Science Friday - Metal-Absorbing Plants Could Make Mining Greener | A Tiny Fern's Gigantic Genome

Episode Date: June 12, 2024

Plants called “hyperaccumulators” have evolved to absorb high levels of metals. Scientists want to harness them for greener metal mining. And, a little fern from New Caledonia is just a few inches tall, but its genome has 160.45 billion base pairs—50 times more DNA than a human.How Metal-Absorbing Plants Could Make Mining GreenerScientists are exploring a somewhat unusual green energy solution: mining metals from the earth using plants.Typically, if soil has high levels of metal, plants will either die or do everything they can to avoid it. But, one group has taken a different path: evolve to be able to safely absorb large amounts of the metals. These special plants are called hyperaccumulators. And their ability to suck metals like nickel from the earth is called phytomining.The Department of Energy’s Advanced Research Projects Agency-Energy announced in March up to $10 million in funding for phytomining research.Ira talks with Dr. David McNear, professor of plant and soil sciences at the University of Kentucky, about these fascinating flora and their promise as a greener option to metal mining.A Tiny Fern Has The Largest Genome Ever DiscoveredScientists just discovered the largest genome of any living thing on Earth, and it belongs to a small, unassuming fern called Tmesipteris oblanceolata. If you were to split open one of its cells and unwind the DNA that’s coiled up in the nucleus, it would stretch out more than 300 feet—taller than the Statue of Liberty.Scientists reported the finding last week in the journal iScience. The fern is only a few inches tall and is found on the island of New Caledonia in the Southwest Pacific. Its DNA is made up of 160.45 billion base pairs—50 times more than the human genome.This finding has left scientists scratching their heads, wondering how and why a fern ended up with so much DNA. Ira Flatow talks with co-lead author of this study Dr. Jaume Pellicer, evolutionary biologist at the Botanical Institute of Barcelona, about this research and why this fern’s DNA is so puzzling.Transcripts for each segment will be available after the show airs on sciencefriday.com. Subscribe to this podcast. Plus, to stay updated on all things science, sign up for Science Friday's newsletters.

Some plants can pull metals out of the earth. Could this be a green solution to mining? I'm a researcher, so I guess I was saying I'm skeptically optimistic. It's Wednesday, June 12th, and you're listening to Science Friday. I'm sci-fi producer Rasha Auretti. Plants, of course, can suck up water and nutrients through their roots, but some have evolved to absorb large amounts of metals like nickel. And scientists are wondering, could we tap into the...

that power and use plants to mine for metals. We'll discuss if and how that could work. But first, a humble organism just broke the world record for the largest genome ever discovered. Here's Iroflato. Scientists just unearthed the largest genome of any living thing on Earth. That means if you split open one of its cells unwound the DNA that's coiled up in the nucleus, it would stretch out more than 300 feet. That's taller than this Statue of Liberty. Now, any guesses as to whom this giant genome belongs? You might be tempted to say maybe a complex being like a person, a human, or a behemoth like a blue whale or a giant squid, or maybe your mind

went to a fancy fungus. Nope. A study in the journal, Eye Science, says that the new record holder is a fern. Yes, a fern found on the island of New Caledonia and the southwest Pacific. To put it in perspective, one of this fern cells contains more than 50 times more DNA than one of ours does. Wow. So how did this tiny fern end up with a giant genome? And what cost? Let's talk about it. Joining me is a lead author on the study, Dr. Jalmei Piathera, evolutionary biologist at the Botanical Institute of Barcelona. Welcome to Science Friday, Dr. Paiythera. Thank you, Wara. It's a pleasure for me to be here. How excited were you by this discovery?

Well, we were absolutely astonished when we found out how big this genome was. Actually, you know, scientists have been working on this field for a long time to expand our understanding of plan genome sizes across a tree of life. But, I mean, this discovery really, really shocked us because we weren't expecting something that big. So how big is the firin to describe it for us? Well, this frame is very small. It's about 10 to 15 centimeters. I don't know exactly how an inch would be because, you know. It's like four to six inches.

Yeah. Yeah. Very, very small plan that you would probably, if you were just walking on the woods, like not focusing on finding this plan, you probably would step over it. Because it's like nothing that would catch your eye. It has no flowers. It's all very greeny. It's like kind of a fish bone structurally.

It doesn't even look like a traditional fern. that you might have in mind. So how did it catch your eye? I mean, what made you not step on it? Yeah, well, I've been always interested in plant genome size diversity and what are the consequences of this trait in the evolution of plants. So we are interested in analyzing giant genomes because they are the exception rather than a rule,

and that's make them very interesting to me. Most plants have very small genomes, and only a very few groups of plants have giant genomes. One of them is mesiptorys and its sister genus Silotum. So how did this sort of small fern end up with so much DNA? Well, that's a great question. That's a one million dollar question. We don't know yet.

