Searching for Life in Mexico's Underwater Caves

Marine biologist Tom Iliffe is on a quest to understand the halocline, a layer of water that may hold the secrets to Earth's earliest life.

By Jennifer Berglund|Friday, May 30, 2014

Tom Iliffe explores waters below Yucatan’s Cenote Taj Mahal. 

Jennifer L. Berglund

About 20 miles south of Cancun, Mexico, on a stifling summer day, Tom Iliffe squints over a limestone ledge and into a giant pool of scuzzy, brown water. Despite the heat, he’s wearing a wet suit that covers everything but his blue eyes and white goatee. A spool of bright-orange nylon line and an assortment of mesh bags carrying glass test tubes, plastic caps and measuring devices dangle at his side. Below, the water temperature is roughly the same as the air. He jumps.


Tom Iliffe

Jennifer L. Berglund

“This water is about as refreshing as piss,” he exclaims with a playful smile after coming up for air. 

For almost 30 years, Iliffe has made a pilgrimage more or less annually to the Yucatan Peninsula, sharing the plane ride with throngs of Jimmy Buffet-loving “Parrotheads” and spring breakers bent on partying. Although they all arrive together, their paths diverge at the airport. Iliffe is here to explore the hidden side of paradise — a vast, underworld frontier mere feet below the hordes in their flip-flops.

Iliffe, an underwater cave biologist, discovers the life scattered throughout a network of caverns beneath the peninsula’s crust. These anchialine, or coastal, caves are filled by both freshwater and saltwater. The Yucatan’s are the most extensive on Earth, yet of the hundreds of miles of documented caves here, scientists have studied only 10 percent of them. Less is known about them, and similar formations, than the ocean floor or even outer space. The creatures living in these caves are just as mysterious. Iliffe discovers new species on nearly every dive. To date, he’s identified nearly 300.

Today, Iliffe and his graduate student, David Brankovits, are collecting specimens from a cave system known as Crustacea. As its name suggests, the system houses a variety of crustaceans specific to the region’s underwater caves. Iliffe and Brankovits are entering through a cenote, or sinkhole. Flying above the peninsula reveals just how plentiful these open pits are — the lush, green landscape is pocked with circular black holes. The cenote here is about the size of a Little League baseball field, lined with ribbons of red mangrove roots drinking the water below. 

As Iliffe and Brankovits prepare to swim below the limestone ledge and into Crustacea, marine biologist Fernando Alvarez and his students from the National Autonomous University of Mexico lower more gear for the divers: four large steel oxygen tanks, each weighing about 30 pounds. Alvarez is counting on the duo to retrieve tiny albino shrimp found only in these caves. Each diver needs two tanks, which they attach to their diving vests and nestle below their armpits to avoid damaging the cave ceiling.

Iliffe nods toward Alvarez. “See you in a couple of hours,” he says. Then, he and Brankovits disappear into the sludgy water. 

Cenote Crustacea is across a small, dirt road from an abandoned shantytown that once housed workers building a nearby mega-resort. The town lacked running water, so residents used the cenote for bathing, drinking and dumping their trash. The evidence still floats in its water and litters the perimeter.

While there is a cenote tourist industry, it’s centered around crystal-clear blue holes better suited for depicting paradise. Most tourists never see the likes of Crustacea. Aside from Iliffe and a small cadre of explorers and scientists, who would want to? It’s gross. The fecal-brown water and smell of stagnant, decaying vegetation would be enough to turn away even the most intrepid adventurer. But about 33 feet below the murky surface, the water becomes beautifully transparent.

Like oil on water, freshwater that seeped into the cave from the surface floats above a denser layer of saltwater from the ocean. These layers meet and mix in a lens of brackish water called the halocline. If left undisturbed, the halocline can be paper thin, yet still visible to the naked eye. Whereas saltwater and freshwater are clear, the halocline appears somewhat like a hazily defined liquid body rippling within the water. It can act like a barrier, preventing leaf litter from the surrounding forest — along with plastic bags, soda cans and other light trash — from sinking into the denser saltwater. Along with the debris, the upper freshwater layer contains more oxygen than the saltwater below, and it supports a completely different set of life-forms.

The halocline divides the freshwater and saltwater throughout the cave system of limestone passageways — so narrow in parts that a diver must detach from his oxygen tanks to fit through — and caverns sometimes large enough to drive a semi-truck through them. Only a few known species live here: a variety of tiny crustaceans, a blind fish and an eel. Life is impossible for all other organisms. In an environment devoid of sunlight, with no obvious energy source for the most basic life-forms, it remains a mystery how life can exist here at all. It’s a puzzle Iliffe can’t resist trying to solve.


Iliffe and student David Brankovits, holding a dive tank, prepare to dive into a coastal cave on the Yucatan. 

The Life Aquatic

As a kid, Tom Iliffe dreamed of life as Jacques Cousteau. The ocean’s mystery excited him, and the prospect of discovery was enthralling. At Pennsylvania State University, where he studied biochemistry, Iliffe saw a scuba class among the course offerings and jumped on the opportunity. He fell in love with scuba diving and started planning his life around it.

