Bioleaching genomics

Mineral ores are full of metals, some very precious – but how to extract them? The Hamersley mines in the Pilbara in Western Australia contain such rich iron ore that it can almost be welded as it comes out of the ground. Traditionally, metals are extracted by ‘smelting’ or pyrometallurgy, the thermal treatment of minerals and metallurgical ores and concentrates to bring about physical and chemical transformations, which then enables recovery of valuable metals. But this process is energy-consuming and generates many undesirable side-products such as toxic gases. Alternatively, bioleaching (or biomining) by microorganisms is used to extract metals from ores by dissolving them into extremely acidic aqueous solution. Bioleaching is a natural process involving acidophilic bacteria and archaea, which have the ability to either oxidize metal sulfides or to oxidize reduced inorganic sulfur compounds (RISCs) to sulfuric acid, or both (Fig. 1, left panel). Acid mine drainage liquors were found to contain bacteria responsible for producing iron-rich acidic waters from coal and metal mines. Bioleaching is used today in commercial operations to process ores of copper, nickel, cobalt, zinc and uranium, whereas biooxidation is used in gold processing and coal desulfurization. The biomining industry has a long-standing interest in the use of extreme acidophiles for metals recovery from ores (for recent reviews see Rawlings, 2002; 2005; Valenzuela et al., 2006; Rawlings and Johnson, 2007). These organisms, with as prime example the mesophilic chemolithotrophic bacterium Acidothiobacillus ferrooxidans, can liberate precious (e.g. gold) and base (e.g. copper) metals trapped in metal sulfides (e.g. iron pyrite and chalcopyrite) through dissimilatory oxidative processes. Biological regeneration of Fe3+ from Fe2+ is the key to chemical attack of metal sulfides. Efficacy in biomining environments also requires tolerance of high levels of toxic heavy metals as well as the ability to assimilate inorganic carbon, as organic sources can be scarce in this environment. A full complement of these desirable traits is not typically present in a single native microorganism, but may be in a consortium. Here we give a brief update of the current status of (meta)genome sequencing and genomics of bioleaching microorganisms and communities.