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

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 spatio-temporal
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.