After college, Iliffe began a master’s degree program in oceanography at Florida State University in Tallahassee. It was the early ’70s, a golden age in underwater cave exploration. Diving technology was now sophisticated enough to support long dives during which divers could be disconnected from an air supply above water. Legendary cave diving pioneers like Sheck Exley began breaking deepwater diving records. Much like the Yucatan, Florida’s panhandle is dotted with wet caves that were then just opening to exploration. Iliffe was simply in the right place at the right moment to find his calling. “It was something that offered an opportunity to go places where no one had ever been before — to do true exploration,” he says. 

Iliffe earned his doctorate degree at the University of Texas and did a stint as a researcher in the Bahamas before landing a teaching gig at Texas A&M at Galveston. At the same time, 22-year-old John Pohlman had just begun graduate school there, but he wasn’t quite sure what he wanted to study. Then he met Iliffe. It was the early ’90s, and Iliffe was just beginning his work in Yucatan’s caves. He needed a diving partner for an upcoming research trip. A few weeks later, even though they barely knew each other, Pohlman and Iliffe hopped in a van and drove south through Mexico. Even 20 years later, “I still think about these things and tell these stories to my friends,” says Pohlman. “It was such a wild experience.” Money was tight, so they slept outside in hammocks. On more than one occasion, Pohlman recalls waking to an unwelcome surprise in his face. One time, it was the snout of a horse. Another time, while they camped outside an abandoned research station, it was the gun barrel of a concerned security guard. 

During those long hours on the road, Iliffe instructed Pohlman, reviewing scientific diving techniques like how to drag a plankton net to collect microscopic crustaceans. By the time they got to Cozumel, an island off the Yucatan’s eastern coast, Pohlman had a pretty good idea of what he wanted to study. He spent the next two years working with Iliffe to figure out what powered life in the deep caves. When he analyzed isotopic signatures of carbon and nitrogen found in the tissues of some of the small cave crustaceans, he discovered that the animals had a food source fueled by something other than the sun. Pohlman believed chemosynthetic bacteria, like the kinds found around deep-ocean hydrothermal vents, must be the answer.


In the Yucatan’s coastal caves, freshwater seeps from the surface through porous limestone into the caves. The lighter freshwater sits atop denser saltwater that flows in from the Caribbean. The layer where the two meet is the halocline, which may host a unique ecosystem. 

Jay Smith

Researchers had thought that since there were no other obvious energy inputs, the fodder for bacterial life must fall from the surrounding forest into cenotes, eventually floating into the deep parts of the caves. This was happening closer to the cave entrances, but Pohlman’s data indicated it was rarely, if ever, the case farther into the system. Iliffe and Pohlman thought a chemical reaction must be happening somewhere in the cave system — not as dramatic as the billowing black clouds of dissolved minerals that erupt from deep-ocean hydrothermal vents, but something more subtle. 

Iliffe believes the answer is in the halocline. “Literally everything that can be measured,” Iliffe says, including temperature, salinity, acidity, biodiversity and more, “is dramatically different above, inside and below [the thin layer].” Such differences across minute distances can indicate chemical activity. What’s more, gelatinous orange, green and brown bacterial mats often rim the halocline on the cave walls. Sometimes clouds of accumulating bacteria can even be seen just above the halocline. Something happening here generates enough energy to feed basic bacterial life, and it’s obviously not sunlight.

The halocline itself is responsible for the formation of these cave systems. When saltwater and freshwater mix together, the result is reactive brackish water that dissolves the calcium- and carbon-rich limestone walls, eroding the rock and enlarging a cave’s passageways. Because different water densities meet at the halocline and both organic and inorganic particulates accumulate there, it’s an intriguing place, chemically speaking. Iliffe and Brankovits haven’t zeroed in on what kinds of chemosynthetic bacteria actually exist there, or what their food sources could be — methane, hydrogen sulfide and ammonia are all potential candidates. But there’s a good chance that the answer, when they find it, might also explain how some of Earth’s earliest life-forms emerged from an environment that was nearly as inhospitable as the caves.

Although a number of scientists study the creatures that divers like Iliffe carry out of the caves, few have ventured into these difficult environments. That puts Iliffe and his students in a unique position to study the halocline’s biological significance. But while Iliffe has a lot of theories, evidence to support them has been slower in coming, hindered by the logistical challenges of studying the halocline and the fact that only a small cadre of people, mostly around Iliffe, share his quest for understanding this obscure natural phenomenon. For now, all we know for sure about the halocline is what has been observed by the naked eye: Bacteria tend to grow there, and crustaceans appear to be eating them. 


An underwater sign warns of hazards in the caves, but fatalities still occur. 

Jennifer L. Berglund

Paradise Losing

Human civilizations have existed on the Yucatan Peninsula for millennia, relying on the freshwater in caves below the limestone crust where Tom Iliffe does his work. But since the 1970s, explosive growth from tourism has damaged many of these fragile ecosystems, at times beyond repair. 

