Hi @Changsu, this is an interesting question. It gets way more into Docker-specifics than QIIME 2, so our support capacity might be a bit limited, but here are some thoughts.
My guess is it isn’t working for you, because of the nature of how docker runs: you have downloaded the QIIME 2 image, and when you run QIIME 2 commands in Docker, you actually launch a container instance, which is based on the image. One thing about Docker though is that containers are generally considered ephemeral, so after you install phyloseq, once you exit the container, your changes get deleted. The next container you launch is sourced off of the original image, so none of your changes are there. 
Option 1: docker commit
After you launch a container instance and make your changes, you could experiment with docker commit - this would let you create a new image, based on our image, but with your changes added in.
Option 2: Dockerfile / FROM
You could also create a new Dockerfile that inherits from ours — then you could programmatically make your changes there.
Like I said before, this really gets into Docker territory, so we might not be your best option for helping you out with the specifics, but please keep us posted. If you come up with a strategy you like, that could make a great Community Tutorial for you to share with your fellow QIIMElings!
Thanks, and keep us posted! 