As far as I understand bioleaching (Bacterial or Fungal) process, bioleaching is considered completely non-polluting, only if the acid produced (acidophilic) by Microorganisms (MO), which intern is used for leaching, is recovered without discarding it into the environment (while extracting heavy metals ).
However, Bioleaching is considered ecofriendly compared to chemical leaching, as the concentration of acids produced by MO is low. There is always a trade off between ecofriendly technology and leaching efficiency (higher the concentration of acids, more is the leaching efficiency).
Bioleaching is preferred over chemical leaching, for low grade ores and for all kinds of wastes (secondary resources) because its more economical and results in significantly less pollution.
Bottom line answer is bioleaching cannot be said non-polluting, until the leaching agent (mostly acids) is not recovered from the leached solution completely (or, the acid concentration should be under permissible limit - EPA).
I hope I have answered your question. Any corrections or suggestions from anybody are always welcome.
Yes it is ecofriendly. But it can't be discussed in journal articles because research papers (especially original article) are meant to advance the knowledge in the relevant fields in a technical perspective rather than explaining the obvious things. Even if it has been explained during the submission of a paper the reviewers will cut it off (or at least suggest the authors to do so) as it will be deviating the objectives or motto of a paper. Nevertheless it will be consuming the space also, which is the most important asset for a publisher.
As far as i know, leaving inorganic acids into the environment is hazardous but organic acids (which bacteria will release during bio-leaching) will get adopted and degraded by the ecosystem itself.
Well lets answer your question in steps. First of all bacterial leaching is mostly use for low grade ores or tailings, which are dumped over land. If bacterial leaching is not done, the ores will still get leached due to environmental conditions and weather conditions which can not be controlled. The leachate will pollute table water and adjoining land and fresh water bodies mostly by percolation. If a controlled leaching process is used then such pollution can be averted. Classical hydrometallurgical leaching is not affordable due to low mineral content. So is the case with other classical extraction processes. Therefore, economically feasible process is the bacterial leaching which does not need any major investment. Here even if the mineral can not be recovered, at least we have saved the environment and hence such a process is ecofreindly. I tell you this because basically I am a geomicrobiologist myself.
YES, it is so, that it allows to avoid the use of cyanides and other toxic chemicals used in traditional leaching to mobilise the metals. Concerning chemicals you use for leaching, there is produced something at industrial scale, we can produce some toxic gases and chemical wastes.Through any speculation one can always say that a natural product (bio leachate) will minimize these emissions and are better than chemical leachates. And bacterial leaching is important ecofriendly technology as we can see it in many our publications.