The Many Lifestyles Of Muck-Dwelling Microbes

Scientists at the University of Leeds are exploring ways to use magnetic bacteria to build biocomputers of the future. Meanwhile, another group of researchers, reporting in Science, write that they have unearthed deep-sea microbe that live off nutrients from the dinosaur age.

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IRA FLATOW, HOST:

This is SCIENCE FRIDAY. I'm Ira Flatow. For the rest of the hour, weird wildlife discoveries. Flora Lichtman is here to tell us more. Hi, Flora.

FLORA LICHTMAN, BYLINE: Hi, Ira. Pack your bags because we are going on safari.

(SOUNDBITE OF ELEPHANT)

LICHTMAN: Actually, it's mostly little game today, starting with bacteria that manufacture magnets in their body.

FLATOW: A magnetic microbe?

LICHTMAN: Yup. And researchers at the University of Leeds are trying to turn these bacteria into biocomputers. So traditionally, computer hard discs use tiny magnets to store information. And the idea is to use these bacteria or magnets made by these bacteria to store data instead.

FLATOW: And here to explain how that would work is Dr. Sarah Staniland, a lecturer in bionanoscience at the School of Physics and Astronomy at the University of Leeds. She was co-author - a co-author of a study on the subject published in the journal Small. She joins us from Leeds, U.K. Welcome to SCIENCE FRIDAY.

SARAH STANILAND: Hello there.

FLATOW: Hi there. How did you use magnetic bacteria to create the beginnings of a biological hard drive?

STANILAND: OK. So what we've actually done is not use the bacteria themselves, but what they have is they have proteins within them that can manufacture these nanomagnets within them, very precisely - precise size and shape. So what we've done is actually extracted and used one of the proteins that does this, and we've actually used that to make an array of nanomagnets on a surface which is then a proof of concept that can be used for a hard drive.

LICHTMAN: So you harvest the protein, and the protein does the sort of magnet manufacture for you?

STANILAND: Exactly. That's right. I mean, what nature is amazing for is that it - if they can have, I suppose, millions, billions of years to experiment through evolution so it's really got a really perfect and elegant way of manufacturing things on the nanoscale. So within these microbes, these proteins can actually control the size and shape of them, really perfectly. So we'll extract that particular protein, and we'll use that on the surface of - actually gold surfaces to make an array of nanomagnets.

LICHTMAN: Let's step back a little bit. So remind me how a traditional hard drive works. Those use little magnets too, I guess.

STANILAND: Yes. So what you have - we have a surface, and it's granulated. And you pattern it with a magnetic signal. And then you obviously read that magnetic signal back. But what we're trying to strive for is if we can use single domain to have the smaller, smaller magnets we can use, then obviously the more density you can fit on a surface. So that's really the driving force - that's the driving force to make all these components smaller. And if we can make them perfectly sized and shaped, so we can use what they call single domain nanomagnets on the surface. And that's something called bit-patterned media where each bit is one tiny magnet.

FLATOW: And so how many more bits can you put on the surface than you could on a hard drive?

STANILAND: Oh, to be honest, I'm not an expert in making hard drives. I'm a material - I'm just making the nanomaterials. I couldn't tell you exactly what is going on in the hard drive at present. But what I'm - I know the bit-patterned media isn't currently a reality in our computers now, and that's something we're striving for.

LICHTMAN: And your - the version that you've made already - so you've actually - you have a prototype of sorts, right?

STANILAND: Well, no. The journal in Small will show you that what we've done is we've got this protein. Now, this protein was actually discovered way back in 2003. Some of my co-workers in Japan, a group there, they found that when they took out the magnets from the magnetic bacteria, they found the protein really tightly attached to the magnetosome, the actual magnetized particle. So they extracted them off, and they grouped lots of it and put that into a chemical precipitation of the particles and found they control the size and shape.

So that that was all ready known. What we've done differently in this study is that - (unintelligible) who's the lead author. She spent her Ph.D. trying to and achieving taking this protein to a surface in the patterned array. So the array that we have is actually on a microbe meterscale, so it's actually too big to be a bit-patterned media as yet.

FLATOW: So...

STANILAND: (Unintelligible) for a hard drive, but we currently have a new Ph.D. student making patterns, as we speak, that are nanoscale. So the aim is to have a single particle per pattern.

FLATOW: How close are you to making a practical memory device?

STANILAND: Well, interestingly, to finish it off, cause my - the Ph.D. student who's just finishing, Jo(ph), who's the lead author. She's actually just won a fellowship to spend two years developing this exact science. So she's actually going to spend some time in the States working on this. So hopefully, we'll have some sort of prototype from her in a couple of years. But I think we're a long way off maybe having it a reality in all our computers, maybe more like 10 years.

LICHTMAN: Do the magnets change if you give the bacteria something different to eat?

STANILAND: Actually, it's funny you should ask, because I started this research because I was interested in trying to change the composition of the magnetite particles. So I was really interested in magnetic bacteria because I'm a chemist, to start with. I wanted to synthesize perfectly-shaped particles. And I saw these bacteria did that for me, but I really wanted them to have a more coercive(ph) magnetic field. I - they make harder magnets. And they do that if you add cobalt.

So I just, very naively as a chemist, thought I could feed these microbes, not just iron, but also feed them cobalt and see if they take it up. And they did take up a small amount before they got poisoned. So that was quite a big study that showed that this is the first time you could actually add something different to the binarization process. And you get these enhanced namomagnets. So the (unintelligible) themselves within the bacteria were actually - that was cobalt. So they were harder magnets.

FLATOW: So it's good that you were ignorant enough not to know, not to ask that question.

