3.1 General description
The Ion platform produced approximately 2,790,479 raw reads for
prokaryotes from 40 samples by sequencing V5-V7 hypervariable region of
the bacterial 16S ribosomal RNA gene. After quality control, denoising,
and removal of chimera sequences, 1,235,434 high-quality sequences were
obtained. A total of 19,367 ASVs recovered in the final dataset were
subjected to taxonomy assignment; 8788 ASVs were assigned to different
genera. Meanwhile, 10,579 ASVs, which could not be identified at the
genus level, were clustered into 2002 OTUs at 97% identity level and
were again subjected to taxonomy assignment. The identified ASVs and
OTUs were subsequently combined, and taxa assigned to non-Bacteria,
Cyanobacteria, Chloroplast, and Rickettsiales were removed from the
dataset. The bacterial dataset agglomerated at the genus level yielded a
new dataset covering 1927 taxa across 40 samples with singletons and
doubletons removed.
Similarly, 3,232,676 raw reads for eukaryotes were obtained from 40
samples by sequencing ITS1 region of fungal ribosomal RNA. After quality
control, denosing, and removal of chimera sequences, 1,704,072
high-quality sequences and 14,801 ASVs were obtained. Out of this, 1747
ASVs were assigned to different fungal species. Meanwhile, 13,054 ASVs,
which could not be identified at the species level, were clustered into
719 OTUs at 97% identity level and were again subjected to taxonomy
assignment. The identified ASVs and OTUs were subsequently combined, and
non-Fungi and plant taxa were removed from the dataset. The dataset
agglomerated at the species level yielded a new dataset covering 843
taxa across 40 samples with singletons and doubletons removed.