What primers / amplicon region are you amplifying? V3V4?
Also, I noticed that there are only ~17 reference sequences in nr99 SILVA reference database for Desmodesmus, and just a few more for the full database. There also appears to be less references within the new SILVA v138.2? Currently, there is no auto download for 138.2, so you'll have to manually follow the instructions under Getting SILVA data: Hard Mode .. .gritty details (click the triangle / drop menu). Then see if 138.2 does any better.
Also, I forgot to mention that the our plugin, by default, downloads the non-redundant SSURef_NR99 SILVA database. You may opt to change the options in get-silva-data to download the full database, SSURef.
-Mike