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.