Mining and mineral processing generates large volumes of waste, including waste rock, mill tailings, and mineral refinery wastes. The oxidation of sulfide minerals in the materials can result in the release of acidic water containing high concentrations of dissolved metals. Recent studies have determined the mechanisms of abiotic sulfide-mineral oxidation. Within mine wastes, the oxidation of sulfide minerals is catalyzed by microorganisms. Molecular tools have been developed and applied to determine the activity and role of these organisms in sulfide-mineral-bearing systems. Novel tools have been developed for assessing the toxicity of mine-waste effluent. Dissolved constituents released by sulfide oxidation may be attenuated through the precipitation of secondary minerals, including metal sulfate, oxyhydroxide, and basic sulfate minerals. Geochemical models have been developed to provide improved predictions of the magnitude and duration of environmental concerns. Novel techniques have been developed to prevent and remediate environmental problems associated with these materials.

The geochemistry of acid mine drainage

Biomining is an increasingly applied biotechnological procedure for processing of ores in the mining industry (biohydrometallurgy). Nowadays the production of copper from low-grade ores is the most important industrial application and a significant part of world copper production already originates from heap or dump/stockpile bioleaching. Conceptual differences exist between the industrial processes of bioleaching and biooxidation. Bioleaching is a conversion of an insoluble valuable metal into a soluble form by means of microorganisms. In biooxidation, on the other hand, gold is predominantly unlocked from refractory ores in large-scale stirred-tank biooxidation arrangements for further processing steps. In addition to copper and gold production, biomining is also used to produce cobalt, nickel, zinc, and uranium. Up to now, biomining has merely been used as a procedure in the processing of sulfide ores and uranium ore, but laboratory and pilot procedures already exist for the processing of silicate and oxide ores (e.g., laterites), for leaching of processing residues or mine waste dumps (mine tailings), as well as for the extraction of metals from industrial residues and waste (recycling). This chapter estimates the world production of copper, gold, and other metals by means of biomining and chemical leaching (bio-/hydrometallurgy) compared with metal production by pyrometallurgical procedures, and describes new developments in biomining. In addition, an overview is given about metal sulfide oxidizing microorganisms, fundamentals of biomining including bioleaching mechanisms and interface processes, as well as anaerobic bioleaching and bioleaching with heterotrophic microorganisms.

Biomining: metal recovery from ores with microorganisms.

Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.

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Thermophilic and alkaliphilic Actinobacteria: biology and potential applications.

Chalcopyrite hydrometallurgy at atmospheric pressure: 2. Review of acidic chloride process options

Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin–Benson–Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.

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Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave.

Some novel actinobacteria from geothermal environments were shown to grow autotrophically with sulfur as an energy source. These bacteria have not been formally named and are referred to here as “Acidithiomicrobium” species, as the first of the acidophilic actinobacteria observed to grow on sulfur. They are related to Acidimicrobium ferrooxidans with which they share a capacity for ferrous iron oxidation. Ribulose bisphosphate carboxylase/oxygenase (RuBisCO) is active in CO2 fixation by Acidimicrobium ferrooxidans, which appears to have acquired its RuBisCO-encoding genes from the proteobacterium Acidithiobacillus ferrooxidans or its ancestor. This lateral transfer of RuBisCO genes between a proteobacterium and an actinobacterium would add to those noted previously among proteobacteria, between proteobacteria and cyanobacteria and between proteobacteria and plastids. “Acidithiomicrobium” has RuBisCO-encoding genes which are most closely related to those of Acidimicrobium ferrooxidans and Acidithiobacillus ferrooxidans, and has additional RuBisCO genes of a different lineage. 16S rRNA gene sequences from “Acidithiomicrobium” species dominated clone banks of the genes extracted from mixed cultures of moderate thermophiles growing on copper sulfide and polymetallic sulfide ores in ore leaching columns.

Autotrophic, sulfur-oxidizing actinobacteria in acidic environments

Ferrous iron oxidation and leaching of copper ore with halotolerant bacteria in ore columns

Novel iron- and sulfur-oxidizing, moderate thermophiles were isolated from an acidic geothermal site and from a previously studied, pyrite-enrichment mixed culture (which also contained the related actinobacterium Acidimicrobium ferrooxidans). The novel species (proposed genus “Acidithiomicrobium”) grew autotrophically with ferrous iron at an optimum temperature of about 50°C, efficiently degraded pyrite at 55°C and also grew well autotrophically on sulfur. The extensive dissolution of pyrite during autotrophic growth contrasted with a requirement for yeast extract for significant growth of the related Acidimicrobium ferrooxidans.

Carol S. Davis-Belmar

Papers

Autotrophic, sulfur-oxidizing actinobacteria in acidic environments

Ferrous iron oxidation and leaching of copper ore with halotolerant bacteria in ore columns

Ferrous iron and pyrite oxidation by "Acidithiomicrobium" species

Pyrite oxidation and copper sulfide ore leaching by halotolerant, thermotolerant bacteria

Ore column leaching with thermophiles: I, copper sulfide ore