The Lives of Extremophiles

As often as she can, Northup and other members of SLIME (Subsurface Life in Mineral Environments), a loose affiliation of cave scientists working on geomicrobiological interactions in caves, don their caving gear and descend into caverns like Lechuguilla and Mexico's Cueva de Villa Luz ("Cave of the Lighted House"). They go in search of bacteria that gobble up hydrogen sulfide gas and other noxious chemicals like we do bread and water. As this interview reveals, she and other SLIME members are finding that these bizarre creatures may hold clues not only to the earliest life on Earth but to the possibility of life in outer space.

A world unseen

NOVA: What drew you to working on cave extremophiles?

Northup: I used to work on cave crickets and things like that, and if you work on insects, occasionally you have to do things to them that aren't very nice, and it's very obvious you're causing them pain. I can't hear microbes scream.

More importantly, I was taking a class at the University of New Mexico on microbial ecology, and the instructor gave me a bunch of little tubes and said, "Why don't you get some water samples out of Lechuguilla, and let's see what's in there?" Well, you look at these in the scanning electron microscope, and there are all these really cool shapes. These are things you can't even see, but they are affecting perhaps how the cave is shaped, formed, dissolved. And some microbes or their products can kill you.

To me, it's fascinating that there's this whole world that is mostly sight unseen, with microbes that are like little puppeteers manipulating things behind the scenes. And extremophiles take it to another level. They can live where we can't live. They can do things we can't do.

"I can go on and on about blue goo and slime balls and 'snottites.'"

Are these cave extremophiles completely outside of the carbon-based system found on the surface?

The ones in Lechuguilla are mainly but not totally outside the surface world. There's obviously no sunlight, and some of these organisms are 1,000 feet or more below the surface. But they get some indirect products from sunshine. Water seeps down through that 1,000 feet of rock and brings a little organic carbon from the surface. Cueva de Villa Luz has some skylights and a stream running through it, so the surface contributes to the food base in that way.

Yet some of the organisms that we study, like the sulfur bacteria in Cueva de Villa Luz, derive their energy from inorganic substances such as hydrogen sulfide, the gas that smells like rotten eggs. So in that respect they are independent of the sun.

Many field biologists become quite attached to their research subjects. Do you feel similarly about extremophile microbes?

Yeah, I get pretty attached to them, because I think they're pretty cool-looking. Some of the ones I see have long stalks; they look like sperm on testosterone. Some of them look like braided ropes. They're really cool. And the stuff they produce is just incredible. I can go on and on about blue goo and slime balls and "snottites," the slimy bacterial stalactites found in Cueva de Villa Luz. My husband teases me about whether he should start enticing me with manganese slime.

What is so cool about snottites and manganese slime?

Well, take snottites. When you're in Cueva de Villa Luz, you see these things that look just like a two-year-old's runny nose, and when you look at them with the scanning electron microscope, they're nothing but bacteria and mucilaginous products and a little bit of minerals that get produced from these microbes. They're so tiny that we can't see them, yet they can build up these snottite structures that can then, if you use your imagination a bit, turn to rock and represent some of the formations we see in caves such as Lechuguilla.

Do any of these extremophiles have medical benefits or other uses for society?

They do, and we're just starting to look into that. This is not restricted to extremophiles. I have a colleague, Larry Mallory, who works in Lechuguilla Cave and elsewhere. His thought was that because these bacteria live in an environment where there's not a lot of organic carbon—that is, there's not a lot to eat—it may be to their benefit to produce compounds that would keep their neighbors at bay. I call them "microbial assault weapons."

Larry thought if they produce these secondary metabolites, as he calls them, those are the ones that are often useful in treating human disease. So he has cultured hundreds of different strains, maybe even thousands, and he and his colleagues have tested those for their ability to kill cancer cells and malaria and stuff like that. And they've gotten really positive results.

The microbes' environment helps to select for organisms that produce some of these compounds. It's a great thing for telling people why they should be careful about contaminating caves.

