Microbes rule in an underground desert.

• Position: Life Sciences

Hidden underneath the hilly grasslands studded with ocotillos and mesquite trees in southeastern Arizona lies a world shrouded in perpetual darkness: Kartchner Caverns, a limestone cave system renowned for its untouched formations, sculpted over millennia by groundwater dissolving the bedrock and carving out underground rooms and passages.

Beyond the reaches of sunlight and seemingly devoid of life, the caves are, in fact, teeming with an unexpected diversity of microorganisms that rival microbial communities on the Earth's surface, according to a study published in the Journal of the International Society for Microbial Ecology. The discovery not only expands our understanding of how microbes manage to colonize every niche on the planet, but could lead to applications ranging from environmental cleanup solutions to drug development.

"We discovered all the major players that make up a typical ecosystem," explains Julie Neilson, a researcher in agriculture and life sciences. "From producers to consumers, they're all there, just not visible to the naked eye."

Neilson and her co-workers have spent years exploring the underground world and its inhabitants. For their latest study, they swabbed stalactites and other cave formations for DNA analysis. Based on the genes they found in their samples, they reconstructed the bacteria and archaea--single-celled microorganisms that lack a cell nucleus--living in the cave. Kept secret for 14 years after its discovery in 1974 by two college students who were hiking in the Whetstone Mountains just south of Benson, Ariz., Kartchner Caverns has been protected from human impact so that scientists can study the fragile environment and organisms inside.

"We didn't expect to find such a thriving ecosystem feasting on the scraps dripping in from the world above," Neilson admits. "What is most interesting is that what we found mirrors the desert above: an extreme environment starved for nutrients, yet flourishing with organisms that have adapted in very unique ways to this type of habitat."

Unlike their counterparts on the surface, cave microbes cannot harness the energy in sunlight to build organic matter from carbon dioxide in the atmosphere...