Terrestrial fungal metagenome

This study aims to evaluate the performance of commonly used bioinformatic pipelines in processing fungal metabarcoding data by comparing their outputs against a high-resolution taxonomic reference. Using a unique dataset from 56 plots, where terricolous lichenized fungi were surveyed both through traditional specimen-based identification and Sanger sequencing, and through environmental DNA metabarcoding, the study assesses how different pipelines influence biodiversity estimates. By doing so, it seeks to inform ecologists about the implications of bioinformatic choices and guide the selection of optimal data processing strategies for accurate and reliable biodiversity assessments in natural communities.