Best practices in metabarcoding of fungi: From experimental design to results

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 experimen...

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Bibliographic Details
Published in:Molecular ecology Vol. 31; no. 10; pp. 2769 - 2795
Main Authors: Tedersoo, Leho, Bahram, Mohammad, Zinger, Lucie, Nilsson, R. Henrik, Kennedy, Peter G., Yang, Teng, Anslan, Sten, Mikryukov, Vladimir
Format: Journal Article
Language:English
Published: England Blackwell Publishing Ltd 01.05.2022
Subjects:
bayesian
Best practice
Biochemistry & Molecular Biology
biodiversity
bioinformatics
classifier
community ecology
Community structure
Computer applications
Design of experiments
DNA barcoding
Ecological function
Ecology
Ecosystem recovery
ecosystems
ectomycorrhizal fungi
Ekologi
Environmental Sciences & Ecology
Eukaryotes
eukaryotic cells
Evolutionary Biology
experiment setup
Experimental design
Fungi
global change
internal transcribed spacer
its2 region
microbial communities
microbiome
Microbiomes
Molecular Biology
molecular identification
Molekylärbiologi
ribosomal-rna
sequence-based identification
soil DNA
statistical analyses
Taxonomy
statistical analyses
biodiversity
experiment setup
molecular identification
bioinformatics
community ecology
ISSN:0962-1083, 1365-294X, 1365-294X
Online Access:Get full text
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Summary: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.
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ISSN:0962-1083
1365-294X
1365-294X
DOI:10.1111/mec.16460