It's still actually an unresolved question. What is exactly the biological meaning of these astounding plant genome size diversity? And this extends into how exactly plants expand their genomes. At a first glance, for example, we can. not see any particularity or any need for this plant to accumulate such dramatic amounts of DNA in its cells, at least not from a functional point of view. You mean it doesn't need all that DNA, is what you're saying? No, it doesn't because the actual functional DNA, which is the one that contains decoding

protein genes, is very small, and it's comparable to plants with very small genus. So the rest is repetitive DNA, which for a long time, scientists call like junk DNA, because it apparently had no function. Now we know it has some roles to play, but it's very, very repetitive, and it has no, it's not the main function. Right. Well, having such a big genome, that's sort of a bad thing for a plant, isn't it? Yeah, it's mostly a bad thing.

And this is because there are several costs that increase. are associated with maintaining and functional large genome. And this is, for example, the requirement for nutrients. For example, nitrogen and phosphorus, which are the main essential contributors to DNA. A plant with a large genome requires lots of these elements, and sometimes they are not available in the environment. And also, for example, every time a soul divides, it needs to copy the whole strand of DNA.

So this is a lot of work to replicate every time the cell. So that slows down their life cycles. So this is a puzzle then about why this has so much DNA? It is indeed, yeah. We know that most plants are very efficient to remove it. So all these repetitive DNA sequences that populate the genome have, some of them have the ability to move around and replicate themselves. So the plant, even if it doesn't have a brain, is very clever.

it has a very efficient machinery that as soon as these elements amplify, they are detected, they are labeled, and they are targeted and removed from genome. But we don't know yet why in some plant groups these processes are not as efficient. Do we know why then this plant has more DNA than animals, let's say? Oh, wow, we don't know yet. We don't know yet. It might be that there is some sort of selective advantage for this fern that lives in a very particular, like, stable environment restricted to it, and it has found the right conditions to

cope with having such a big genome. Does this discovery challenge anything we know about genomes or plant DNA? Well, it will definitely. I mean, not just the discovery, but it will challenge how do we see the structure of the DNA in the nuclei? Because from a DNA sequence point of view, we have the technology to produce massive amounts of DNA sequences. We have the potential, the computational power to analyze and assemble probably these genomes, but we don't know yet how the 3D structure of the nuclear stands up, what are the intimate relationships between all the molecules that enable the integrity of this nucleate to be maintained given the vast amount of DNA. And for that, we will need like

high microscopy technologies that probably will help us understand a bit more. Because right now, we are pretty ignorant about the overall structure. How is this maintained and regulated? Are you just amazed that you could have stepped on this firm that you didn't and missed the whole discovery? If I'm honest with you, if I had been walking on the woods, without looking for it, it would have gone missing. And that is something I have to acknowledge to our new Caledonian colleagues because they were critical contributors to this work because they showed us where these plants grow

and help us to make this story successful. Otherwise, it would have been unknown. You know, noblist physicist Richard Feynman once talked about the beauty of flowers and plants and how you might look at the outside and love it, but there's also a complicated beauty that goes on inside the plant that needs to be discovered and amazed that also. Yeah, and this is the case. This very humble plant hides a very, very powerful and shocking secret in its genome.

Yeah. Well, thank you very much, and congratulations on finding this. Well, thank you very much for reaching out, and it's been an absolute pleasure talking to you today. Thank you, Dr. Jomei Piafthera, evolutionary biofuscary. at the Botanical Institute of Barcelona. Hey, Ira here with an update that Cephalopod Week is just around the corner, and it's going to be inc credible. All squitting aside, I'd like to invite you to join the Cephalop Party

by sponsoring some virtual cephalopods. Here's what I mean. Our talented team of digital producers has built a sea of support on our website, giving each of you the chance to sponsor a Cephalopod for just $8. With each donation, you'll get to pick from one of eight beautifully illustrated sea creatures, which will post on our site, along with your first name and city. We're aiming to raise $8,000 here, folks, which will go to support all the great work we do at SciFri. So we do hope you'll conscriptor making a gift.

Sorry for all the puns. We're cracking up over here. Just head to ScienceFriiday.com slash see of support to join us and help us reach our $8,000 goal. Again, that's Science Friday.com slash see of support. On my Rofleto, squitting you farewell. And thanks.

