I recently sequenced the hypervariable V9 region of the 18s SSU gene. eDNA samples were taken from diseased coral tissue and non diseased coral tissue and I need to assess the fungal species richness and relative abundance between the two communities. I am however having quite a bit of trouble with the bioinformatics side of things. The primers I used were universal to eukaryotes due to the communal nature of the study which left me with both libraries almost entirely saturated by the host organism. I have found 17 fungal OTUs out of >8000 between the two groups. Additionally, a third of these OTUs exist as singletons and doubletons. I) Is it worth estimating species richness and abundance? II) If so, what would be the best approach to make the most of my situation?
I apologise if my terminology is wrong. Both environmental sequencing and this level of bioinformatic analysis are entirely new to me and I'm finding it quite intimidating.
