Bacteria in a petri dish.

Bioleaching: How Microorganisms Eat Pollutants

Steve Russell - April 22, 2025

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Bioleaching harnesses microorganisms to eat hazardous pollutants, keeping them out of the environment while converting mineral processing waste into valuable solid metals. Its applications and implications are promising. 

The Problem That Bioleaching Is Poised to Solve

There are only so many pockets of minerals and heavy metals on Earth. Even though they are finite, miners often leave a lot behind when extracting them from underground deposits. These leftovers are called mineral processing waste. 

While mineral processing waste is often a combination of topsoil, worthless alloys, and finely ground rock, it is also usually made up of trace amounts of valuable metals. Porphyry copper deposits — large bodies of low-grade, copper-rich ore — generally contain less than 1% of copper. However, they are typically massive, making extraction via open-pit mining profitable. 

An open-pit mine.
An example of open-pit mining.

Generally, sifting through mineral processing waste to find low-grade ore is more expensive than it is worth. As a result, trace amounts of valuable heavy metals and rare earth elements get left behind in the mine. The problem with this is that many of these materials are toxic. 

Hazardous trace metals and mineral pollutants leach into the surrounding air, water, and soil. Research shows they can spread far beyond the mining site. What’s worse, they can remain in local ecosystems for centuries or even thousands of years, causing untold damage generations after the mine closes. 

Mining is not the only source of these pollutants. Agriculture, industrialization, and urbanization also contribute. This means the problem is not isolated to the ecosystems surrounding mining operations. Rather, they exist on farms, in industrial parks, and within cities.

How Microorganisms Eliminate Toxic Pollutants

Bioleaching uses microorganisms to extract valuable metals from mineral waste. The living bacteria essentially eats pollutants, dissolving waste material in an aqueous solution. It only needs water, light, oxygen, and nutrients to multiply. This process — which takes place in a specialized bioreactor — transforms trace metals into a soluble, extractable substance. 

How bioleaching works. Source: brgmTV

Scientists start with finely ground mineral processing waste and end with an aqueous solution. They can chemically filter the watery material to produce solid metals. While the bacteria produce sulfuric acid — this is how they break down substances — this substance is easily taken care of in a laboratory setting, where the entire process takes place. 

Factors like pH, carbon dioxide, temperature, oxygen, and nutrients are important. The medium needs a proper balance for bioleaching to be effective and efficient. It is still relatively slow — small batches take days, while large ones take months — but monitoring is essential to avoid unnecessary delays. 

Phytomining Goes Hand in Hand With Bioleaching

Phytomining is another emerging remediation method. It involves cultivating hyperaccumulator plants — greenery with a natural ability to uptake minerals and metals from the soil. After they absorb the pollutants, they can be cut or burned. Those cuttings or ash piles contain valuable element compounds that professionals can refine into pure metals. 

A yellow flower.
Buckler Mustard (Biscutella laevigata), a hyperaccumulator plant that absorbs Thallium.

All plants are natural purifiers. Most can uptake heavy metals and toxic pollutants through their root systems. However, only some can accumulate exponentially more — up to 1000 times higher concentrations — than nonaccumulators. 

Hyperaccumulator plants are essentially living biorefineries. Unlike factories, which require an energy-intensive refinement process to extract, isolate, and refine pure nickel, phytomined ore contains chemically pure nickel. In this way, it lowers the final product’s carbon footprint. 

While bioleaching must occur in a laboratory environment, phytomining can occur on-site where soil pollution has already happened. They can even be planted in areas unsuitable for growing crops. The United States has approximately 10 million acres of barren, nonarable land with a high nickel concentration. Hyperaccumulator plants could passively harvest it. 

The Benefits of Bioleaching and Phytomining 

The benefits of bioleaching are twofold. For one, metals and metalloids are finite, so it performs a vital duty by preventing shortages and keeping costs down. Its environmental benefits are far more notable. It keeps toxic pollutants from leaching into the water and soil, improving the well-being of humans, livestock, and wildlife. 

A green fern.
Old World Forked Fern (Dicranopteris linearis), a hyperaccumulator plant that absorbs rare earth elements.

Phytomining is just as good for the planet, if not better. While the plants are often ultimately destroyed, they are typically replaced. Moreover, they absorb carbon dioxide while alive, helping combat climate change. Planting acres of hyperaccumulator plants is also relatively affordable since some are weeds. 

Conventional approaches are often too expensive, complex, energy-intensive, or restricted to be effective at scale. For instance, while bleach is effective at killing bacteria and viruses, it cannot remove chemicals, particulates, or heavy metals from the environment. Unlike alternatives, green biological methods are environmentally safe and economical. 

Emerging Opportunities for This Extraction Method

While bioleaching is catching on in the mining and mineral extraction sectors, there are other industries in which it could be effective. For instance, it could eliminate toxic pollutants originating from cities’ wastewater. When used as a pretreatment for sewage sludge, it preserves the fertilizer value while removing pathogens. 

A pile of Nickel ore.
A pile of nickel ore.

In one study on sewage sludge, it removed over 67% of zinc, 64% of cadmium, 56% of manganese, 50% of copper, 49% of nickel, 20% of arsenic, 10% of lead and 6% of chromium within 10 days. It is even more efficient and effective when combined with existing pollutant treatment methods.

Electronic waste remediation is another promising application. Electronic devices contain rare Earth elements and precious metals like gold and lithium. With bioleaching, workers could extract these valuable materials. 

Consumers only recycle 25% of their electronics, according to the United States Environmental Protection Agency. The rest becomes waste, which pollutes landfills for centuries. Since e-waste is a global issue, it presents a unique opportunity for scientists to prove bioleaching is an effective remediation method at scale. 

Will Bioleaching and Phytomining Catch On?

Bioleaching and phytomining are promising alternatives to existing remediation methods because they are cost-effective, environmentally friendly, and can integrate into existing processes. They also have a relatively small physical footprint — professionals do not need to invest in a giant factory and numerous specialized machines.

Already, these processes have moved beyond research and are being used in the field. Although they have yet to become industry staples, they have been the focus of many studies and trials in recent years. Soon, they may replace industry-leading extraction and refinement processes, paving the way for more sustainable industrial and urban areas. 

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About the author

Steve Russell

Steve is the Managing Editor of Environment.co and regularly contributes articles related to wildlife, biodiversity, and recycling. His passions include wildlife photography and bird watching.