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Cave slime. Credit: Kenneth Ingham, 2001

Cave Slime

By: Stephen Hart
Penny Boston and Diana Northup taking a pH or ORP measurement in the Ragu passage
Penny Boston and Diana Northup taking a pH or ORP measurement in the Ragu passage (Cueva de las Sardinas. Tabasco, Mexico).
Credit: Kenneth Ingham, 2001

Cold, slimy and pitch dark. Just add some acid and you'll make Diana Northup and Penny Boston happy.

Northup, Boston and their colleagues -- the self-named slime team -- study cave-dwelling microbes. In some cases the bacterial growth is so abundant the walls drip slime. What's making this mucus-like substance?

"The snot? The bacteria are making sort of a biofilm in which they exist," says Northup, a microbiologist, librarian and avid caver at the University of New Mexico in Albuquerque.

Caves provide one of the most constant of environments; the temperature and humidity remain the same. But in some caves, hydrogen sulfide combines with oxygen to produce sulfuric acid. Some bacteria add their own acid as a waste product. To protect themselves, bacteria produce their own microenvironment within the slimy biofilm.

"It acts as a place for them to conduct their own little chemistry labs, so to speak, regardless of what is going on outside of the film," says Boston, a microbiologist at New Mexico Tech, in Socorro. "We protect ourselves (sometimes ineffectually) against the byproducts of our metabolism, everything from simple waste products like feces to the toxic substances resulting from our industrial efforts," Boston says. "In essence, the bacteria are doing the same thing."

While that acid-producing bacteria appear to etch away the limestone of caves -- helping to produce the soft, crumbly stone cavers call punk rock -- some cave bacteria create crystals, actually producing new rock, much like dripping water deposits limestone stalactites. If the colony is growing on the underside of a ledge or on a roof, they build a slimy projection the team calls a snottite. The mineral portion of a snottite carries a bacterial signature in its crystal formation, so a snottite sample from Mars, say, could be distinguished from a small stalactite.

Snottites -- slimy, dripping stalactites made of goo that contain bacteria in abundance and beautiful microscopic gypsum crystal formations
Snottites/Biovermiculations are slimy, dripping stalactites made of goo, that contain bacteria in abundance and beautiful microscopic gypsum crystal formations. Credit: Diana Northrup
Walls dripping with slime may seem like a scene from a horror movie to some, but not to Northup. Vast colonies of bacteria coat the walls of some Hawaiian lava tubes, Northup says. "They're really cool because when you shine your light on them at certain times of the year it looks like somebody has silvered the walls. It's just breathtakingly gorgeous. It's so thick, I saw where people had written their names in the slime."

Other caves, such as Lechuguilla in New Mexico -- the deepest cave in the continental United States and a favorite of the slime team -- may appear nearly devoid of life, Northup says. "In a cave like Lechuguilla, if you didn't know from microscopy that there were microbes there, you would never guess it. The only place you see them is a place called Pink-Dot Pool, where there are actually colonies of bacteria floating. Whether that's a matter of contamination or not, we don't know," Northup says. Nonetheless, both bacteria and archaea call Lechuguilla home, many using gasses as sources of energy: hydrogen sulfide, carbon monoxide and formaldehyde, for example.

Northup extracts and sequences DNA from bacteria in the several caves the team studies. In some cases, the bacteria represent new species. But even in the age of desktop DNA analysis, if the researchers want to learn how the bacteria eke out a living, they still need to grow them in the lab -- not always an easy chore.

"DNA analysis provides no information on the metabolism, physiology, ecology, biochemistry, or geomicrobiology of a strain, Boston says. "It cannot reveal the amazing chemical and mineralogical talents of organisms. Only growing them in the laboratory and hoping to induce them to perform feats of bacterial derring-do reveal those processes."

So Boston cooks up new recipes for growing the bacteria in the lab, all the while maintaining the constant temperature and humidity of the original cave. The process should begin, the team found, even before they bring the bacteria out of the cave. Larry Mallory, of Biomes, Inc., a pharmaceutical company formed to search for novel drugs made by cave microbes, discovered that starting the bacterial culture in the cave produces better yields of difficult-to-grow species. "The results are consistently better by using their natural cave environment as their first 'incubator,'" Boston says.

In Lechuguilla, the team has kept bacteria growing in cultures in the cave for almost a year. Furthermore, they have begun growing bacteria on faux cave rock, and even glass slides, hoping to bring out even richer bacterial samples.

Caves on Mars

Microbial filaments and green slime on a rock
Microbial filaments and green slime on a rock.Credit: Diana Northrup
Boston sees caves as more than just another extreme environment. "We have thought about what the life might look like on the surface [of other worlds], but in light of the huge biodiversity of microorganisms in the subsurface of Earth, the subsurface in general and caves in particular will be an important place to look for life on other bodies. I believe that there may be many planets, including Mars, where the only life on the planet will be restricted to the subsurface." As the team finds out more about how cave microbes thrive in the extreme environment of earthly caves, they'll learn more about what chemical and crystalline signs to look for in what may be the normal environment of other planets.

What's Next?

Northup is extracting DNA from bacteria collected by Boston in a cave with such a high carbon dioxide in the air that cavers need special breathing equipment. "We think we'll probably turn up some really interesting bugs there," she says. The team plans to continue exploring known caves and to search for caves with unique environments. Each environmental extremity offers new challenges to microbes living there and therefore new challenges in growing those microbes in the lab. But the effort may pay off in new clues to look for in the search for life on other planets.

Cave microbe research wouldn't be complete without a space mission, and Boston has one in the works. "The experiment was originally scheduled for the Space Shuttle this summer," she says. With the shuttle fleet grounded, Boston's experiment will instead ride to the Space Station aboard an unmanned Russian Progress vehicle. Boston will grow a bacterial strain that produces unique mineral crystals in the microgravity of near-earth orbit. "Because microgravity is known to affect the growth of crystals," she says, "we hope to gain insight into the fundamental crystal-producing mechanisms of our organisms."

"In the meantime, Boston says, "We are plowing through laboratory analyses of samples from previous trips. For every hour in the field, you can figure on about 100 hours of lab followup or more, so we are always behind."

NASA's Astrobiology Magazine