Researchers explored pitch-black pits in Yucatán's labyrinthine underwater caves to unlock the secrets of the rivers that provide drinking water to millions

• The Yucatán Peninsula's underwater caves cover over 900 miles.
• Its cenotes, or sinkholes, are an important drinking water resource for the region.
• Researchers mapped unique communities of microbes in a dozen areas of the cave system.

The Sac Actun cave system on Mexico's Yucatán Peninsula contains many wonders, from a 13,000-year-old skeleton to human artifacts and fossils of giant sloths.

It's also part of the Yucatán Peninsula Aquifer. Its cenotes, or water-filled sinkholes, provide drinking water for millions of people in the region.

"Caves — and especially these caves — are really important groundwater resources for everyone that lives there," Magdalena R. Osburn, an associate professor of Earth and planetary sciences at Northwestern University, told Business Insider.

She and several colleagues at Northwestern University mapped communities of bacteria and other microbes that live in the aquifer's waters, from methane-producing methanogens to sunlight-loving cyanobacteria.

It's an important first step to understanding how the microbes function and how to keep the crucial aquifer healthy. They published their findings in the peer-reviewed journal Applied and Environmental Microbiology.

The underwater cave microbial community

The cave system is a network of over 900 miles of connected caves that contain a mix of freshwater and saltwater. The Yucatán Peninsula is a giant limestone platform, Osburn said. "When you have a land surface that's built of a porous and dissolvable rock, you end up with caves," she said.

The system has isolated reservoirs, dark pits, and sections exposed to the sun. It took a team of scientists, including half a dozen divers, to collect the samples and sequence the microbes' DNA.

After taking 78 samples from a dozen sites, they found different niches with different organisms. Caves flooded with coastal seawater had different microbes than The Pit, a deep cenote exposed to the surface, for example.

The interesting part was that different types of organisms in different environments were all performing similar functions.

"We found that often the ecological roles were being performed by different organisms in different sites, but those roles were always being performed," Osburn said. These functions help balance the environment's microbiome.

Preserving a critical water source for millions

Osburn hopes future samples will allow them to sequence more of the microbes' genes to learn more about their specific functions within these communities.

One consistent bacteria showed up all over the place. Comamonadaceae were found in several locations, playing different roles and teaming up with various microbes. "That one had different partners depending on which cave system you were in," Osburn said.

That could mean Comamonadaceae bacteria function as a "keystone species" whose presence is fundamental to the health of the ecosystem, the authors wrote in the study.

"What happens in these underground river systems is directly important to the drinking water of the populations that live above."

For example, she noted that a planned train system from Cancún to the Yucatán Peninsula could affect the cave system. One concern is that diesel could leak into cenotes, Reuters reported. "Groundwater contamination is always a concern," Osburn said.

The introduction of any type of new substance, like diesel, or organic matter, like human waste, can influence a microbial community, Osburn said.

"That organic matter is going to be oxidized, either with oxygen or with things like sulfate or nitrate," she said. "The end product of those are things like ammonia and things like sulfide or organic nitrogen compounds."

All of those pollute drinking water.

Chemicals from medication, drugs, shampoo, and other sources have been showing up in the aquifer, a 2011 study found. As digital nomads flock to the peninsula, the contamination will likely get worse.

The potential for contamination is a problem anywhere there are caves, Osburn said. In Kentucky, she said, where she's done a lot of caving, people once treated sinkholes like landfills — throwing in everything, even the kitchen sink.

After a big storm, Osburn said, "The underground rivers flood, and then you find washing machines in caves because they don't just go away when you put them in the sinkhole."