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Updated: Aug 17, 2025

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
Whole-Genome Sequencing of Bacterial Endophytes From Fresh and Preserved Plant Specimens
Bram Danneels1,2, Aurélien Carlier3,4
1LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
Abstract:
Many plants harbor symbiotic bacteria in their leaves, sometimes within structures visible with the naked eye. These bacteria play critical roles for host development and defense, but are often not amenable to culture. Gaining insight into the functions of these obligate endophytic bacteria hinges on culture-independent omics approaches, which have seen tremendous development in recent years. We describe in this chapter a set of protocols for the extraction and bioinformatic analysis of bacterial genomic DNA from leaf samples of various origins, including fresh, silica-preserved, or herbarium specimens.
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