Acid and metalliferous drainage (AMD) is a global environmental problem associated with mining activities that causes significant damage to ecosystems and human health. AMD involves the production and seepage of highly acidic leachate (pH < 2) and toxic metals from waste rock at active and closed mines, with liability costing over $650 million annually in Australia. Microorganisms are central to the AMD dilemma; extremophile chemolithotrophic bacteria such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans thrive in low pH and metal laden waste streams and accelerate the oxidation of iron and sulphide minerals, contributing to acid generation. Alternatively, there exists guilds of microorganisms that promote favourable reactions in mine-stressed environments that immobilize toxic metals from flow paths and contribute to acid reduction when combined with traditional treatment methods. Thus, microbes and their communities act as both antagonists and protagonists in the realm of mining-related pollution. As AMD environments exhibit relatively low microbial diversity due to the extreme conditions, the total extractable RNA:DNA ratio can be a bioindicator of antagonist acidophile activity. We’ve established than in cultures of L. ferrooxidans, the RNA:DNA ratio peaks prior to iron-oxidation events. Thus, the RNA:DNA metric can be applied as an on-site prediction tool while fulfilling the complementary objective of building sample libraries for sequencing. This work is being applied to meso-scale lab experiments with mine sponsor-supplied waste rock, flagged as acid-generating, with the primary objective of establishing the connection between microbially-driven oxidation events and RNA:DNA yields on a community scale, and a secondary objective of applying metagenomics to discover novel acidophilic species. Field-scale studies will also be presented, specifically, a review of a metagenomic investigation of a microbial-mineralization mechanism for cleaning Zinc from a legacy mining discharge site in Western Australia sediments. This work emphasizes the significance of chemolithotrophic microbes to Australia’s largest industry sector.