Oh, oomycete are part of Eukaryota. Whoops!
Yes, the greengenes will not work well for those. Chris is asking the right question; which gene was amplified?
If the 18S gene was amplified, using the 18S part of SILVA might work well. If the ITS gene was used, UNITE is a pretty good database. Qiime compatible version of both databases are listed on this page:
If a specific gene was used, say COI, you will need to find a matching database. Hopefully someone has already made a qiime compatible version of this database.
Any advice here, Chris? I've mostly worked with common marker genes.