You know, typically, if soil has high levels of metal, plants will either die or do everything they can to avoid it, but there is another option. Evolving to be able to safely absorb high amounts of the metals, and these special plants are called hyperaccumulators,

and their ability to suck metals like nickel from the earth, is called phytomining. Joining me now to talk about these fascinating flora and their promise as a greener option to metal mining is Dr. David McNier, Professor of Plant and Soil Sciences at the University of Kentucky in Lexington. Welcome to Science Friday. Hi, Ira. Thanks for having me. You're welcome. Can you explain how plants absorb metal from the soil without causing harm to the plant? That's a good question, Ira, and actually something that we're still trying to figure out. So you mentioned, you know, these plants grow in soils and they have a couple strategies that they've evolved.

One of those is to exclude the metal, so don't take it up at all. And that happens at the plant soil, you know, root interface. But the other option is to take it up and take it up in large quantities. So the mechanisms of that process, you know, we're still trying to figure out. Yeah, yeah. And where do they store it when they take it up? So mostly, you know, they store it in the leaves, really in the skin of the leaf, if you will, the cells on the outside of the leaf, they have these compartments like a closet. It's called

a vacuil, and they take that metal up and they store it in those compartments in the leaf. Wow. And about how many plant species are actually able to do this? There are probably upwards of 500 species that have been identified and counting. That's, you know, hyperaccumulate metals. There's about 400 of those that are described mainly for nickel hyperaccumulation. What are other kinds of metals? Yes, so you have plants that take up zinc and cobald and arsenic, selenium. So there are a variety of plants out there that take up a variety of metals.

And how big are these plants? Are they giant trees? What do they look like? So generally, the plants that I'm normally working on are fairly small. You know, they might get as high as knee or waist high. So they're not massive plants. They inhabit an environment that's pretty harsh. Many of those are found in dry or Mediterranean climate,

so they have to be drought-tolerant. So they're not huge plants. They're not corn. They're not sorghum or some of these grasses. Yeah. Are they all related species? So there's probably 42 different plant families that these hypercumulators come from. The main ones are brassica-type plants,

or mustard or, you know, rabbitopsis might be a variety that you've heard in a lot of research that people do. And so the plants accumulate the nickel or the other metal, they store it in their leaves. Then how do you go about getting the metal out for using it, you know, for other purposes? So the agronomy, and you mentioned phytomining. I think that the common term now at least was coined in 2013 is agro mining. So, you know, this is the process where you grow plants that hypercumulate metals. And there's agronomy involved or the production.

You have to grow it. You have to harvest it. Right. And then you have to extract that metal from the plant. Right. So you have to, well, once it's grown and harvested, you have to send it out, so to speak, to get the metal removed? Yeah, it's a pretty neat process.

There's a couple ways in which you, you know, the plant is beneficial in that process. So a farmer can go out and bail this crop. of nickel into a bale, a classic hay bale, but this is a nickel bale, and they can burn that for energy. And then they take that ash, that ash that contains now about 20% nickel, and they can using, you know, refining processes that have been developed for rock with metal in it, they can then, you know, extract the nickel from the ash. Did you say that the plant is actually 20% nickel? So the plant can take up, ideally, for a phytomining or agromining operation, you would like that plant to take up 2% and some plants take up more. But after it's been bailed and burnt, the ash that

comes from that plant can have upwards of 20% or more nickel in it. And this is, this is a significant amount? This is a significant amount. And the beauty of that ash is, you know, it's a plant. It's a carbon-based life form. So there aren't many other impurities in there. Like when you go and mine rock, you have silica and all these other elements that you have to try to get rid of. But when you burn this plant and, you know, it's just carbon and nickel essentially. Right. How much energy does it take to do mining in the conventional way, then do it with a plant? Yeah, that's a great question. That may be a little bit out of my wheelhouse, but I think that is actually what has sort of raised the interest in phytto mining, particularly from the Department of Energy in the U.S., is that, you know, current

mining and extraction processes for mainly low-grade orders is a pretty energy-intensive process. So, you know, compared to, I think, nickel's the fourth most CO2 emitted for a unit of nickel extracted in the mining process. That's followed, you know, platinum gold and then steel and then it's nickel. So they're pretty energy-intensive processes. Is there something that was found out recently or have we known about this for years? So I think that the process of, are the idea or the identification of plants that take up metals, I think first occurred in 1945, where they identified at a plant where they had a whole bunch of nickel in it. The term phytomining or the concept of phytomining was really, I guess, brought about in 1983 by some researchers at the USDA here in the United States.

