Skip to main content
Log in

Taxonomic assignment of arbuscular mycorrhizal fungi in an 18S metagenomic dataset: a case study with saltcedar (Tamarix aphylla)

Mycorrhiza Aims and scope Submit manuscript

Cite this article


Many studies describing communities of arbuscular mycorrhizal fungi (AMF, Glomeromycota) based on high-throughput sequencing target the V4 variable region of the 18S ribosomal gene. However, an accurate taxonomic assignment of these short 18S sequences is challenging. Here we describe a simple approach based on a phylogenetic analysis using a backbone of reference sequences with taxonomic names updated in MycoBank to improve the taxonomic assignment of amplicon sequence variants (ASVs). As a case study, paired-end sequencing (2 × 250 bp) was carried out to describe the community of AMF associated with Tamarix aphylla from Algerian steppe ecosystems. AMF from root and soil samples were targeted with a nested PCR, using the AMF-discriminating primers pair AML1/AML2 for the first amplification and a new primer pair for the second. The proportion of the sequences assigned to Glomeromycota was 85.9%, representing a total of 87 ASVs. Seven well-defined genera (Claroideoglomus, Dominikia, Funneliformis, Innospora, Microkamienskia, Rhizophagus, Septoglomus) and seven phylogenetic divergent clades of Glomus (27% of the ASVs) were identified with the proposed approach. This taxonomic assignment was in sharp contrast with querying the MaarjAM or GenBank databases. Out-of-date taxonomy led the MaarjAM database to attribute 85% of the ASVs to the genus Glomus and the GenBank database to assign 18% of the ASVs to unclassified taxa. We recommend using the simple workflow presented in this study so that up-to-date taxonomic information is accurately assigned to AMF communities analyzed by high-throughput sequencing.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5


Download references


We are grateful to Marie-Josée Bergeron and James Tambong for insightful comments on an early draft of the manuscript; Susan Young for her assistance in literature review; Kitty Cheung and Julie Chapados, from the Molecular Technology Laboratory (Ottawa-RDC, AAFC), for their assistance with MiSeq library preparation and Illumina sequencing. The authors thank the two anonymous reviewers for their useful comments.


This work was supported by funding from the Agriculture and Agri-Food Canada through the projects J-002272 and J-002295.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Franck Stefani.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Franck Stefani is the Curator of the Canadian Collection of Arbuscular Mycorrhizal Fungi.

Electronic supplementary material


(DOCX 1.93 mb)

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Stefani, F., Bencherif, K., Sabourin, S. et al. Taxonomic assignment of arbuscular mycorrhizal fungi in an 18S metagenomic dataset: a case study with saltcedar (Tamarix aphylla). Mycorrhiza 30, 243–255 (2020).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: