Microbe samples sit in petri dishes at a Cemvita laboratory. Image: Cemvita factory
Environment Technology

Biotechnology: using microbes as mining equipment

Marny Reakes explains how synthetic biology can change the way we mine. From the micro fracturing of rocks, to exploration and advanced bioleaching, we are just at the tip of the iceberg

“We just took part in a two-week virtual workshop with a major mining company based on how to mine without actually creating a mine,” Marny Reakes told me.

Cue a slightly stunned silence from me. I thought this interview would be mainly about bioremediation but, boy, was I wrong.

Let’s rewind a little…

Marny Reakes is VP of biomining at Cemvita Factory
Marny Reakes is VP of biomining at Cemvita Factory

Reakes and I met earlier this year through Moji Karimi, CEO of biotechnology company Cemvita Factory. Reakes had recently joined the Cemvita team as vice president of biomining, and Karimi had introduced her to me as a “fearless leader… who is passionate about sustainable mining”.

Fearlessness is an important quality when your mission is to instigate change in a famously stoic industry. And Karimi was not exaggerating.

Reakes’ previous role saw her managing BHP’s legacy mine sites which account for over half of the company’s tailings dams; a job that carries an immense weight of responsibility, particularly at a time when global tailings management practices are under the microscope.

Having originally trained as a chemical engineer in her home country of New Zealand, Reakes began her career in mining accidentally – as many do – while backpacking around South Africa. She landed a three-month job as an environmental engineer at the Palabora Mining Company and ended up staying for five years.

“I started off working for Rio Tinto and then, the last 20 years, at BHP, I did all sorts of things from operations management to commissioning plants and implementing an enterprise-wide IT management system… I also did some supply and marketing,” she told me.

“The last six years I was based in North America looking after the company’s legacy mine sites. That really opened my eyes to the fact that, as miners, we need to do things differently.”

Upon leaving BHP, Reakes’ intention was to get into angel investing, supporting clean tech companies, and she does that today alongside her role at Cemvita.

Improving mining processes

“When I first joined Cemvita, the mining vertical was just about bioremediation and I’ve worked to expand that,” she explained. “I’m so excited to tell you about some of the trends I’m seeing and how people are starting to get their head around the possibility of microbiomes as mining equipment.”

The feeling was mutual. We were 20 minutes into an hour-long interview slot and, pre-written questions discarded, we were almost talking over each other to share our latest projects.

Biotechnology for carbon sequestration was the topic of my first blog post in 2020. Karimi wrote a guest article based on Cemvita’s work in this area, and we had agreed to catch up later in the year as the project progressed.

“We’re seeing huge traction on the carbon sequestration and utilisation side,” Reakes told me. “But I’ve also started to see interest in biomining and mineral processing as well. Some big companies have come to me saying ‘we don’t want to do normal biomining or bio-mineral processing ’, which, as you know, are based around bioremediation, bioleaching and bio-oxidation.

“I’ve had people ask for designer microbes for use in exploration and for the in-situ fracturing of rock. Another wanted synthetic biology to remove impurities from their metal in bio-beneficiation…

“There seems to be a trend: companies are looking at reducing their carbon impact, energy intensity and cost base in all the usual ways, and now they’re asking, how they can copy what nature already does to support this and scale up.”

Mining without ‘mines’

In copper, Cemvita is engaging in work on to optimise recovery from bio-heap leaching of mixed sulphides, finding ways to augment the naturally occurring or existing microbial consortia. And that work translates into in-situ leaching application as well.

Which is how we came to talk about mining without mines… well, not as we know them today anyway.

“In-situ leaching is already done in mining, because you’re only extracting the metals you need,” said Reakes. “And if you’re doing it using microorganisms, there’s a higher likelihood that you’ll be able to restore the microbiome afterwards. It’s much more sustainable in the long term.”

