Hi @zcw15774723795 ,
I suggest reading the forum FAQs, which answers several common questions about taxonomy classification:
On the one hand, incomplete classification is typical for 16S data.
On the other hand, your reads are probably in mixed orientations and this is why you get one hit to Eukaryota. You can use the action qiime rescript orient-seqs to harmonize the orientation of your sequences and see if this improves classification.
You can use the action qiime taxa collapse to collapse your feature table in QIIME 2 before exporting to R. This will solve this issue by binning your taxonomic groups appropriately. If you collapse at genus level, you would get one feature like this: d__Eukaryota;p__Retaria;c__Foraminifera;o__Rotaliida;__;__