Hi Everyone i have run through QIIME2 with some fungi data and after using DADA2 and not trimming because of the variability of the ITS region I filtered by quality. I hardly lose any read (around 20-30%). I end up with around 1700 OTUs after filtering out the unclassified fungi etc. But the observed diversity between treatments is fairly low , just over 100 species? The ecosystem i am studying is peatlands.
Is it possible that due to the anaerobic nature of peatlands there just isn't many species there?