Mining with aliens

C&I Issue 4, 2013

Mention aliens and the most likely image that will spring to mind is Sir Ridley Scott’s film Aliens – creatures with fangs, claws, and sundry other sharp bits, whose obsidian exoskeleton hosts body fluids that can burn through plate steel. And yet there is an industry much closer to home that is coming to rely ever more closely on organisms that, by the standards of Earthly evolution, are similar in that, despite having cytoplasm of about pH 7, they thrive in fluid with a pH of 2 or less. It is the mining industry.

The business of biomining

Mining has been an essential technology since ancient times and without it, the industrial and technological revolutions could not have happened. But that success comes at a price. It is now becoming ever more expensive to extract ores by conventional chemical means. Furthermore, many economically accessible ore deposits have long since been exhausted, and smelting and mining are both energy intensive processes. Until recently, for example, copper ore bodies were considered worth mining if they contained >5% of the metal, but now many of the major copper mines, such as the Swedish operated Aitik mine 60km north of the Arctic circle, are processing ores containing <1% copper.

With the rising costs of energy, mining is becoming more expensive by the day. Consequently biomining, where bacteria and archaea are used to extract metals from their ores, is enjoying a resurgence of interest.

Travis Bayer, of Imperial College London, points out that there are two major categories of biomining: bioleaching and bio-oxidation. ‘Biomining is the umbrella term for using biological methods in mineral recovery. Bioleaching refers specifically to using microbes to solubilise metals from ores, such as copper, nickel, and zinc. Bio-oxidation is where the target metal is actively exposed to the action of oxidising bacteria or archaea, which then concentrate the mineral of interest. Gold is the main metal recovered on a commercial scale using bio-oxidation.’

But there is nothing new about biomining. Barrie Johnson at Bangor University in North Wales points out: ‘Biomining has been around for 50 years.’ And this is just the modern industrialised version when biomining was ‘discovered’ in the mid-20th century. The Romans, and possibly the Phoenicians before them, regularly used microbes to leach copper from ore without even being aware that it was microbial activity that was releasing the metal.

The first recognised application of modern industrialised biomining was undertaken by Kennecott Copper in the US during the 1960s. The company obtained a patent for using Thiobacillus (now Acidothiobacillus) bacteria to extract copper from its waste rock dumps at the Bingham Canyon mine in Utah and later at the Chino mine in New Mexico. Since then, similar bioleaching operations of low-grade copper ore from waste dumps have been established elsewhere in the world, including China and South America.

Johnson points out that interest in biomining is cyclical and in recent years interest has blossomed mainly because of the soaring energy costs. Initially this interest focused on bioleaching copper and nickel using various species of the bacteria Acidithiobacillus, which oxidise sulphur, and species of Leptospirillum, which oxidise iron. These organisms and other bacteria and archaea are very effective at extracting metals even at low concentrations of 0.3%. ‘This means,’ as Johnson points out, ‘that former spoil heaps are now fertile grounds for biomining. What was once waste is now potentially valuable.’


Some species of bacteria and archaea of relevance to biomining are extremophiles. They can live in extremes of temperature, salinity or acidity. And most of them are also mesophilic: they flourish in a temperature range of 20–50°C. Hyperthermophile biomining organisms tend to be archaea, which can live at temperatures of up to 90°C. These microorganisms offer the advantage of vastly enhanced reaction speeds, with clear cost benefits to companies increasingly seeking to improve yields from low grade ores.

Biomining organisms have several biological and chemical similarities. All can use ferrous iron or reduced inorganic sulphur sources, or both, as electron donors. The byproduct of these reactions is sulphuric acid, so these organisms are acid tolerant and grow best in a pH range 1.5–2. Most biomining bacteria thrive in highly aerated aqueous solutions and require both oxygen and carbon dioxide.

In biomining operations, a bacterial cocktail tailored to the type of ore that needs to be separated is used. Thus, a combination of Leptospirillium and A. ferrooxidans can degrade both pyrite (iron sulphide) and chalcopyrite (copper iron sulphide) ores, something that neither species can do alone.

There are currently moves afoot to establish consortia of bacteria that are tailored to particular mine environments. These consortia will include naturally occurring populations and genetically engineered populations.

Designer microbes

Since different species have different requirements of temperature and pH, there is a natural selection of the most appropriate organism, according to the substrate that is being mined. Thus the species composition needed for the degradation of nickel will not be the same as, for example, that needed for copper waste.

Johnson and his team are interested in what the bugs are metabolising when it comes to biomining extraction. They have done experiments in which they added up to 20 species to the biomining soup and then monitored how the relative concentrations of particular species changed. After about 20 days, says Johnson, three or four species tend to dominate the consortium and these are the ones that are most active in breaking down the waste.

