mining microbiome
Dan Letchworth, Illumina, John Steen, University of British Columbia, Elizabeth Deyett, Allonnia, Aria Hahn, Koonkie Cloud Services
Let's actually talk about the actual boot on the ground and honestly about the genetic sequence. I mean, it's been part of the introduction to the show for long enough. This is pretty close to magic. By taking a small sample of organic matter, you can identify the chemical components adenine, thymine, guanine, cytosine, and uracil if you are feeling high. You can also determine in what order they are placed. From there, we can determine the organism and the part of the organism from which the sample came. So the applications seem endless. And thanks to our new best friends at the biotech company Illumina, over the next few months we'll be taking a deep dive into what cutting-edge sequencing technology can reveal about our world.
Will – So here's an idea. Let's talk about the boots you actually wear in the field. Let's be honest, genetic sequencing now has been part of the introductory part of the show for long enough. This is pretty close to magic. By taking a small sample of organic material, you can identify the chemical components adenine, thymine, guanine, and uracil when you're feeling high. Their order also allows us to identify the organism and part of the organism from which the sample comes. So the applications seem endless. And thanks to our new best friend at the biotech company Illumina, over the next few months we'll be taking a deep dive into what cutting-edge sequencing technology can reveal about our world. I'm sure this line sounds familiar. Anyway, let's start with the story. As I mentioned earlier, the range of applications for gene sequencing is tremendous. So what would you say if I asked you, what big role do you think gene sequencing is currently playing in shaping our future? Identifying diseases, absolutely. Forensic science is 100 percent. But how many people have thought about mining? Mining, especially coal mining, is a controversial subject and has a reputation for irrefutably contributing to global climate change. But if we are to step into the clean new world of renewable energy, we will need coal.
Dan – You need coal to make steel. One wind turbine requires approximately 5 tons of copper and over 300 tons of steel. And to make that steel you need coal.
Will – By the way, that's Dan Letchworth from Illumina. He will tell us about this matter in considerable detail. So if we have to continue mining coal, at least for the time being, we also have to contend with other materials that appear when we dig big holes 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 crush rocks and expose much more selenium to the surface than would be exposed naturally. Then, as the mining process breaks the rock into smaller pieces, the surface area suddenly increases significantly. And they're usually just exposed to the atmosphere, exposed to air and water. Precipitation from rain and snow runoff can then carry these remaining selenium fragments into water supplies and into rivers and streams.
Will – By the way, if you're not sure, that's bad.
Dan-Selenium is an element necessary for animal cell function. All animals, including humans, use selenium as a natural part of their metabolism. But as the saying goes, the dose makes the poison. High enough concentrations of selenium can cause growth defects in fish, which can have a negative impact on fish populations. And unfortunately, when selenium levels get too high in water supplies, they can have negative health effects on the communities that rely on that water for drinking as well.
Will – So what should we do with this excess buildup?
Dan – The companies I talked to were Teck Resources and Rio Tinto. Specifically, Teck implemented bacteria that eat selenium. What Teck does is introduce this bacteria into the waste rock pile, along with a small amount of carbon-based food for the bacteria to eat. Then, as part of their metabolism, these bacteria take up dissolved selenium and convert it into a harder, solid form of selenite crystals. This makes the crystals heavier and easier for humans to keep away from water supplies.
Will – Some bacteria can process metals like selenium. That's pretty amazing. But perhaps it's not that surprising. John Steen of the University of British Columbia explains:
John – Microorganisms have been around metal for a long, long time. They have evolved to interact with metals, and some very specifically use metals in their metabolism. They use metals for their energy systems. The reason there are iron ore deposits all over the world is because of microorganisms and what they were doing billions of years ago.
Will – So the question arises… what else? If there really are a trillion species of undiscovered microorganisms under our feet, as some estimate, What can you do? That's where Illumina and the Mine Microbiome Analysis Platform (M-Map to its friends) come in. The plan is to find out if what's underground can help us above ground. Aronia's Elizabeth Dayette explains it a little more clearly.
Elizabeth – I think microorganisms have untapped potential in many different fields. And what M-Map is really trying to do is understand that potential at a much deeper level than we've ever done before. And often our abilities are limited by what we can do and what we can tell from our own samples. But what M-Map seems to do is preserve data security parameters while allowing all the samples provided by the collective community and various sources to help enhance personal projects. It's something.
Will – Yes, that's right. And of course, genetic sequence plays a big role in this.
Dan – So it all starts with targeting 15,000 soil and rock samples from various mine sites. And what Illumina does is extract the DNA present in those soil samples and sequence it. Then, through secondary analysis software, we can piece together the original sequence of all life forms present in that soil. From what we've heard so far on this project, about 80% of the life forms they've discovered are previously unknown and undescribed bacterial species.
Will – So there are already a lot of new microorganisms that could be useful. And if we can sequence a new microbe, we can learn what it does, and perhaps more importantly, we can share that knowledge with groups. So it says Koonkie Cloud Services, Aria Hahn.
Aria – We have developed statistical software to find new genes with known functions. So you might be interested in the production of methane, for example. So we're now able to find new genes that we didn't know what they were doing before, and we're now confident that this one is producing methane, as an example. Once I discover these new genes as well, I can put them back into the M map, so I can benefit from all of that prior knowledge when I'm trying to see what's going on in my sample.
Will – and the knowledge shared is already bearing fruit.
Dan – Approximately 20% of the copper mined in the world is mined using hydrometallurgy. Hydrometallurgy uses strong acids or, more often these days, bacteria to leach copper from the source rock. It's a much more environmentally friendly method. When bacteria bind fine sand particles, they can become airborne, creating a potentially dangerous breathing situation for miners. They can use bacteria to suppress dust.
Will – But what if we discovered a gene that was useful for detoxification, but was in a bacteria that was still harmful to humans overall? That might be OK too.
Dan – Suppose a scientist analyzing data from M-Map discovers a potentially useful gene that could clean up a toxic compound in, say, a mine's soil, but it's not a bacterium that's harmful to humans. exists within. Genetic engineering scientists can transfer the gene into another bacterium and encourage that bacterium to reproduce with that gene. This means that a new type of bacteria has been created that can purify toxins without harming humans.
Will – This is a rapidly developing field, but one that is already showing great potential. And isn't it fascinating to think that the keys to clean energy development may already be at our feet?
Aria – It's so easy to focus on the visible world, and everyone does it in everyday life. Because it has to be done and it's realistic and makes sense. But the more we learn about microbes, the more we realize that this is their planet, and that they are, in fact, responsible for their maintenance and health. They were here long before we were here, and they will be here long after us. Therefore, understanding them means in many ways understanding what gave life to us and our planet and everything we see. And there's something about that concept that I find existentially beautiful.