Synthetic biology is a multi-disciplinary science. Image: Cemvita Factory
Synthetic biology is a multi-disciplinary science which brings together bioengineering, bioinformatics, microbiology and more… Image: Cemvita Factory

At the aforementioned workshop, Reakes presented on the use of synthetic biology for bioleaching and also in preconditioning orebodies, using organisms to induce micro fracturing.

How?! I asked her. How can tiny organisms crack rocks in a commercially feasible timeframe?

“Nature already weathers rock,” she told me with a smile. “Microbes dissolve minerals, they bind to minerals, they bore their way into rock. We just need to accelerate that.

“There’s a subset of microbes called endoliths that live and grow in cracks in rocks. There’s one particular species that can actually wedge themselves through cracks in rocks that are smaller than their diameter, then grow on mass and potentially crack them.”

The really exciting part is that, currently, we only know about 2% of the world’s microbial life, and there’s a big portion of that 2% that we don’t even fully understand yet.  

Geomicrobiology is further behind than some of the other microbiology fields. It’s lagging by about 20 years,” said Reakes. “So, there’s probably a whole lot of really exciting species out there doing amazing things in rock that we don’t even know about yet.

“They might not be the dominant strain in the rock, but maybe we can make them dominant or over express some genes to make them function more efficiently, better, at a faster rate…”

What is synthetic biology?

Redesigning organisms or enhancing systems that occur in nature falls under the field of synthetic biology.

“Synthetic biology is a multi-disciplinary science,” Reakes explained. “It includes: bioinformatics [the application of computation and analysis to interpret biological data]; bioengineering or the programming  of cells using DNA; and microbiology, which involves looking at how you can stimulate and augment organisms to work more efficiently.

“There’s also a lot of data processing and artificial intelligence required to search and really understand the functionality of these microbes, to work out their metabolic pathways and optimise them.

“It’s a combination of really diverse pieces of science all coming together to understand and programme microbes to do what you want.”

Given how stringent regulations surrounding genetic modification are today, synthetic biology mainly involves the manipulation of characteristics that organisms already possess or express. For example, horizontally transferring a gene from one organism to another, or putting two microbes into an environment where they might not have met naturally to encourage interaction.

“We’re accelerating some of the evolutionary pathways,” Reakes explained. “For mining applications, we start by examining the native microbiome and then looking at how we can enhance that.”

Other industries that are harnessing synthetic biology to improve their processes include agriculture and food production (fake burger, anyone?), pharmaceuticals and cosmetics. Theoretically, we should be able to learn from these applications and apply that knowledge to heavy industries too.

“We’re already seeing the CO2 utilisation market developing,” said Reakes. “For example, companies like LanzaTech that source carbon dioxide from off-gas points and use synthetic biology to convert that into fuel.

“There’s quite a lot going on in low-carbon chemicals too, specifically the precursors to polymers and plastics, one example being Cemvita’s work for production of carbon-negative bioethylene from CO2. Another interesting area is the treatment of waste, like the biodegradation of plastic or recycling of batteries and other e-waste.”

The recycling framework is also applicable in mining as, going forward, it’s likely that more mining companies will pivot their business models to take in and recycle waste (see Boliden and Umicore for an example of current work) to close the loop on metal production.

“We’re also seeing interest from mining companies wanting to repurpose their tailings and get more metals or water out,” added Reakes. “And there are companies in the oil and gas industries that are potentially looking to extract metals like cobalt or lithium from the brines they produce at onshore operations as well.”

Making mining more sustainable

There are a myriad of ways that synthetic biology could impact or even disrupt the mining industry, many of which I had not remotely considered prior to this interview. It truly opened my eyes.

“There’s a lot of work to be done to scale up these technologies and make them commercial but, yes, it opens up completely new ways of mining,” Reakes agreed. “Mining deposits in-situ, or heap leaching and processing can completely eliminate the need for comminution or fine grinding down to 75 microns, which is what many copper operations require today.”

