Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere

  • Wafa Achouak
  • Feth el Zahar HaicharEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2046)


Stable isotope probing of microbial nucleic acids applied in the rhizosphere enables (a) the identification of the active microbial community involved in root exudate assimilation and those involved in soil organic matter degradation, and (b) the study of the impact of plants via root exudates on the in situ expression of microbial functions. By incubating plants under 13CO2, fresh carbon exuded by the plant will be labeled and hence the microbial community assimilating 13C-root exudates will incorporate 13C into their cellular macromolecules. Labeled DNA, RNA, and proteins can be used to identify microorganisms that assimilated the root exudates. We provide a step-by-step protocol on how to apply stable isotope probing of DNA and RNA in the plant rhizosphere to identify the active microbial communities and analyze their gene expression.

Key words

Stable isotope probing 13CO2 plant labeling Root-adhering soil Root system Root exudates DNA RNA CsCl equilibrium density-gradient centrifugation Isotope Ratio mass spectrometry 16S rRNA 18S rRNA 



We thank French National Research Agency (ANR-18-CE32-0005, DIORE) for providing funding to the project.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Aix Marseille University, CNRS, CEA, UMR 7265 BVME, LEMIRE, ECCOREV FR 3098Saint-Paul-lez-DuranceFrance
  2. 2.Laboratoire d’Ecologie MicrobienneUniversity of Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, UMR CNRS 5557Villeurbanne CedexFrance

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