Zayda, there is a good blog about it.

http://blog.mothur.org/2016/01/12/mothur-and-qiime/

In short, no really. But you have to make sure that you justify why you chose your clustering approach. Personally, I use a combination of multiple programs/algorithms, since that gives me more what I am looking for. I use Usearch's uparse for clustering OTUs, use some functionalities of Qiime for working and filtering through my OTU tables and mothur more for sequence summaries and other quality measures (as some of the data has to be formatted differently between Mothur and Qiime) and then R for downstream analysis (phyloseq has nice graphics and some statistics, but also other packages).

And the fungal and bacteria part of it...it really comes down to the reference databases you are using and how they are formatted. For fungi, Unite has their databases formatted for both. Depending on your primers for fungi, check if using the ITSx (ITS extractor is useful). I think the same applies for bacteria, where in some cases the best to do is use the SILVA databases.

Let me know if you want to talk more about this! I could keep going foreverer ;) 

Thank you for your answer, it was really useful 

E-mail me if you have more questions!