The microbiome of mining

Let’s actually talk about some actual boots on the ground, honest to god genetic sequencing now. I mean, it’s been part of the introduction to the show for long enough. This stuff is pretty close to witchcraft by now. By taking a tiny sample of some organic material, you can then identify the chemical building blocks, Adenine, Thymine, Guanine, Cytosine, and uracil if you’re feeling feisty, but also the order in which they are… ordered. From that you can work out the organism, and the part of the organism that the sample came from. I mean, the applications seem endless. And thanks to my new best friends at Biotechnology company Illumina, over the next few months we are going to delve into just what the cutting edge of sequencing technology can reveal about our world.

Will - And hey, here's an idea. Let's actually talk about some actual boots on the ground. Honest to God, genetic sequencing now, I mean, it's been part of the introduction to the show for long enough. This stuff is pretty close to witchcraft by now. By taking a tiny sample of some organic material, you can then identify the chemical building blocks, adenine, thymine, guanine, and uracil if you're feeling feisty. But also the order in which they are ordered from that you can work out the organism and the parts of the organism that the sample came from. I mean, the applications seem endless. And thanks to my new best friends at biotechnology company Illumina, over the next few months, we are going to delve into just what the cutting edge of sequencing technology can reveal about our world. I know that line sounded familiar. Anyway, let's begin with a story. Like I said, the applications of genetic sequencing are absurdly wide reaching. And so if I asked you where you think genetic sequencing is currently playing a huge part in shaping our future, where would your mind go? Disease identification, absolutely. Forensics a hundred percent. But how many of you thought of mining? Mining, particularly coal mining is a controversial subject and has a reputation for contributing to global climate change that is irrefutable. However, for us to venture into a clean new world of renewable energies, we will need coal.

Dan - We need coal to make steel. A single wind turbine requires nearly five tons of copper and over 300 tonnes of steel. And to make that steel, you need coal.

Will - That's Illumina's Dan Letchworth by the way, he's going to be talking us through quite a lot of this. So if we must continue to mine for coal for the moment at least, we must also contend with the other stuff that appears when you dig a big hole in the ground.

Dan - So one of the harmful byproducts of mining is selenium. Selenium is a naturally occurring element, but the problem is that mining tends to grind and chew up the rock and expose a whole lot more selenium to the surface than would naturally be uncovered. And because the mining process breaks up the rock into tiny pieces, suddenly the surface area is vastly multiplied. And those are usually just exposed to the atmosphere, exposed to the air and water. And so precipitation from rain and snow runoff that can, uh, carry these leftover bits of selenium into the water supply into rivers and streams.

Will - By the way, if you weren't sure, that's bad.

Dan - Selenium is a required element for cell function in animals. All animals, humans included, use selenium as a natural part of their metabolism. But just like the phrase goes, the dose makes the poison. High enough concentrations of selenium can cause growth defects in fish, and it can adversely affect their population numbers. And unfortunately, if selenium levels get too high in the water supply, communities that rely on that water to drink can also have negative health effects as well.

Will - So what to do then with this excess buildup?

Dan - The companies I spoke with were Teck resources and Rio Tinto. Teck in particular has implemented selenium eating bacteria. What Teck does is they introduce this bacteria to the waste rock piles with a small amount of the carbon based food that the bacteria eat. And as a part of their metabolism, these bacteria take the dissolved selenium and convert it into a harder, more solid form selenite crystal, which is then heavier and it's easier for humans to keep outta the water supply.

Will - A species of bacteria is capable of treating metals like selenium. That's pretty amazing. But perhaps not all that surprising. As the University of British Columbia's John Steen explains...

John - Microbes have been around metals for a long, long, long time. They're evolved to interact with metals and, some quite specifically, they use metals for metabolism. They use metals for their energy systems. The reason why we have deposits of iron ore around the world is because of microbes and what they were doing billions of years ago.

Will - And so that begs the question... What else is out there? If there really are, as some have estimated, 1 trillion species of microbes undiscovered beneath our feet, what might they be capable of? Well, that's where Illumina and the Mining Microbiome Analytics Platform, or M-Map to its friends, comes in. A plan to find out if anything underground can help us out on the surface. Here's Allonnia's Elizabeth Deyett to explain that a bit better.

Elizabeth - I think that microbes offer an untapped potential in a lot of different areas. And what M-Map is really trying to do is understand that potential at a much deeper level than we've ever been able to have before. And a lot of times our capabilities are limited by what we can, what our own samples can tell us. But what M-Map is doing is sort of allowing the collective community and all of the samples that come in from various sources to help enhance an individual's project while still having data security parameters on it.

Will - Yes, exactly. And naturally genetic sequencing has a huge role to play in this.

Dan - So it all starts with the target being 15,000 samples of soil and rock from different mine sites. And what Illumina does is extract the DNA present in those soil samples and sequence it. And then through the secondary analysis software, you can piece together the original sequence of all the life forms present in that soil. From what we've heard so far in the project, about 80% of the life forms they found have been previously unknown, undescribed, species of bacterias.

Will - So that is a lot of new potentially helpful microbes already. And if you can sequence new microbes, you can find out what they do and perhaps more importantly share that knowledge with the group. So it says Koonkie Cloud Services, Aria Hahn.

Aria - We've developed statistical software that will find novel genes of a known function. And so you might be interested in methane production, for example. And so we're able to find new genes that were previously we didn't know that that's what they were doing and say like, we're pretty sure that this is doing methane production as an example. As we find those novel genes as well, we're again able to put that back into M map so that if you try to see what is happening in my samples, you can benefit from all of that prior knowledge.

Will - And the shared knowledge is already bearing fruit.

Dan - About 20% of the copper being mined in the world is being mined through hydrometallurgy, which uses either strong acids or, more frequently these days, bacteria to leach the copper from the source rock, which is, as you can imagine, a much more environmentally friendly way to do it. Bacteria can bind the fine sand particles that would otherwise get tossed up into the air and create a potentially hazardous breathing situation for mining workers. They can use bacteria to help with dust suppression.

Will - But what if you found a useful detoxifying gene but in a bacteria that is on the whole still harmful to humans? That might not be a problem either.

Dan - If the scientist analysing the data from M-Map discovers a potentially useful gene that could, for example, clean a toxic compound that is found in mine soil, but it's in a bacteria that would be harmful to humans. Genetic engineering scientists could transport that gene into a different bacteria and then encourage that bacteria to reproduce with that gene. So you have a new kind of bacteria that performs that toxin cleaning function without being harmful to humans.

Will - So this is a rapidly developing field, but one that has already shown immense promise. And isn't it so enticing to think that a key to clean energy development could already be there just beneath our feet?

Aria - It's really easy to focus on the world that we can see and we all do this in our, in our day-to-day lives. because we have to, and it's practical and it makes sense. But the more that I learned about microbes, the more that I learned that this is their planet and they are actually responsible for its maintenance and health. They were here long before we were, and they will be here long after us. And so to understand them is to understand in a lot of ways what has given life to us and our planet and everything that we do see. And so there's something I think just existentially beautiful about that concept.