And they proposed this idea of metal hypercumulator as a plant species to use for soil and remeastern. mediation in that case. But then the idea of extracting the metal from that plant and recovering it. I know that ARPA-E, the federal government program that invests in research, announced in March up to $10 million in funding for more phytomining research, you know, to the average person that sounds like a lot of money, but to researchers, it's not a whole lot of money, is it? You know, spread across several folks, you know, several researchers, it's not, but it is nice You know, as someone who did their PhD research on metals and soils and hyper-accumulating plants and have spent my academic career trying to find funds to support that research,

it's nice to see this resurgence of interest in plants as a mechanism for extracting metals from soils. You know, a lot of the impetus from the DOE was from the carbon footprint of conventional mining. But I think greater impetus for, you know, your listeners is the batteries and the drive. that we need more of these metals to produce the electric power vehicles and electric storage. Huh, that's a really interesting point. And my question about that, are we thinking of whole fields of plant that get harvested for the metals in them, or do we plant them in areas where there's a lot of nickel that we know of is in the ground and we want to get it out? I think people are thinking all of the above. So, you know, these soils that have a lot of nickel in them, if they have been

farm, they are typically very low producing fields. They're not very agronomically productive. They're not producing much, you know, feed or fiber or fuel. If you could grow a crop of nickel on those soils, that would be great. You have to think about there are widely dispersed regions across the world that have soils that are naturally enriched in metals. Those are sensitive environments. They're unique environments. I don't think you'd want to go plowing over all of these soils and start growing nickel in them. But there are some places where, again, if they have been already put into production and they need an alternative thing to do on that land, that might be an option. But also, I will just add that, you know, there have been places where there have been contamination around

smelters or historic mining operations where these plants could be employed to help remediate, but also remove metals from those soils. And is it possible to tweak the genome of these plants, to make them better miners at what they're doing? I would say certainly, yes. There is a way. I mean, that's the science of gene editing, I think, could certainly play a role in this process. There's obviously some regulation issues you have to deal with down the road. But so little focus has been put on metal hypercumulation as, you know, towards agro-mining.

I mean, we have, if you think about it, right? Corn used to be a wild species that we domesticated and now we grow in mass. population. So if focus is put on, you know, developing either conventional breeding or like you're saying gene editing to get a plant that's bigger, that takes up more metal, that could be beneficial. But that's part of probably what some of these folks who are getting this grant are going to look at. Well, what about the unexpected consequences? I'm sure there must be some ecological concerns, right, about planting fields of hyperaccumulators to mine out the metals. No, for sure. And, you know, the area or the of phytal mining or as an industry has sort of had some fits and starts and mistakes, really, where we've taken, some folks have taken, you know, non-native species and started planting them in places where there's nickel-rich soils and they've escaped. So they've become invasive. So you have, you know, there are certainly ecological considerations. You're also introducing metal from the soil now into a plant. So what impact does that have then on transferring metal to this?

grounding environment. So there are still a lot of questions that need to be explored. Good, good points. But you feel optimistic then, though? I'm a researcher, so I guess I'm skeptically optimistic. I mean, about the ability to make a dent and the need to mine so much of this metal from the earth, possibly. Yeah, I think it definitely could play a role. I mean, I think it should play a role in where we're already doing surface mining for some of these metals that you could have from the tailings, you could be growing this plant and also continuing the extraction process of nickel from those, or in regions where smelters or refineries have contaminated large areas

of soil around those facilities. You could, you know, grow crops of nickel there. So that, yeah, there are places. You know, and they talk about the rare earth metals that are needed so much these days, and it's not that they're rare, but it's very difficult to get them out of the ground and process them, could this be one way to do that? Absolutely. Yeah, and I think that's some of the focus. So we're starting at nickel, which maybe is the low-hanging fruit

of metals, because there are so many of them and we have some that are well characterized and have been deployed, honestly, you know, there are places where they are currently phytomining, not in the United States. So I think that with an eye towards what we could learn from this research, learning about the

mechanisms of metal uptake from soils or whatnot could be applied to, then, you trying to find plant species that are taking up and concentrating rare earth elements, exactly. Well, wow, fascinating, Dr. McNair. Thank you for taking time to be with us today. Of course. Thanks for having me, Ira. Dr. David McNier, professor of plant and soil sciences at the University of Kentucky in Lexington. That wraps up today's episode. Lots of folks help make this show happen, including Jordan Smudjick.

Diana Plasker. Santiago Flores. Melissa Mayors. On tomorrow's episode, How Sound Rules Life Underwater. Join us. I'm Safarai producer Rasha Auredi.