IRA FLATOW, host:
You're listening to Talk of the Nation: Science Friday. I'm Ira Flatow. You know, we're all taught about the web of life, the famous food chain where animals at the top devour those below them as sources of food. But this week, researchers report that they have found one place, at least, where that kind of interaction just doesn't occur, and doesn't need to. They've found a bactera - bacterium that is self sufficient.
These bacteria contain all the tools they need to eat, and grow, and reproduce, and these bacteria live virtually entirely by themselves in one little spot. Joining me now to talk about it is Dylan Chivian. He's the bioinformatics lead at the Joint BioEnergy Institute, as part of the Lawrence Berkeley National Lab in Berkeley. And he joins us by phone from there. Welcome.
Mr. DYLAN CHIVIAN (Bioinformatics Lead, Joint BioEnergy Institute): Hello.
FLATOW: Tell us about these bacteria. Where did you find them?
Mr. CHIVIAN: So, these bacteria are found in South Africa, and the way they were found was by going into gold mines, going down 2.8 kilometers, and drilling into fluid-filled fracture that's down there. These mines have to avoid blowing into these fractures, because otherwise, it'll flood the mines.
So they carefully avoid them, but they were able to get a shaft close enough that we were able to drill through into it, and extract out 5,000 liters of water and filter it out, and collect that DNA, and sequence it. And so, when we did this, we discovered from that DNA that there was really only one organism present in that DNA. It's very exciting.
FLATOW: Wow! So what does it live on?
Mr. CHIVIAN: So, it lives on sulfate. So, here at the surface, most organisms are going to be dependent on oxygen as a terminal electron acceptor, and so they extract energy by moving electrons from chemicals that, you know, at which there are higher potential, and move them to oxygen which is greedy for electrons.
Well, there's no oxygen down there, and in fact, earlier before (unintelligible) bacteria changed the atmosphere, there really wasn't any oxygen to speak of. So, organisms had to use and have to use down in the deep, other chemical species, in this case, sulfate.
FLATOW: It sounds very much like the kinds of things we hear growing in the bottom of the ocean in those hot climates, you know, where they're living off the sulfate.
Mr. CHIVIAN: That's right. And in fact, one of the things that's sort of special about this genome, is that it's managed to assemble the blueprint it needs for a single species' ecosystem, partly by combining those genes it's inherited from it's bacterial lineage. But additionally, it's picked up genes from archaea, these extreme halophilic archaea.
So, for example, the nitrogenates it has is - most closely resembles high-temperature archaeal-type nitrogenates. So it can fix nitrogen from the - its environment to that.
Mr. CHIVIAN: It also has genes for the sulfate utilization that look like archaeal genes, and also, it's carbon-fixing machinery. Part of that also looks like that from extreme halophilic archaea.
So it's managed to piece together this solution, but it's done it by combining pieces from different kingdoms.
FLATOW: When you say it's done it by combining pieces, does that mean that it once co-existed with these archaea, or is part of them, or subclass, or lived with them, or came the same time they did? Take a choice.
Mr. CHIVIAN: So - yeah. Exactly. So, it seems like a bit of conundrum, right?
Mr. CHIVIAN: And here it is, living by itself and yet, its solution for this ecosystem is combining things from different organisms. Well, the solution here is actually that the ancestor to this organism, Desulforudis audaxviator, was living in contact with our archaea in the past.
Mr. CHIVIAN: And so, that's when those genes made their way into this genome, and eventually were brought with this colonizing ancestor into this fracture.
FLATOW: Do we then might believe that they were at the bottom of the ocean in these hot thermal vents too, at some point?
Mr. CHIVIAN: Well, so, if we look at scraps of marker genes that you can find flowing out of vents in these various surveys that are done, we actually find that there are not exact relatives, but sort of a little bit beyond the genus level relatives…
Mr. CHIVIAN: To Desulforudis that are coming out of (unintelligible) vents, and coming from fluid seeps from the Gulf of Cadiz off Spain…
Mr. CHIVIAN: And there's similar relatives in Denmark and in an aquifer in New Mexico.
Mr. CHIVIAN: Yeah.
FLATOW: Wow. It's all over the place. And it gets its energy from the sulfur, but you say, it can also fix the nitrogen and the carbon on its own?
Mr. CHIVIAN: That's right.
FLATOW: How long do we think it's been down there?
Mr. CHIVIAN: Well so, it's hard to say. It's fairly diverged from surface organisms, but probably the best minimum estimate would be that isotopic studies of the water date the youngest water, meaning the last time it saw the surface, at at least three million years, possibly up to ten million years. So, it's probably somewhere in that range.
But it's hard to really pinpoint it, because we can't…
Mr. CHIVIAN: We don't know the division rate, we don't know…
Mr. CHIVIAN: It's hard to measure based on the divergence of the genome without knowing several factors.
FLATOW: So, I guess it has no interest in evolving into moving up to the surface anymore?
Mr. CHIVIAN: No, it doesn't really need to. I mean, what it's really found here is - you know, there's this concept in ecology of a niche, right? Well, this is essentially a literal niche. I mean, it's perfectly optimized to this one spot, and so it's coming and taking it over, and it's really happy right where it is.
FLATOW: Do you think that if you'd - that you have found this in this gold mine, it's probably in lots of other places then?
Mr. CHIVIAN: Well, it's hard to say exactly how similar its relatives would be in other locations. You have to sequence the entire gnome, and there's a lot of variation, even in very close organisms, and we're finding this as we sample more and more from different - like in the ocean for example.
But we - numerous very, very similar strains at one level, but if you actually go and look at the genome…
Mr. CHIVIAN: The genes that are present in it are quite different, and so their capabilities are somewhat different.
Mr. CHIVIAN: So, that may be the case.
Mr. CHIVIAN: We may find similar organisms throughout the deep subsurface, but the exact content of the genes, the exact abilities of those organisms may be slightly different.
FLATOW: Why is it living alone? Is it because that's the only thing that can survive under those conditions?
Mr. CHIVIAN: Well, it's a very interesting question. It's not quite possible to say right now. One possible explanation is that you would think that, well, it has these gifted genes from, you know, extreme halophilic archaea, well, why aren't we finding them there? And one possible explanation is that, well, archaea can't form endospores.
This is an ability that's been granted to it from its gram-positive Firmicutes lineage. So, it's possible that it's this combination of bacterial abilities and archaeal abilities…
Mr. CHIVIAN: That has really given it the ability to survive.
FLATOW: Mm-hm. And it's - you gave it a very interesting name, and has an interesting derivate.
Mr. CHIVIAN: Yes. So the genes' name, Desulforudis, is based on the fact that it uses sulfate for its energy, and then the rudis-system morphology, the shape is a rod-like shape. And then the audaxviator, we were inspired by Jules Verne's "Journey to the Center of the Earth." There's a message that inspires their journey, which tells them to descend, bold traveler, which in Latin is audaxviator.
This is a message given in Latin. So descend, audaxviator, and you will attain the center of the earth.
FLATOW: That's a very good place to end, and thank you very much, Dr. Chivian, for taking time to be with us.
Mr. CHIVIAN: Thank you.
FLATOW: Dylan Chivian is the bioinformatics lead at the Joint BioEnergy Institute. That's part of the Lawrence Berkeley Lab in Berkeley, California.