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.