Bioinformatic analyses
The adapter and primers from the raw sequence reads were trimmed using
Cutadapt v2.10 (Martin et al., 2011). Bioinformatics pipeline was run
using DADA2 v1.16 (Callahan et al., 2016) to infer amplicon sequence
variants (ASVs) with single-nucleotide resolution. For quality trimming,
a more relaxed filtering option was applied on the reverse reads as
maxEE = c (2, 5), and the low-quality sequence tails were removed from
the forward and reverse reads with truncLen = c (270, 210). Bacterial
taxonomy was assigned to representative ASV sequences using DADA2
implementation of RDP naïve Bayesian classifier based on the EzBiocloud
database (Yoon et al., 2017). Sequences matched to the Eukaryota,
Archaea or Cyanobacteria were removed from the dataset. Sequences are
available in the NCBI Sequence Read Archive (SRA) database under
accession number PRJNA753257.