How to enrich my 18S extemophile metagenome

Hi everyone!

I have performed a metagenomic classification on several extreme enviromentes (halophilic, Acidophile, radioactive and minery). I have even trained the SILVA database. But the taxonomy resolution I obtain is very low for some of the samples (for instance in the halophilic medium I get D_0__Eukaryota;;;;;; | 100.000%)

I was wondering if theres ANY way of enhacing this results, either with qiime2 or other external software.

Thanks in advance, Jose.