Hi @nvtravan!
In QIIME 2 we can treat some artifacts as metadata. These are typically artifacts that you can think of as mapping some ID to some piece of data (like a spreadsheet). This includes almost everything we call FeatureData[...].
Additionally, we can merge metadata in QIIME 2 making it easy to pair up pieces of data by their ID. In fact we have a tutorial example that does exactly what you are trying to do, merge your rep-seqs with your taxonomy:
https://docs.qiime2.org/2018.2/tutorials/metadata/#exploring-feature-metadata
Let me know if that’s what you’re looking for!