Introduction

Background¶

Arbuscular mycorrhizal fungi (AMF) are ecologically and economically vital symbionts that enhance plant nutrient uptake and play a key role in maintaining soil health (Smith & Read, 2010; Martin & van der Heijden, 2024). As with other fungal groups, molecular techniques have become the standard for characterizing AMF diversity (Tedersoo et al., 2022). Global initiatives focused on mapping the distribution and diversity of AMF—such as GlobalAMF (Větrovský et al., 2023), SPUN, and the Australian AMF Mapping Project (Frew et al., 2024)—emphasize the need for accessible, robust, and reproducible workflows. These efforts also highlight the growing demand for trained personnel capable of conducting community-level AMF analyses in this rapidly advancing field.

In this tutorial you’ll use the amplicon distribution of QIIME 2 to perform an analysis of AMF diversity in the rhizosphere microbiome. This tutorial was developed as a part of seminar course BIO 698-063 and BIO498-008 4249 in Spring 2025, Northern Arizona University by Professors Manju M. Gupta, Nancy Johnson and Catherine Gehring. Where available, links to instructional slides and recordings are provided. The tutorial also includes a guest lecture by Greg Caporaso. View this here. A high level introduction to the QIIME 2 project may be found here

The dataset used in this tutorial originates from the study by Parvin et al. (2021) and represents a small, curated subset of the original data available on NCBI SRA, chosen to allow rapid processing on a personal computer. This dataset comprises 18S rRNA amplicon sequences targeting AMF in rice root samples, generated using the Illumina MiSeq platform ( ~3.1 MB download). A 350 bp fragment of the small subunit (SSU) rRNA gene was PCR-amplified using Glomeromycota-specific primers AMV4.5NF and AMDGR, each tagged with sample-specific indices to enable dual-index sequencing. For video context for this study refer to this video.

References Smith, S.E. and Read, D.J., 2010. Mycorrhizal symbiosis. Academic press. Martin, F.M. and van Der Heijden, M.G., 2024. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. New Phytologist, 242(4), pp.1486-1506 Tedersoo et al., 2022. Global patterns in endemicity and vulnerability of soil fungi. Global change biology, 28(22), pp.6696-6710. Větrovský et al., 2023. GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high‐throughput sequencing metabarcoding studies. New Phytologist, 240(5), pp.2151-2163. Frew et al., 2024. AusAMF: database of arbuscular mycorrhizal fungal communities in Australia. bioRxiv, pp.2024-09. Parvin, S., 2021. A comparison of the arbuscular mycorrhizal fungal communities among Bangladeshi modern high yielding and traditional rice varieties. Plant and Soil, 462, pp.109-124.

License¶

AMF analysis tutorial (©2025) by Caporaso Lab is licensed under CC BY-NC-ND 4.0.