Hi @Negin,
Thanks, that would be great!
Remember that in both QIIME 2 and phyloseq, -by design- the taxonomy of your features is kept in a separate file and is only called on when taxonomy info is required. Meaning that if you are working with phyloseq, then you’ll need to import a separate taxonomy file, and not have this part of your biom table. Even though you CAN add taxonomy to your biom table, this isn’t the recommended approach.
Since you are operating from Qiita to QIIME 2/phyloseq, have a look at this tutorial here to see how you can create taxonomy file in QIIME 2, importing that into R/phyloseq is easy following the links you posted earlier.