How life began?

Are you finding new species all the time, and are they very different from known bacteria?

We do, and they are. I produce what are called phylogenetic trees. Each is like a family tree, and it tells me how the genetic sequences that I pull out of microbial material from the caves fit in with known life. So, for instance, right now I'm looking at a family tree of the Archaea that we produced. [Editor's note: The Archaea are extremophiles and other unusual microbes that are so different from bacteria that Carl Woese of the University of Illinois assigned them their own domain on the tree of life, along with Bacteria (organisms with no nucleus) and Eukarya (organisms, including humans, with nuclei).]

About ten years ago it was discovered that there are low-temperature or mesophilic Archaea—ones that live at, say, room temperature—that no one's been able to figure out how to grow in pure culture. We have a whole bunch of those in Lechuguilla. From a little thimble-full of material I collected there, I have a family tree that spans two Kingdoms and has a Family-level grouping that's off all by itself. Its closest known relatives are some other uncultured microbes from the South African gold mines.

Does this suggest a great antiquity among these microbes?

I would like to say that, but I've been told by people who are more expert in this than I am that that's really going out on a limb. These microbes share a common ancestor with marine bacteria, which makes me speculate that maybe these were around when that area of New Mexico was under the sea. But that's really speculation, I've been told. Wild speculation!

"If you live at pH 0, to us that's extreme. But if you think about it from the microbes' point of view, it's just everyday."

Is the theory of the Archaea forming a third domain of life fully accepted by scientists?

It's accepted by many but not all. Many of the scientists I work with accept this as the way, and it's now starting to appear in textbooks. But there are some fairly well known critics of it, including [University of Massachusetts, Amherst, microbial biologist] Lynn Margulis, who looks at the tree of life differently. Which is healthy. We find out all the time that we are wrong.

Carl Woese has also argued that extremophiles are closely related to the very first single-celled organisms that arose on Earth and therefore may represent the most ancient form of life. Did life begin as an extremophile?

I believe that it did. When you look at the tree of life, humans are out at the tips of the newest branches; we are a fairly new innovation in my view of the world. If you look farther down the tree, more towards the roots, the organisms that are down there, which we believe are more ancient, tend to be thermophiles and chemolithotrophs, those that derive their energy by oxidizing inorganic chemicals.

By thermophiles do you mean heat-loving organisms?

Right. And they tend to be extreme thermophiles, those that exist above 80°C [176°F]. They like it really hot. From what we know about conditions on the early Earth, it was probably hot, and there was a lot of ultraviolet (UV). It was a reducing atmosphere, so things like hydrogen sulfide as an inorganic source of energy are probably what was available to use. So I think some of the evidence from the tree of life and what we know about the way the Earth likely was at that time support this idea that the first microorganisms probably were extremophiles.

What it means to be extreme

How exactly would you define "extremophile"?

An extremophile is an organism that lives in conditions that are outside of a normal range. So, for instance, above 40°C [104°F] is considered a thermophile and above 80°C [176°F] is a hyperthermophile. We have ones that like to live in really cold temperatures, near or below zero. We have ones that live in different pHs, the so-called acidophiles. That is what we have in Cueva de Villa Luz, microbes that produce sulfuric acid and live in an environment that's just like the inside of your car battery.

"Extremophile" is a very human-centric term. If you live at pH 0, to us that's extreme; we couldn't survive in that. But if you think about it from the microbes' point of view, it's just everyday.

So what are the most "extreme" of extremophiles?

The highest temperature that I see routinely—though this waffles a bit in the literature—is 113°C [235°F]. In terms of pH, I think they've found organisms that can live below zero pH. I realize that sounds impossible, but there are actually negative pH values. And there are ones that live, I believe, at 13 and 14 pH, but I am less familiar with them.

And there's an organism, Dinococcus radiodurans, that can live at really high UV concentrations. Carlton Allen of the Johnson Space Center in Houston once did experiments to determine how he could be sure that future space missions weren't bringing back organisms from Mars to Earth. He subjected organisms to really high UV rates, and Dinococcus could still grow. He found that he had to up the amount of sterilization, because this organism can live at really high radiation levels.

