There’s an alien world beneath our feet. What could it teach us about life?

So-called extremophiles, like blind, transparent shrimp that thrive deep within the cavernous bowels of the Mexican jungle, are stretching the limits of where life can flourish.

Deep in the dense jungle of Mexico, pools of water that dot the thick vegetation may resemble the shallow ponds found in forests all over the world. But these seemingly boring puddles are actually deep sinkholes, or cenotes as they are known locally, and form portals to another world.

Thomas Iliffe and David Brankovits aren’t hesitant to enter these watery portals. Clad in wet suits and headlamps, and lugging multiple oxygen tanks and sample jars, the two biologists and their colleagues have plunged into the murky cenote waters many times.

As they dive down, sometimes as deep as 80 feet below the surface, the water becomes so crystal clear it almost seems as if they could remove their respirators and take a breath – despite being sometimes as far as 1,000 feet from breathable air.

At times they have to wriggle through tight spots in the rock to enter roomy caverns or dodge stalactites and stalagmites, relics of a time before this subterranean world was flooded. At more than 160 miles long, the Ox Bel Ha cave system that lies beneath the Yucatán Peninsula is the longest explored underwater cave system in the world.

“To be down there is otherworldly, to put it mildly,” says Dr. Iliffe of Texas A&M University, who has been diving in caves like these for more than 30 years.

As the divers glide through this pitch-black watery world, their electric lamps occasionally alight on a tiny flash of white in the water. This is what they came to study: life.

In this seemingly inhospitable environment, a menagerie of microbes and tiny crustaceans, just millimeters in length, share a home with fish that grow up to 6 or 8 inches long. All the animals are blind and many are white or partially transparent, as they have no adaptive need for sight or flashy colors in the pitch dark.

Biologists have puzzled over the presence of this extensive biodiversity in such a dark, forbidding place. What could there possibly be down there to sustain such an ecosystem? Dr. Brankovits has part of the answer for the Ox Bel Ha system, in a paper published last week in the journal Nature Communications. His research found evidence of a methane-based food chain with a surprising link to the above-ground biosphere in this cave system.

But understanding the food web for all kinds of caves across the globe could hold much broader implications. Studying life that survives in these seemingly inhospitable subterranean worlds expands our understanding of what life is capable of – and where else we might find it.

An otherworldly window

“[Caves] are kind of like a whole other planet underneath our feet,” says Penelope “Penny” Boston, director of NASA’s Astrobiology Institute, who was not part of this study. “These worlds, these little planet-lets under our feet, have the potential for being proxies for radically different planetary environments.”

One thing that makes caves otherworldly is their isolation. “In the subsurface, it’s all geologically partitioned,” explains Dr. Boston, who is also a cave biologist. These underground caverns and crevices are enclosed in rock. But caves aren’t always completely sealed off from the surface world. Water can seep through pores in the rock, and some caves have passageways that connect them to the surface. Still, life dwelling in these subterranean caves is relatively isolated from the biological processes occurring above on the surface of the Earth. And that includes the process that we often think of as the biological linchpin of the food chain: photosynthesis.

Without any sunlight reaching deep into these caves, there can be no photosynthetic organisms. Instead, scientists have found chemical-eating microbes at the base of the food chain. In some of the dry cave systems that Boston studies, like the Cueva de Villa Luz in Tabasco, Mexico, bacteria munch on hydrogen sulfide gas – which is highly poisonous to humans – then everything else lives off that bacteria either directly or indirectly. That gas is produced by geological systems, so the food web in that cave is quite isolated from the biology at the surface.

But Brankovits, now a researcher for Woods Hole Oceanographic Institution and the US Geological Survey, found that the same is not entirely true for the water-filled Ox Bel Ha cave system.

During his PhD studies at Texas A&M University at Galveston with Iliffe as his adviser, Brankovits studied the diet of a few cave-adapted shrimp, all members of the genus Typhlatya, as a window into the food chain in the cave system. He and his colleagues found that much of the shrimp’s diet came from bacteria that was munching on methane.

But, Brankovits says, that methane isn’t geologically produced. Instead, it originated on the surface. The process goes something like this: Plants in the jungle die, falling to the forest floor to decay. In the rot process, the plants are broken down into smaller and smaller parts, largely by microbes. Then, water dissolves this organic matter down even farther, washing it through the permeable rock and further breaking it down into tiny molecules, including methane. That methane and other dissolved organic material then seeps through the limestone into the caves below, where more microbes eat it.

So, despite being deep underground, the Ox Bel Ha shrimp are still benefiting from sunlight and photosynthesis.

But Iliffe suggests other mechanisms might be at play, too – ones that might not be connected to the surface biosphere.

The Ox Bel Ha cave system’s very waters might reveal such mechanisms.

Because the caves are near the coast, ocean water has seeped into them. Freshwater seeps in from above, too. But the two don’t mix much. Instead, a layer of fresh, slightly brackish, water sits atop a denser layer of saltwater.

There is a sharp divide between the two waters, called a halocline. Swimming in the freshwater and looking down at the saltwater, Brankovits describes, “it’s almost like you are swimming above a lake in a cave.”

Some of the cave-adapted organisms don’t cross this boundary, which makes it a site for much ongoing and future research. And learning more about what happens at and around that boundary might reveal mechanisms sustaining the cave life that have no connection to surface photosynthesis.

Stretching the bounds of life

“If we actually want to better understand how life can exist in different environments, then caves provide a good natural laboratory for that,” Brankovits says. Between intriguing formations like these stratified waters, the absence of sunlight, limited organic matter, limited oxygen, biology’s use of inorganic sources to sustain itself, and the isolation of caves even from each other, each cave a biologist studies could provide a unique new model of an ecosystem.

“Caves are really beautiful windows into this underground world,” says Jennifer Macalady, a geomicrobiologist at Pennsylvania State University, who was not part of the Ox Bel Ha research team. There are crevices and pore spaces all over the world that probably contain similar biological processes, she explains, but caves are “human-sized voids” where scientists can actually explore and conduct experiments.

And exploring these caverns could help expand our knowledge of the organisms that we share this planet with. Estimates vary dramatically, but microbiologists say there are probably some 1 trillion different species of microbes on Earth. And about 99.999 percent of those microscopic organisms have yet to be discovered by scientists, so studying life in caves could help close that knowledge gap.

Scientists aren’t just discovering new microbe species in caves, though. The crustaceans and fish are also unique, cave-adapted species. Many of them only reside in one cave system in the world, making them critically endangered because pollution or another sort of destruction of that one cave could drive all the species within it to extinction, Iliffe says. (So, please don’t try to eat the fish, he adds with a laugh.)

Biologists look for undiscovered organisms all over the world, particularly in extreme environments. “It helps us understand what the boundaries of Earth-like life really are,” Dr. Macalady explains.

Caves are just one example of these extreme environments where life can be found, but with their variety of seemingly-inhospitable environments, caves attracted the attention of astrobiologists, like Boston.

In searching for life on another planet (or moon), it’s important to establish the broadest boundaries of where life might exist and not make assumptions based on what conditions are comfortable for humans. In caves here on Earth, for example, Boston has found a diverse array of organisms while wearing a gas mask and covering every inch of her skin to protect from conditions that could kill a human.

“These environments seem extreme to us,” Boston says, “but for them, it’s home sweet home.”