I have recently completed an analysis of Illumina 16S amplicon data with Qiime2. I am working in R on the beta-diversity and I'm trying to figure out how to make an NMDS or CCA ordination of my OTU's that accounts for the environmental data. Originally I was working with phyloseq but I am unable to perform this task using it. I know that people use vegan functions like env.fit and metaMDS but I'm not really sure what I should be doing. If anyone could point me in the right direction or provide assistance that would be much appreciated.