If natural consortia can sort themselves into an optimum spectrum of species for a particular mining task then it is conceivable that they can be pre-engineered to do the job with even greater efficiency.

‘Biomining could benefit from the use of synthetic consortia [of naturally occurring species] because natural consortia have already been shown to play a crucial role in it. We already know that, in many situations, two or more species can only complete metabolic reactions to gain energy when they work together. So the design of synthetic biomining consortia is the logical next step,’ Bayer explains.

This need not involve an genetic modification of individual species. Bayer points out that it should be enough to engineer synthetic consortia out of naturally occurring species. ‘The use of consortia assembled from naturally occurring species is interesting because they would not be considered genetically modified and are hence not susceptible to regulatory procedures,’ he says.

He points out that a synergistic effect has been documented during chalcopyrite leaching with a defined consortia of the common biomining extremophiles L. ferrooxidans and A. thiooxidans. The mixed culture was more efficient at leaching chalcopyrite than pure (or clonal) cultures of each species alone. Scientists speculate that that co-culture reduced the formation of inhibiting layers by generating sulphuric acid due to sulphur oxidation of A. thiooxidans.

Despite the problems of regulation of gene engineered extremophiles, there are reports of successful genetic alteration of the Acidithiobacillus species in the literature, particularly from Chinese laboratories and Biosigma in Chile. Emphasis is on changing the way that bacteria communicate with each other via the process of ‘quorum sensing’ (C&I, 2007, 4, 24); this would in turn influence the development and composition of bio-engineered populations. At the moment the success rate is low, but that is likely to change as more is understood about the genetic basis of quorum sensing.

So is the future of biomining to be with gene engineered consortia? Johnson is emphatic: ‘Not a chance, there is no way to contain them and they will escape into the environment.’

With the current concerns about gene engineered crops it does seem that gene engineered consortia may be unlikely to get the green light. But this should not affect designed consortia of non-genetically engineered species. Indeed, using evolution to our advantage is certainly on the cards. ‘Once an initial consortia has been established,’ says Bayer, ‘the power of evolution can be used to drive novel species interactions, potentially resulting in increased consortia stability and productivity.’

Bayer also points out that the benefits of using engineered populations of bacteria extend far beyond mining. ‘Designing microbial communities has many attractive possibilities for biomedical and energy applications,’ he says. ‘Studies like this are likely to provide insights into how natural microbial consortia function. Cell signalling and communication pathways, for example, quorum sensing, between different bacterial and archaeal species are likely to be the key processes, which we can alter to design novel functions in synthetic and natural consortia.’

Whether or not synthetic biology and gene engineered consortia are ever introduced or not, one thing is sure. With rising extraction costs, biomining is likely to be close to the top of the industries agenda for many years to come.

So next time you settle down to scare yourself silly with a repeat viewing of Aliens remind yourself that there really are creatures who love concentrated acid, and they are a lot closer to home than planet LV426.

Biomining extraction made simple

In comparison with chemical extraction, which involves several steps, biomining involves simple percolation or agitation techniques to extract the mineral or metal. A lixiviant – fluid inoculated with extremophiles – is either percolated through a static bed of relatively coarse particles, or in the case of finer particles, agitated mechanically with them to extract the metal.

Percolation techniques are cheaper of the two options, and until recently, much preferred by the industry. They are used for in situ, dump, and heap leaching, while agitation techniques are used in vat leaching.

In situ leaching is the simplest and cheapest and involves pumping the lixiviant together with air under pressure into a mine or into ore bodies which may have had their porosity and permeability enhanced by explosive charges. The resulting metal-enriched solutions are recovered through wells drilled below the ore body.

Dumps of uncrushed waste rock can contain up to 0.1–03% copper, too low to recover profitably by conventional procedures but ideal for bioleaching. Some of these dumps are huge, containing in excess of 10m t of waste rock. There are also heap mines, where the ore surface area has been maximised by mechanically arranging the materials into a heap. Heap leaching also requires size reduction of the ore to maximise mineral–lixiviant interaction and  a impermeable base to prevent lixiviant loss and pollution of water bodies.

Both dump and heap leaching involve adding the lixiviant at the top of the dump or heap surface and the recovering the metal laden solution that seeps at the bottom. Dilute sulphuric acid is sprinkled on top and percolates down through the dump, lowering the pH and promoting the growth of acidophilic microorganisms. The acid run-off is collected at the bottom of the dump, from where it is pumped to a recovery station.

Vat leaching involves the dissolution of crushed ores in a confined tank. Enhanced recovery can be achieved by using bioreactors, though these necessarily involve higher costs.

Richard Corfield is a science writer based in Oxfordshire, UK.

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