´ Claude Bernard Lyon 1, 69622
Villeurbanne Cedex, France
L. Intertaglia
Observatoire Oce ´anologique de Banyuls sur Mer UPMC/CNRS – UMS
2348, Plateforme BIO2MAR, 66650 Banyuls-sur-Mer, France
P. Lebaron
Observatoire Oce ´anologique de Banyuls, Laboratoire de Biodiversite ´ et
Biotechnologie Microbiennes (LBBM), Sorbonne Universite ´s, UPMC
Univ Paris 06, USR CNRS 3579, 66650 Banyuls-sur-Mer, France
P. Normand
Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364,
Universite ´ Lyon 1, 69622 Villeurbanne, France
P. Peyret
EA CIDAM 4678, CBRV, Universite ´ d’Auvergne, 63001 ClermontFerrand, France
L. Urios
Institut des Sciences Analytiques et de Physico-chimie pour
l’Environnement et les Mate ´riaux (IPREM), UMR CNRS 5254,
Universite ´ de Pau et des Pays de l’Adour, B.P. 1155,
64013 Pau Cedex, France
* Chapter Coordinator
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_17, # Springer Science+Business Media Dordrecht 2015
757
in the Environment
17
Fabien Joux, Jean-Claude Bertrand, Rutger De Wit, Vincent Grossi,
Laurent Intertaglia, Philippe Lebaron, Vale ´rie Michotey, Philippe Normand,
Pierre Peyret, Patrick Raimbault, Christian Tamburini, and Laurent Urios
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
F. Joux* (*)
Laboratoire d’Oce ´anographie Microbienne (LOMIC), UMR 7621
CNRS-UPMC, Observatoire Oce ´anologique de Banyuls,
66650 Banyuls-sur-Mer, France
e-mail: fabien.joux@obs-banyuls.fr
J.-C. Bertrand V. Michotey P. Raimbault C. Tamburini
Institut Me ´diterrane ´en d’Oce ´anologie (MIO), UM 110, CNRS 7294
IRD 235, Universite ´ de Toulon, Aix-Marseille Universite ´,
Campus de Luminy, 13288 Marseille Cedex 9, France
R. De Wit
E ´ cologie des syste `mes marins co ˆtiers (ECOSYM, UMR5119),
Universite ´s Montpellier 2 et 1, CNRS-Ifremer-IRD, 34095 Montpellier
Cedex 05, France
V. Grossi
Laboratoire de Ge ´ologie de Lyon: Terre, Plane `tes, Environnement,
UMR CNRS 5276, Universite ´ Claude Bernard Lyon 1, 69622
Villeurbanne Cedex, France
L. Intertaglia
Observatoire Oce ´anologique de Banyuls sur Mer UPMC/CNRS – UMS
2348, Plateforme BIO2MAR, 66650 Banyuls-sur-Mer, France
P. Lebaron
Observatoire Oce ´anologique de Banyuls, Laboratoire de Biodiversite ´ et
Biotechnologie Microbiennes (LBBM), Sorbonne Universite ´s, UPMC
Univ Paris 06, USR CNRS 3579, 66650 Banyuls-sur-Mer, France
P. Normand
Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364,
Universite ´ Lyon 1, 69622 Villeurbanne, France
P. Peyret
EA CIDAM 4678, CBRV, Universite ´ d’Auvergne, 63001 ClermontFerrand, France
L. Urios
Institut des Sciences Analytiques et de Physico-chimie pour
l’Environnement et les Mate ´riaux (IPREM), UMR CNRS 5254,
Universite ´ de Pau et des Pays de l’Adour, B.P. 1155,
64013 Pau Cedex, France
* Chapter Coordinator
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_17, # Springer Science+Business Media Dordrecht 2015
757