STANILAND: Exactly.

(LAUGHTER)

LICHTMAN: Why do the microbes have this ability? Do you have any sense?

STANILAND: It's a really good question. Most times when I give a talk about this subject, people do always ask that, because they are intriguing little things, and they're beautiful to look at. I mean, if you can pull up an image on the Internet, if any of your listeners there, you'll see the - like, wiggly worms with all this, like, spine down them, of magnetic particles. And they were first discovered in the late '70s by an American scientist called Blakemore. And he saw they're magnetic, so he proposed - quite fairly - that he assumed it was navigation, because they actually grow at a very specific oxygen tension. So they'll be in a pond, possibly even outside your studio. You might find some. They're very near the sediment in the pond, so quite near the bottom. Actually...

FLATOW: Yeah. You here on 5th Avenue, I think.

(LAUGHTER)

STANILAND: But they grow without a very chemistry-defined area, with only 1 percent oxygen. So it's supposed that they would use this to navigate to that area. But then they don't actually make the magnetosomes at higher oxygen tension - so aerobically, when there's normal oxygen, like, in the air. So I don't think that that's actually probably true. So there are a lot of different theories floating around. People thought that it might be because iron is quite toxic. It's a way of storing iron out of the system. But then when there's actually very low amounts of iron, they will scavenge iron. So like my cobalt experiment, reducing the iron, and they made magnetosomes. So I don't think it's that, either. I'm angling more towards metabolism. It might be something to do with them getting energy from the surface. But I genuinely don't know. It's still mystery.

FLATOW: That's - we love mysteries in science. Thank you very much, Dr. Staniland, for taking time to be with us.

STANILAND: That's all right. Thank you.

FLATOW: You're welcome. Dr. Sarah Staniland is lecturer in Bionanoscience at the School of Physics and Astronomy, University of Leeds, and co-author of the study published in the journal Small.

(SOUNDBITE OF SPLASHING)

LICHTMAN: Now diving to the bottom of the Pacific Ocean to meet a colony of microbes that got stuck in the mud. Nice work, Ira.

FLATOW: Thank you.

LICHTMAN: Eighty-six million years ago is when it happened, when the dinosaurs were roaming the planet. And to make matters worse, this community of microorganisms hasn't gotten any fresh food since they sunk, and yet they're still alive - although life is pretty slow down there. It takes one of these microbes 10 years to use as much oxygen as we inhale in a single breath.

FLATOW: Here to tell us more is Dr. Hans Roy, a microbiologist at Aarhus University in Denmark. He was part of the team that unearthed this deep-sea microorganism, and is co-author of the study published in Science. He joins us from Denmark. Welcome to SCIENCE FRIDAY.

HANS ROY: Thank you.

FLATOW: Doctor Roy, you found some really old communities of microbes, didn't you, when you were looking?

ROY: Yes, we were probing the sediment, and saw this sediment sitting, like, 6,000 meters below the sea and 30 meters into the sediments, and lots of them.

LICHTMAN: Is it clear how - when you say that these communities are millions of years old, does that mean - what does that mean, exactly? How old is an individual in this group?

ROY: This is a - this is, I think, one of the most intriguing questions that we are getting here, because we have really no way of judging the age of the individual organisms. We know that the community is that old, and we know that due to this very slow metabolism, that the actual cells must also be very old. But we cannot really extrapolate the age from calculating their - from their metabolism, because the only thing we have to compare it to is something that grows very fast.

Normally, we would think about how microbes grow and what their energy budget is. We kind of ignore their idling metabolism or their maintenance metabolism, because it's such a small fraction of their growth. And that's probably a good way of doing it if you have something that will double its cell every 20 minutes. But if it's something that's not growing at all, you just cannot ignore that maintenance energy. And then that means that we have really now way of judging how old the individual organisms are.

LICHTMAN: Do we know what they're eating down there?

ROY: The only thing that they really have access to is just, you know, the remnants of algae and the shells of crustaceans and whatever fell down through the water column 86 million years go and got incorporated, like, maybe half a percent of organic content, organic carbon in these sediments. That's what they had from the start, and that's what they're still eating.

FLATOW: Very slowly, I imagine, then. I mean, it's 86-million-year-old food.

ROY: That is exactly - that is 86 million-years-old food, and it has been undergoing various chemical processes and it's been polymerizing and turning into something that's very, very complex and very, very hard to eat. And I don't think it's because they're really - that they are clever and they're saving it, but it's something that's very, very hard for them to actually break down.

LICHTMAN: When they, I mean, when they sunk down there, presumably, their metabolism was faster, right? This has to - I guess that's the part that confuses me. Did they go down with a slow metabolism, or this is an adaptation once they were down there, the ones that survived, stuck around?

ROY: That is another one of these things that we don't know. Up at the surface, there's about 1,000-millionth(ph) in a cubic inch. And when we get down 30 meters below, 86 million years later, there's maybe 10,000 per cubic inch. So you could say, well, is that then a small fraction of those that once were? Or is it somebody who has been then - a living community that has been keeping itself alive and dividing for that many years? We - it's hard to imagine that they should be 86 million years old. So we kind of - we imagine that these are, indeed, active organisms. They are just adapted to this very low rate of metabolism. (unintelligible) where they come from.

FLATOW: Dr. Roy, thank you very much - it's fascinating - for taking time to be with us.

ROY: Thank you.

FLATOW: Doctor Hans Roy, microbiologist at Aarhus University in Denmark. He was co-author of a study published in Science. I'm Ira Flatow. This is SCIENCE FRIDAY, from NPR.

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