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Updated: Sep 25, 2025

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Published on: May 2, 2018

High-Throughput Profiling of Root-Associated Microbial Communities.

Felix Getzke¹, Stéphane Hacquard²

¹Max Planck Institute for Plant Breeding Research, Cologne, Germany.

Methods in Molecular Biology (Clifton, N.J.)

|April 25, 2022

Summary

This study details methods for analyzing root microbial communities in plants. Researchers developed protocols for sequencing bacterial (16S rRNA) and fungal (ITS) DNA, aiding plant health research.

Keywords:

Amplicon sequencing Arabidopsis thaliana Bacteria Dual indexing Fractionation Fungi Microbiota Next-generation sequencing Root

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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

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Last Updated: Sep 25, 2025

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Published on: May 2, 2018

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

Published on: July 24, 2018

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Area of Science:

Plant microbiology
Microbial ecology
Molecular biology

Background:

Plant roots host diverse microbial communities (root microbiota).
Root microbiota composition is influenced by environmental factors, host genetics, and microbe-microbe interactions.
Root microbiota assembly is directly linked to plant health.

Purpose of the Study:

To present detailed methods for preparing 16S rRNA and ITS amplicon libraries.
To characterize bacterial and fungal communities associated with Arabidopsis thaliana.
To analyze microbial communities along the soil-root continuum.

Main Methods:

Marker gene amplicon sequencing was employed.
Protocols for 16S rRNA gene amplicon library preparation were developed.
Protocols for internal transcribed spacer (ITS) amplicon library preparation were developed.

Main Results:

Detailed methods for characterizing plant-associated bacterial and fungal communities are provided.
The study focuses on Arabidopsis thaliana, examining communities along the soil-root continuum.
The presented protocols are adaptable for various plant organs and species.

Conclusions:

The developed methods facilitate the characterization of root microbiota.
These protocols are valuable tools for studying plant-microbe interactions and plant health.
The adaptability of the methods broadens their applicability in plant science research.