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

Wafa Achouak (1) , Feth El Zahar Haichar (2)

1 LEMIRE - Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes
2 LEM - Laboratoire d'Ecologie Microbienne - UMR 5557

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 (CO2)-C-13, fresh carbon exuded by the plant will be labeled and hence the microbial community assimilating C-13-root exudates will incorporate C-13 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.

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

Domains: Life Sciences [q-bio]

Wafa Achouak, Feth El Zahar Haichar. Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere. Dumont M., Hernández García M. (eds). Stable Isotope Probing. Methods in Molecular Biology, 2046, Humana, pp.233-243, 2019, ⟨10.1007/978-1-4939-9721-3_18⟩. ⟨cea-02327672⟩