Hi @Francis29029!
Of course! Generally speaking, we recommend that all plugin dependencies be published as conda packages - mothur is available on the bioconda channel, so you're all set there. You'll be able to register the appropriate citations within your plugin, so the mothur team (and any other tools you integrate) will be cited as appropriate!
We are busy working on the revamped Library (link) - one of the major goals there is to allow for plugin developers to get automatic building and testing of their conda packages, so keep your eyes peeled for further information on that (I'm going to get back to work on it as soon as I finish responding here!).
If you have any questions, or run into any hurdles, you know where to find us.
PS - bookmark dev.qiime2.org, there are some developer docs and notes available there