Proton driven pumps with electro-neutral turnover might benefit from higher pH gradient.
Misha is right. There are many proton-driven transporters in microbial membranes. Also, since the pH is lower than inside the cell, that's a stress condition. It's proven that many stress conditions leads to better handling face other stressing conditions. So, the low pH may benefit the removal of heavy metals by and indirect way.
I concur with the Misha and Rui Fillie. In addition, it will depend on the specific bacteria. If it is an acidiophilic species the lower pH is essential for its growth. In part for the proton driven pumps, but for other metabolic functions as well. If you know the exact species you are using, you can do a search on its specific cellular functions to assess the exact impact the pH has on the organism.
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