A Micro Universe on Earth: Harnessing the Smallest Life Forms for Reducing Environmental Impact in Mining

Mining Microbiome,

While Elon Musk plans to explore the cosmos, researchers at UBC are discovering a new universe right under their eyes here on earth, the microcosmos. 

According to Dr. Aria Hahn, there are about 1022 stars in the known universe, while here are the earth there are 1030 microbes. This is an eight-fold order of magnitude and yet labs have barely developed the capacity to explore and map this micro universe right here on Earth.

With advances in computing power and DNA sequencing, Dr. Steven Hallam and his lab are uncovering this universe of microbes, tracking their genetic memories to find out how the earth and life here were formed. This research is revealing the potential for a new generation of environmental solutions for mining that harnesses the smallest life forms that developed in the unique micro habits around the world.

Dr. Hallam is part of the Department of Microbiology and Immunology at UBC. He is a University of California Santa Cruz and MIT trained molecular biologist, microbial ecologist, entrepreneur, and innovator with over 20 years of experience in field and laboratory research.

In a recent conversation, BRIMM had a chance to sit down with Dr. Hallam to explore how his research is uncovering this micro universe.

What is the microbiome?

I’ll try to demystify things a little bit, but I will start at the high level of maybe the mystical here, because I think it’s a pretty foundational awareness. Everyone should have at least an inkling of. Do you want to know the earth moves around the sun, it is a pretty transformative way to look at the world. It is a different framework for how we interact with the world around us. 

The ability to see into the microbial world is relatively new and only began in the seventeenth century, when Anton van Leeuwenhoek gazed through the first microscope, revealing an invisible microbial world, the microcosmos.

Through a convergence of things like traditional microscopy, accounting and sequencing technology. So you know, just like there’s been this huge big data revolution with geospatial analyses like satellites that can look down on the earth and see contours, coordinates, land forms.

We are becoming aware that microbes are the dominant form of life on earth through sequencing. We have these sequencers for exploring DNA just like satellites exploring the earth. 

The cost of sequencing technology has gone down while the ability to scale and handle larger data has gone up. We now have this unprecedented ability to look at and map the DNA of microbes, and it’s a new awareness.

“Today, there are an estimated nonillion (or 1,000,000,000,000,000,000,000,000,000,000) prokaryotic microorganisms on Earth. Their abundance eclipses the number of stars in the known universe, the number of neurons in our brains, and all of our synapses combined.

– dr. steve hallam

And so now we have this unprecedented look at the DNA fabric of the earth. And it’s telling us we live on a microbial planet and so that to me is a profound awareness

That to me is the wow moment that says, I want to learn more and not just what can it do for me? But what can I learn about the earth as a system? What I learned about the past? 

What can I learn about the future based on this awareness that we live in a microbial world. And so when I talk about the microcosm, this is essentially what I mean.

The microbes that inhabit the microcosmos represent 3.5 billion years of evolution, during which time these microorganisms developed ways to harness energy and materials from the world around them. This transformed the surface chemistry of Earth, and it has generated a deep reservoir of genomic diversity. 

These very small things give rise to global resource systems, create the atmosphere, change the elemental composition of the earth, banded iron formations that created oxygen in the Earth’s atmosphere.   

Do they display any of the geological patterns or minerals of the environment they inhabit? Are rocks alive?

Your question about site specificity is actually pretty important. When we think about the mining industry, it may be that there is no one solution that you can apply across all mines. In fact, what you might want to do is go into your local site, which has a particular history and a particular geochemistry and a particular seasonality. 

You might want to try and use the indigenous microorganisms that are already there. They have adapted to those conditions and we could harness them, and find a way to make them work in a positive way to bioprocess waste instead of using chemicals.

I would argue that that’s what the Mining Microbiome Analytics Platform (M-MAP) wants to do. If we were really truly successful that would be it. Our research would empower local solutions to global problems.

How would or can microbes recover metals or even store carbon?

Microbes are critical components of the carbon cycle, they do it in several ways. Photosynthesis, a fundamental process and bio-cementation processes, can be done in the lab. 

One of the tensions is whether you put that carbon in the ground or whether you cycle that carbon from carbon dioxide into biomass for some value added. From a policy point of view, I hear lots of talk about locking it away for thousands of years.  

What is the future for this research?

Progress being made on microbe metal interactions and identifying, there is a huge push to find these proteins to use them in bio processes to waste resource recovery, that is a very fertile place to develop the technologies, it is going to take a lot of investment and work.

What are the challenges of research in the university?  

If you think about what I have learned from studying the microbiome, there is no one way to do it, there is no microscope that tells us the complete story, some are computational, some are scientific, statistical, there are tons of interdisciplinary approaches, to see this you have to have an ecosystem of research, you have to have a very complicated process

We’re not like health research here where there are a lot of resources over long-term grant periods. When we talk about natural sciences and engineering projects, they tend to be shorter term with industrial applications with industry partnerships. It is hard to drive research at scale that develops long-term programs because results are wanted on a shorter timeline. Plus, we are also here to train the next generation of scientists. This is a lot to ask of small teams.

Universities are positioned to be innovation brokers, if they want to take that risk. It is difficult to get the institutional mandate to take that risk. BRIMM is a unique situation to take this type of risk. It is willing to underwrite risk and find these breakout opportunities. 

It is very empowering to have someone like John Steen, someone who knows about innovation. You have to make calculated risks, not blind risks, that would not be productive.  We have to overcome the monolithic inertia of established research in academia.

Redundancy is also a problem. BRIMM creates an institutional environment for innovation that brings together different departments, it does not do it at the expense

This research appears to cut across a lot of fields of knowledge? What are the benefits and challenges of this type of work?

The power of cooperation, it is just really hard to do it and maintain it, that how, it is terrible at growing them. Once you have some traction, how do you realise the next level of potential, how do you do it? You need organisations like BRIMM. 


BRIMM would like to thank Dr. Hallam for taking the time to help explain the microbial work, he is uncovering.

By working across the UBC campus, BRIMM have access to top minds in the fields of Mining Engineering, Microbiology, Geology, Business, Policy, Data Science and more. It is through these connections that we can find the perfect team of researchers for the big mining problems of today.

If you are interested in connecting with BRIMM, contact us.

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