Related Experiment Video
Updated: Sep 5, 2025

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments
Published on: July 24, 2018
Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach
13PHM, INSERM, Faculté de Santé, Université Paris Cité, Paris, France. victoriamesa@gmail.com.
Abstract:
The diversity of microbes associated with plant roots is in the order of tens of thousands of species. It is estimated that only 0.1-1.0% of the living bacteria present in soils can be cultured under standard conditions. The microbial marker-gene sequence data and the next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes. Molecular techniques can be used to generate comprehensive taxonomic profiles of the microorganisms present in roots. The aim of this chapter is to provide a standard method for the obtention of rhizosphere and endosphere fractions, and a generic workflow of the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software to analysis of 16S rRNA marker-gene.
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