I am studying the diversity of organisms colonizing seagrass leaf surface and wish to target eukaryotic SSU, among other markers, using a metabarcoding approach.
Article Coprophilic amoebae and flagellates, including Guttulinopsis...
but several others exist all with pros and cons...
in the end, if you have a good question and target the organisms of interest the primer pair shouldnt matter even if a lower diversity is recovered than with other primer sets...
Hope that helps!
More news on the proposed primers in a few months :)
I would recommend the primers described in Piredda et al. 2016 that target the V4 region of the 18S rRNA gene (Article Diversity and temporal patterns of planktonic protist assemb...
). We are using them now routinely with excellent results. Although the V9 region is also possible, I would rather recommend V4 which is longer and for which more sequences are available in the databases. See also :
Article Comparison of coastal phytoplankton composition estimated fr...
I strongly agree with Stefan that there is no "ONE primer pair that targets everything".
What sequencing platform will you be using, because the length of primers are also important to consider, if you want to use overlapping for MiSeq for example? A colleague of mine had very good results with these primers targeting marine benthos, while avoiding some planktonic taxa, targeting V2: Article Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in ...
For longer amplicons sequenced with 454, we recently used the primers F566 and R1200 with very good results in terms of universality, but they are not as suitable for MiSeq since the amplicons are too long to overlap: Article Characterization of the 18S rRNA Gene for Designing Universa...