Issues Magazine

Microbial Mining

By Carla Zammit

Microbes can operate in the toughest conditions on Earth, including among the acids and heavy metals of the mining industry.

The first microorganisms appeared on Earth 3.7 billion years ago at a time when there was no free oxygen and the atmosphere was composed of methane, carbon dioxide, ammonia and hydrogen. They have since evolved to inhabit almost all parts of the globe, developing many systems to deal with life at the extremes.

Some microorganisms can grow in strongly acidic conditions, withstand levels of heavy metals lethal to most other life forms, live in temperatures above the boiling point of water and withstand radiation levels much greater than we can tolerate.

Many microorganisms make significant contributions to environmental cycles, such as the fixation of nitrogen, the cycling of carbon and the transformation of a range of metals such as iron, manganese, gold, copper and uranium.

Microorganisms are used in a vast number of industrial processes, ranging from chocolate production to gold extraction. Since ancient times we have used them in the manufacture of alcohol, bread and cheese.

Microorganisms can catalyse reactions that, in energy terms, are only marginally favourable. We have the technology to upscale what microorganisms in the environment do and to apply it to our industrial processes, encompassing all of those billions of years of evolutionary refinement into simple solutions for seemingly complex problems.


Around 3000 BCE, mining along the banks of Spain’s Rio Tinto River began. Miners sourced ore and place it in beds along with water from the local river. Unbeknown to them, the microorganisms in the river water were breaking down the sulfide-containing ores to extract copper. The river is very acidic and rich in heavy metals, so no vegetation or animals live along its shores. Not until the 1940s was it recognised that microorganisms there played a role in the dissolution of metals from their ores, a process termed “bioleaching”.

The microorganisms commonly associated with bioleaching and bio-oxidation (see below) are chemolithoautotrophs. As the name suggests, their energy is obtained by oxidising inorganic iron and/or sulfur and using the freed electrons in energy production and using carbon dioxide from the atmosphere as their source of carbon. Generally, the pH of bioleaching operations is within the range of 1.2–2.0, and hence these microorganisms are acidophilic.

As a result of the oxidation of iron and/or sulfur at low pH by these bioleaching microorganisms, minerals trapped in the ore become soluble. These solubilised metals can then be processed using traditional methods, such as solvent extraction and electrowinning.

By the end of the 19th century, Rio Tinto was a full-scale mining operation and was providing materials to fuel the development of Europe. When the English took over the mine, they switched from bioleaching to modern metal-processing techniques such as smelting.

These changes caused a vast amount of pollution from the mine to leak into the environment. The main problem was the emission of sulfur dioxide gases, which affected anybody within 15–20 km. The people of the area demonstrated against the mine, calling for better health and safety conditions. The military retaliated against the people and at least 200 men, women and children were killed. Soon after this, the Rio Tinto mine closed down, but the method of bioleaching was just about to make its way out of Europe.

In 1959 the first commercial bioleaching operation began at the Bingham Canyon Mine in Utah, USA. Since that time it has been an expanding industry driven heavily by the benefits of using the technology over traditional mining processing methods.

Scientists have since been able to use their knowledge to expand the application of these microorganisms to the extraction of many types of metals. Currently it is estimated that ore processed using microorganisms accounts for 20% of the world’s copper supply. A number of other metals have now been extracted using bioleaching, including gold, silver, uranium, nickel, zinc, lead and cobalt.


Bio-oxidation is another method in which microorganisms help to extract a metal of interest. However, during bio-oxidation the metal of interest remains in an insoluble form. Hence, bio-oxidation is often used as a pretreatment method prior to metal extraction, such as the extraction of ores containing gold. After bio-oxidation, the gold is extracted by a more traditional method such as cyanide extraction.

Bio-oxidation is a relatively new technique, with the first commercial operation opening in the 1960s in Utah. During the past 20 years the method has expanded rapidly, specifically for the treatment of refractory gold ores.

BIOXTM is the most commonly used bio-oxidation process, and has been used since 1986 to recover gold from sulfide-containing ores. During this process, flotation concentrate is mixed with nutrients to promote microbial growth. This is then added to a series of reactors where a selected mixture of microorganisms break down the sulfide within the ore. The product is then cleaned and leached by traditional metal extraction methods, such as cyanidation. Finally the waste products are pH-adjusted and made safe for disposal in a tailings dam.

Stirred tank bio-oxidation is the fastest method of bioleaching but, due to higher costs, is only appropriate for some operations and is currently being used at ten different sites across the world.

The Optimal Process

Although bioleaching and bio-oxidation processes have a long history, the mechanisms that drive the microbial–metal interactions are still not fully understood. Research into the microorganisms within bioleaching/bio-oxidation communities, their interaction with each other and their environment is necessary if the optimisation of the processes are to be realised.