In a pine forest on Michigan’s Upper Peninsula, the only active nickel mine in the US is nearing the end of its life. At a time when carmakers want the metal for electric-vehicle batteries, nickel concentration at Eagle Mine is falling and could soon drop too low to warrant digging.

But earlier this year, the mine’s owner started testing a new process that could eke out a bit more nickel. In a pair of shipping containers recently installed at the mine’s mill, a fermentation-derived broth developed by the startup Allonnia is mixed with concentrated ore to capture and remove impurities. The process allows nickel production from lower-quality ore. 

Kent Sorenson, Allonnia’s chief technology officer, says this approach could help companies continue operating sites that, like Eagle Mine, have burned through their best ore. “The low-hanging fruit is to keep mining the mines that we have,” he says. 

Demand for nickel, copper, and rare earth elements is rapidly increasing amid the explosive growth of metal-intensive data centers, electric cars, and renewable energy projects. But producing these metals is becoming harder and more expensive because miners have already exploited the best resources. Like the age-old technique of rolling up the end of a toothpaste tube, Allonnia’s broth is one of a number of ways that biotechnology could help miners squeeze more metal out of aging mines, mediocre ore, or piles of waste.

The mining industry has intentionally seeded copper ore with microbes for decades. At current copper bioleaching sites, miners pile crushed copper ore into heaps and add sulfuric acid. Acid-loving bacteria like Acidithiobacillus ferrooxidans colonize the mound. A chemical the organisms produce breaks the bond between sulfur and copper molecules to liberate the metal.

Until now, beyond maintaining the acidity and blowing air into the heap, there wasn’t much more miners could do to encourage microbial growth. But Elizabeth Dennett, CEO of the startup Endolith, says the decreasing cost of genetic tools is making it possible to manage the communities of microbes in a heap more actively. “The technology we’re using now didn’t exist a few years ago,” she says.

Endolith analyzes bits of DNA and RNA in the copper-rich liquid that flows out of an ore heap to characterize the microbes living inside. Combined with a suite of chemical analyses, the information helps the company determine which microbes to sprinkle on a heap to optimize extraction. 

In lab tests on ore from the mining firm BHP, Endolith’s active techniques outperformed passive bioleaching approaches. In November, the company raised $16.5 million to move from its Denver lab to heaps in active mines.

Despite these promising early results, Corale Brierley, an engineer who has worked on metal bioleaching systems since the 1970s, questions whether companies like Endolith that add additional microbes to ore will successfully translate their processes to commercial scales. “What guarantees are you going to give the company that those organisms will actually grow?” Brierley asks.

Big mining firms that have already optimized every hose, nut, and bolt in their process won’t be easy to convince either, says Diana Rasner, an analyst covering mining technology for the research firm Cleantech Group. 

“They are acutely aware of what it takes to scale these technologies because they know the industry,” she says. “They’ll be your biggest supporters, but they’re going to be your biggest critics.”

In addition to technical challenges, Rasner points out that venture-capital-backed biotechnology startups will struggle to deliver the quick returns their investors seek. Mining companies want lots of data before adopting a new process, which could take years of testing to compile. “This is not software,” Rasner says.  

Nuton, a subsidiary of the mining giant Rio Tinto, is a good example. The company has been working for decades on a copper bioleaching process that uses a blend of archaea and bacteria strains, plus some chemical additives. But it started demonstrating the technology only late last year, at a mine in Arizona. 

While Endolith and Nuton use naturally occurring microbes, the startup 1849 is hoping to achieve a bigger performance boost by genetically engineering microbes.

“You can do what mining companies have traditionally done,” says CEO Jai Padmakumar. “Or you can try to take the moonshot bet and engineer them. If you get that, you have a huge win.”

Genetic engineering would allow 1849 to tailor its microbes to the specific challenges facing a customer. But engineering organisms can also make them harder to grow, warns Buz Barstow, a Cornell University microbiologist who studies applications for biotechnology in mining.

Other companies are trying to avoid that trade-off by applying the products of microbial fermentation, rather than live organisms. Alta Resource Technologies, which closed a $28 million investment round in December, is engineering microbes that make proteins capable of extracting and separating rare earth elements. Similarly, the startup REEgen, based in Ithaca, New York, relies on the organic acids produced by an engineered strain of Gluconobacter oxydans to extract rare earth elements from ore and from waste materials like metal recycling slag, coal ash, or old electronics. “The microbes are the manufacturing,” says CEO Alexa Schmitz, an alumna of Barstow’s lab.

To make a dent in the growing demand for metal, this new wave of biotechnologies will have to go beyond copper and gold, says Barstow. In 2024, he started a project to map out genes that could be useful for extracting and separating a wider range of metals. Even with the challenges ahead, he says, biotechnology has the potential to transform mining the way fracking changed natural gas. “Biomining is one of these areas where the need … is big enough,” he says. 

The challenge will be moving fast enough to keep up with growing demand.