In desert cave, microbes feed on water, rocks, and air

"We didn't expect to find such a thriving ecosystem feasting on the scraps dripping in from the world above," says Julie Neilson. (Credit: Bob Casavant/Arizona State Park Service)

A cave system in southeastern Arizona is home to a diversity of microorganisms that rival microbial communities on the earth’s surface.

Kartchner Caverns is known for its untouched formations, sculpted over millennia by groundwater dissolving the bedrock and carving out underground rooms and passages.


“We discovered all the major players that make up a typical ecosystem,” says Julie Neilson, associate research scientist at the University of Arizona. “From producers to consumers, they’re all there, just not visible to the naked eye.”

For the study published in the International Society for Microbial Ecology Journal,  Neilson and colleagues 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.

“We didn’t expect to find such a thriving ecosystem feasting on the scraps dripping in from the world above,” Neilson says. “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 can’t count on photosynthesis to harness the energy in sunlight to build organic matter from carbon dioxide in the atmosphere.

Antje Legatzki samples below the Throne room. (Credit: Bob Casavant/Arizona State Parks)
Antje Legatzki samples below the Throne room. (Credit: Bob Casavant/Arizona State Parks)

Cave’s limited nutrients

In the absence of light, bacteria live off water runoff dripping into the cave through cracks in the overlying rock and harvest the energy locked in compounds leaching out from decaying organic matter in the soils above and minerals dissolved within the rock fissures.

“Kartchner is unique because it is a cave in a desert ecosystem,” Neilson says. “It’s not like the caves in temperate areas such as in Kentucky or West Virginia, where the surface has forests, rivers, and soil with thick organic layers, providing abundant organic carbon. Kartchner has about a thousand times less carbon coming in with the drip water.

“The cave microbes make a living off the extremely limited nutrients that are available,” she says. “Instead of relying on organic carbon, which is a very scarce resource in the cave, they use the energy in nitrogen-containing compounds like ammonia and nitrite to convert carbon dioxide from the air into biomass.”

The researchers found evidence of cave microbes engaging in all six known pathways that organisms use to fix carbon from the atmosphere to make food and structural material.

Rocks for food

Although the nitrogen-driven pathway is probably the most dominant in the cave, there might be others. Some microbes even eat rock—to derive energy from chemical compounds such as manganese or pyrite.

The team expected to find the overall microbial diversity in the cave to be only a fraction of that found in the soil on the surface, says Raina Maier, professor in the department of soil, water, and environmental science and a member of the BIO5 Institute.

“We expected the surface community many times more diverse than the cave. Instead, we found the cave is about half as diverse as the terrestrial environment where there is sunlight and soil and vegetation.

“At the same time, the two ecosystems share only 16 percent of the microbial species. In other words, there is a difference of 84 percent between the two, which is amazing.”

Previous studies had shown that, to the cave microbes, the stalactite they live on is like an island: Restricted to the stalactite they happen to be on, there appears to be little mixing between populations, resulting in different assemblages from one cave formation to another.

Rod Wing, professor in the department of plant sciences and director of the Arizona Genomics Institute at BIO5 helped Neilson and colleagues analyze the DNA swabbed from the cave formations.

Barely enough DNA

“When you work in extreme starving environments, you barely get enough DNA,” Neilson says. “In some of our samples we got about half of what is considered the minimum amount for DNA sequence analysis. But, we said, let’s just try it.”

She said technicians in Wing’s lab “managed to get us a data set even from the dry rock, where there is no drip water and where there are very few microbes living to begin with.”

In addition to encountering all the major players that make up a complex food web in the cave, the scientists discovered what likely are microbes yet unknown to science.

“Twenty percent of the bacteria whose presence we inferred based on the DNA sequences were not similar enough to anything in the database for us to be able to identify them,” Neilson says.

“On one stalactite, we found a rare organism in a microbial group called SBR1093 that comprised about 10 percent of the population on that stalactite, but it represented less than 0.5 percent of the microbes on any of the others.”

Nobody has been able to culture that organism in the lab, and its DNA sequence has only ever been found three times in history: in a stromatolite—a special type of sedimentary rock involving microbial communities—in the hypersaline waters of Shark Bay in Australia; in a site contaminated with hydrocarbons in France; and in a sewage treatment plant in Brisbane, Australia.

Beyond Earth

“This suggests there are many microbes out there in the world that we know almost nothing about,” she said. “The fact that these organisms showed up in contaminated soil could mean they might have potential for applications such as environmental remediation.

“The most abundant microbe that we found in our taxonomic survey was closely related to a microbe that produces erythromycin, an antibiotic.

“That is not what it is doing in the cave, but it shows you that not only is there a potential to find microbes that are new to science, but studying them in those extreme and poorly studied environments could lead to new applications.”

The implications of the research reach far beyond Kartchner Caverns, as far as other planets, Neilson says.

“There is a lot we have to learn about microbes and how they control processes of global importance, and by studying microbes in extreme ecosystems such as Kartchner Caverns or in the Atacama Desert in Chile, it helps us study some of the capabilities we don’t yet understand in rich ecosystems here on the surface. It shows the flexibility of microbes. They have conquered every niche on the planet.”

“When you think about exploring Mars,” Maier says, “and you look at all those clever strategies that microbes have evolved and tweaked over the past 4 billion years, I wouldn’t be surprised if we found them elsewhere if we just keep looking.”

The National Science Foundation Microbial Observatory helped fund the project.

Source: University of Arizona