From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing

In recent years, DNA sequencing technologies have advanced considerably with the rise of Next-Generation Sequencing (NGS) platforms, which have transformed microbial ecology research. These approaches enable the characterization of entire communities by using DNA traces to identify organisms taxonomically from a single sample. Arbuscular mycorrhizal fungi (AMF) are no exception and represent one of the most extensively studied groups of soil fungi. This chapter presents protocols for high-throughput, sequence-based analysis of AMF communities, covering the complete workflow from DNA extraction in plant or soil samples to the bioinformatic processing of sequencing data. It particularly focuses on rRNA gene metabarcoding, the most common strategy to provide estimates of AMF diversity and community composition through the amplification of DNA with taxon-specific primers followed by sequencing of barcode regions. Alternative strategies are described to accommodate different research objectives, including the selection of molecular markers.