DNA metabarcoding data processing
Sequencing data were processed using QIIME 2.0 2021.8 (Bolyen, et al.
2019). Raw reads were demultiplexed and quality filtered using the
q2‐demux plugin, and in the case of fungal datasets, the ITS region was
extracted using the q2-ITSxpress plugin (Rivers et al. 2018).
Afterwards, reads were denoised using the DADA2 algorithm (Callahan, et
al. 2016) and a feature table with counts of amplicon sequence variants
(ASVs) per sample was produced. Taxonomy was assigned using the
q2‐feature‐classifier classify-sklearn (Bokulich, et al.2018) using a
trained naïve Bayes classifier against the SILVA_138_SSURef_Nr99
bacterial reference database and UNITE QIIME release for Fungi version
8.0. Rarefaction analysis of final ASV tables was performed to assess
the completeness of the dataset and the admissible data resampling level
for statistical analysis.