Does that suggest it or other extremophiles could live on Mars?

I honestly believe that there could be organisms in the subsurface of Mars, especially if, as has been suggested lately, it has water.

What about on Jupiter's moon Europa, which has been suggested as a possible haven for microbial life?

That's a fascinating question, considering that they think Europa could have liquid water under its surface of ice. I certainly think it's possible. Why not? The chemical conditions could be similar to what early Earth was like.

How deep in our planet have extremophiles been found?

I think it's like seven kilometers [4.3 miles] or more down. You're probably familiar with the work of [Cornell University professor emeritus of astronomy] Tommy Gold, who has suggested that he thinks there's as much biomass below the surface of the Earth as there is above the surface. We don't have a lot of proof for that yet, but I suspect that he's at least partially right.

What we're seeing is yes, there are lots of organisms deep within the Earth, but maybe there aren't as many as we might have thought at one time. And I think that we don't have a good handle yet on how active those guys are, how dynamic the ecosystem is. Many organisms that live in low-nutrient caves, for instance, likely live life at a slow pace.

"Cueva de Villa Luz is actually much more of a danger than Lechuguilla. You can die really easily in that cave."

You mentioned earlier that there are low-temperature Archaea that no one has been able to grow in pure culture. What does it mean not to be able to culture something?

Well, it's like we've got this whole grocery store, and we're pulling things off the shelves and putting them on the microbes' dinner plates, and they're turning up their noses. We just haven't gotten the environmental conditions correct. We have it too hot or too cold or too much salt, too much this or that, so they don't want to live. It also might mean that they require another organism to live together, in which case we may never get pure culture.

What is the most exciting avenue in extremophile research at the moment?

Well, I think in the study of the origin of life the discovery that organisms have done what's called lateral gene transfer, where they just swap genetic material all the time, which has sort of obscured the roots of the tree of life—to me, some of that research is incredibly fascinating.

From a human point of view, the fact that these organisms that we're discovering all the time can do things with chemical bonds that are very difficult for us to do. They can go in and break some of these really difficult chemical bonds and make products that are hazardous to our environment or benign. The idea that biotechnology can help us clean up our environment with microbes, to me that's really exciting. It might give us the opportunity to undo some of our folly. It may also give us the means to produce drugs that will help us out.

It's hard to pinpoint one avenue, because there are so many exciting things going on with microbes. E.O. Wilson says at the end of his autobiography Naturalist that if he had it to do over again, he'd be a microbial ecologist.

Captivated by caving

Do you have to be a spelunker at heart to be a cave scientist?

No, but it helps. By the way, cavers call themselves cavers, not spelunkers. People who don't cave call them spelunkers. It's reverse snobbism, as far as I can tell.

Are you an active caver?

I've been a caver since 1966. I started caving in college.

So what was it like to work inside Cueva de Villa Luz?

You know, it's really interesting. I am terrified of heights, so Lechuguilla is nothing but a terror experience to me the whole time. Yet Cueva de Villa Luz is actually much more of a danger. You can die really easily in that cave, because our respirators are only protective against hydrogen sulfide, yet [geologist] Louise Hose has discovered that there is carbon dioxide at high levels, there's formaldehyde, there's sulfur dioxide, there are lots of other things that our respirators don't protect us against. And, of course, you can die from hydrogen sulfide in a matter of seconds.

And yet you still go in.

I do, and I love it. I have no sense of danger there, because everywhere I look there are these colonies of bacteria—blue, red, yellow, white, orange—that are like a terrestrial version of the Yellowstone hot-spring pools. In caving you usually have to really scrape to get lots of organisms, but in Cueva de Villa Luz it's nothing but goobers of bacteria. You don't have to work; you just have to turn around. Everywhere you look there's some really cool process. It's like a whole other world.