High-Throughput Profiling of Root-Associated Microbial Communities.

Roots of healthy plants are colonized by a great diversity of bacteria and fungi but also other microorganisms that are collectively referred to as the root microbiota. Root microbiota composition is shaped by environmental cues, by host genetics, but also by microbe-microbe interactions, and recent evidence indicates that a direct link exists between root microbiota assembly and host health. In order to characterize the root microbiota or to study the complex interplay between plants and their associated microbes, the assessment of microbial community structure via marker gene amplicon sequencing has become a key tool. Herein, we present detailed methods for the preparation of 16S rRNA gene and internal transcribed spacer (ITS) amplicon libraries to characterize Arabidopsis thaliana-associated bacterial and fungal communities along the soil-root continuum. The protocols can be easily adapted for different host organs or plant species.