The use of naturally occurring organisms to augment or enable mining processes, as opposed to using chemicals like cyanide, also offers mining companies the chance to improve their environmental credentials and expedite permitting; something which is becoming ever more difficult.  

“I was recently working on some proposals for some gold companies, and my research led me to microbes that can actually produce cyanide, and also those that can degrade cyanide afterwards,” Reakes told me. “So, you could create a completely biological process, even with cyanide.”

Exploring the possibilities

I wanted to know more about the application of synthetic biology in mineral exploration too…

“It expands on some of the work that Moji did in one of his previous startups called Biota,” explained Reakes. “The team used bioinformatics to add another dimension to oil exploration.

“If you extrapolate that… we found that some microbiomes in plants, rocks and soils will change depending upon the metals available in their environment. Based on that, we should be able to find biological signatures that indicate what’s in the ground.

“For example, if companies did biological analysis as well as chemical analysis on their drill core samples during exploration, that could add another dimension to their exploration programmes.

“With microbes, because we’re talking about genomes in their tens of thousands, that’s a lot of extra information that could potentially be pulled into a geological model.”

During recent research work, Reakes came across technical paper on a microbe that can transform gold from its mineral state by consuming it to create a nanoparticle. It then transferred the particles downstream where it built them back up to create a gold nugget.

The Cemvita team in action. Image: Cemvita Factory
The Cemvita team in action. Image: Cemvita Factory

“It took only decades for the microbes to make a gold nugget,” Reakes said, excitedly.  

“Wow!” I leaned closer to my computer screen. “How could we use that ability in mining?”

“There are a couple of ways,” she said. “One is the location of a biosignature that could help us find gold deposits. People have also been looking at ways that nanoparticles can be used healthcare and, maybe… and it’s a little bit further away, but we could potentially use them for in-situ mining or heap leaching as well.”

Untapped potential

The long and the short of it is that we’re not currently exploiting all of the different ways that microbes interact with minerals. There are opportunities available that we don’t even know about yet.

It’s very much an emerging subject.

“In the past month, I’ve been overwhelmed with mining companies asking for proposals on different ways of biomining,” Reakes said. “I’ve seen people starting to use the language of synthetic biology and understand it. That’s only happened in the last six months and it’s really encouraging.”

The team at Cemvita is thinking big, but the company is, for now, still early stage.

“We’re currently in a Series A funding round. That will allow us to do some internal R&D, grow our team and lab equipment and expand our knowledge base,” Reakes told me.

“I recently brought a geo-microbiologist into our team and, through her, I’ve learnt so much about micro-mineral interactions. There’s such a huge scope for innovation and discovery in this space.

“I think, the only reason people haven’t gone down that path yet is because there hasn’t been an incentive to make big step changes in the footprint (physical, chemical and climate) left by mining.

“But there is now, and I think applying focus and energy in this area will come up with some really amazing discoveries that can change the face of mining.”

I couldn’t agree more, I told Reakes.

Mind. Blown.

4 comments on “Biotechnology: using microbes as mining equipment

  1. Cautious Reader

    Synthetic biology to mine seems like a Black Swan risk waiting to happen. You mess with nature. . . it hits back in greater force.

  2. Herman Lombard

    What an incredible article Carly. I am a Chemical Engineer that also found my way into Mining many years ago. I recently got very interested in Biomimicry and it is fascinating to see how little we are yet to discover on how nature really works. I think for many people would not see any connection given the reagents and chemicals in use so very interested in this field. Will certainly follow this field of research as it develops and what Marny and team gets up to. Thanks for this article.

  3. Thank you for this article and all the best to Marny Reakes with this work. Absolutely fascinating.


    No doubt, the length and breadth of the subject is fascinating. Yet at places, where legal and social issues limit the mine excavation geographically, can this subject be of help to avoid drilling, blasting, magazine maintenance and the relevant security costs by breaking the rock on a commercially viable scale with microbes.
    Fear, may be a long way to go!

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