Heap bioleaching technology has been successfully applied at an industrial scale for over 30 years, and is generally considered to be the most effective engineering option to bio-process low-grade copper sulfide ores. Heap bioleaching was established at the Escondida mine in Chile in 2006, and culture-independent analysis of liquid samples had previously provided some information of the composition of the indigenous microbial communities. In the current project, six prokaryotes belonging to three bacterial genera and one archaeal genus were isolated from the heap bioleaching plant at Escondida and studies carried out comparing their responses to those of known species and strains of mineraldegrading bacteria to some environmental stress factors, in order to understand how the indigenous microflora are able to successfully colonize and exploit the bioheaps. Stress factors examined including elevated concentrations of heavy metals and osmotic potentials. One of the isolates, identified as a strain of Acidithiobacillus ferrooxidans, was able to grow at more extreme conditions of pH and temperature than reported for most other strains of this species. Copper tolerance observed in a Leptospirillum ferriphilum isolate was found to be comparable with other strains of this important mineral-oxidizing acidophile, and far greater than in strains of other Leptospirillum spp. (L. ferrooxidans and “L. ferrodiazotrophum”), which helps to explain why only L. ferriphilum rather than other species is found in this (and many other) copper bioleach operation, even though the relatively low temperatures might favour other species. Studies carried out on osmotic stress response by several mineral-degrading acidophiles identified the disaccharide trehalose as a major organic osmo-protectant synthesized by several unrelated species of bacteria, including L. ferriphilum, At. ferrooxidans, Sulfobacillus thermosulfidooxidans and Acidiphilium sp. SJH. In contrast, the major organic solute that accumulated within the sulfur-oxidizer At. thiooxidans in response to salt stress was the monosaccharide glucose, together with smaller amounts of proline. Micro-representational difference analysis (MRDA) was used to elucidate the genetic response of a L. ferriphilum isolate to copper-induced and osmotic stress. Data obtained suggested that certain metabolisms related to lipopolysacharide synthesis, transport systems and nucleic acid processing were activated in response to these stress factors.