Abstract

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

Keywords

biodiversity; bioinformatics; community ecology; experiment setup; molecular identification; statistical analyses

Published in

Molecular Ecology
2022, Volume: 31, number: 10, pages: 2769-2795
Publisher: WILEY

SLU Authors

• Bahram, Mohammad

  • Department of Ecology, Swedish University of Agricultural Sciences
    
  • University of Tartu

UKÄ Subject classification

Ecology


Publication identifier

DOI: https://doi.org/10.1111/mec.16460

Permanent link to this page (URI)

https://res.slu.se/id/publ/116815