Bioinformatics
Illumina adapters and primer complements were trimmed using ‘cutadapt’
(Martin
2011). Illumina sequences were then processed with the DADA2 pipeline to
remove low quality reads, filter chimeras, and to resolve amplicon
sequence variants (ASVs)
(Callahanet al. 2016; Pauvert et al. 2019). Taxonomy was assigned
to each ASV against the UNITE database
(Kõljalget al. 2013). Sequences that were not categorized as fungi at the
kingdom level (23 ASVs) were removed for downstream analyses. The fungal
data were rarefied to an even depth of 14,689 sequences per sample.