Short 16S rRNA analyses tutorials - links - useful packages - this pipeline below feels like a fractal - I will try to zoom in at several points (while I work on this, please click to enlarge).
All tools, packages and sites described here (and more), can be found under the links section - and don't forget to check out their tutorials!
In addition I'll list and link some of the methods paper describing the specific use and approach:
Also, please read this paper if you are interested in multivariate analyses in microbial ecology: Multivariate analyses in microbial ecology by Alaban Ramette (2007) and if you are hooked, then take a look at this paper and the corresponding homepage: A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses Buttigieg & Ramette 2014 - GUSTA ME.
Microbial communities in sponges
Redfield stoichiometry in phytoplankton
The Mytilus complex
16S rRNA analyses
Local BLAST database
Sponge Sampling 2016