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Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities

Furneaux, Brendan and Bahram, Mohammad and Rosling, Anna and Yorou, Nourou S. and Ryberg, Martin (2021). Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities. Molecular Ecology Resources. 21 , 1833-1849
[Research article]

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Abstract

Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.

Authors/Creators:Furneaux, Brendan and Bahram, Mohammad and Rosling, Anna and Yorou, Nourou S. and Ryberg, Martin
Title:Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities
Series Name/Journal:Molecular Ecology Resources
Year of publishing :2021
Volume:21
Page range:1833-1849
Number of Pages:17
Publisher:WILEY
ISSN:1755-098X
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
URN:NBN:urn:nbn:se:slu:epsilon-p-112012
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112012
Additional ID:
Type of IDID
DOI10.1111/1755-0998.13387
Web of Science (WoS)000647966000001
ID Code:25023
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Ecology
(S) > Dept. of Ecology
Deposited By: SLUpub Connector
Deposited On:25 Aug 2021 13:25
Metadata Last Modified:25 Aug 2021 13:31

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