At the same time that freshwater is being pumped out of the caves for drinking water, sewage is being pumped in. The peninsula’s porous limestone surface allows contaminants from golf course herbicides and motor oil from roads to seep into the cave systems, causing further contamination. 

“Humans are extending their reach with their garbage faster than they can explore the caves,” says Iliffe. More than once over the years, Iliffe has swum into masses of plastic bags floating inside previously unexplored coastal caves. The tainted water also flows out to the Caribbean, smack into the Mesoamerican Barrier Reef System, the second-largest barrier reef in the world. Where these outflows are the most voluminous, coral reef has largely been overtaken by green algae, which has destroyed habitat for an untold number of marine species.

Ironically, species threatened by increased human stresses to their environment are a big draw for tourism in the region, and that only drives the already staggering rate of development. The population of Quintana Roo, the Mexican state that extends 240 miles along the eastern coastline of the Yucatan Peninsula, grew from 88,150 people in 1970 to 1.3 million in 2011. Many suspect this is just the beginning of a major environmental catastrophe that might extinguish the biodiversity, effectively ending tourism on the coast.

“All of these cave systems — the cave systems, the coral reefs, the mangroves, the seagrass habitats, the jungle — are all interlinked and intermeshed together. It’s like a chain of dominoes,” says Iliffe. “If you push one over, it’s going to knock everything over in its path.” — JB


Iliffe collects a remipede from Cenote Crustacea during a 2009 expedition. Adapted to a lightless environment, the inch-long animal has lost all pigmentation.

Tamara Thomsen

Underwater cave biology as a field is still relatively new, and Iliffe sees himself as an evangelist, responsible for promoting as many areas of research within these unique environments as possible. As a result, he spends a lot of time in the field, and not nearly as much in the lab, so he needs to collaborate with a variety of more specialized researchers. “When I find something really cool, I try and get the best people in the world to work with me,” Iliffe says of his strategy to do good science across multiple fields.

Alvarez, a crustacean biologist, is one of these experts. After Iliffe’s dive into the Crustacea system, the shrimp specimens he gathers will go back to Alvarez’s lab to be identified and studied. Iliffe relies on the expertise of microbiologists, geologists, other marine biologists and even archaeologists, among others, to complete his work.

Collaboration is also something Iliffe encourages in his students. “He finds students and identifies what their interests might be, and then he tries to align those interests with experts he knows from his years of interaction and experience in the field,” says Pohlman. Case in point: Pohlman, who is now a biogeochemist for the U.S. Geological Survey, studies global distributions of methane deposits, stored in the seafloor as solid methane hydrates, and how the destabilization of those deposits could impact climate change. Currently, he is informally co-advising Brankovits, who is investigating energy inputs for microbial life within the caves. 

Playing It Safe

Preceded by a swirl of air bubbles, Brankovits emerges from Crustacea. He lost sight of Iliffe moments earlier. Unable to see through Crustacea’s polluted water, Brankovits was hoping his adviser was still right behind him. But it’s a few suspenseful minutes before Iliffe emerges. He’s unscathed — and unaware he was missed. 

“Where were you?” Brankovits asks.

“Oh, I was just following a shrimp,” Iliffe says. 

Despite the occasional distraction, Iliffe has managed to stay safe for more than three decades diving into environments that have claimed nearly 400 lives since 1969 just in the U.S. Among cave divers, it is often said there are no accidents, only fatalities.

Knowing when to turn around keeps Iliffe alive, says Jill Heinerth, an underwater cave filmmaker and explorer who has dived with him for years. Just last year, Iliffe traveled to Christmas Island, a remote spot in the Indian Ocean, for a high-profile, National Geographic-funded expedition to discover life in the island’s underwater caves, and in particular to find a small crustacean called a remipede. It was an expensive expedition — the entirety of which was documented by professional underwater filmmakers, including Heinerth — for a potential TV special. But conditions weren’t right for finding the remipedes and, when his window of opportunity for diving closed, Iliffe left empty-handed but undaunted.

Iliffe is a persistent scientist, but he also knows when to step back. “That’s the earmark of a good explorer,” says Heinerth. And it’s the mark of a researcher in it for the long haul: Iliffe returns to Yucatan’s coastal caves this summer, hoping to unravel more of their secrets.

The Cave Critters of Crustacean Nation

Tom Iliffe spends much of his time documenting the biodiversity in underwater caves, including these ghostly, unique species. 


Tulumella unidens

The front legs of these shrimp-like crustaceans look like paintbrushes. Iliffe thinks the tiny creatures — about the size of a pencil eraser — might use these appendages to clean themselves and then eat whatever bacteria they’ve cleaned off their bodies. 

Fernando Alvarez/Instituto de Biologia, UNAM

Speleonectes tulumensis

This primitive centipede-like crustacean, which can grow up to an inch, uses venomous fangs to capture prey. No other crustacean has this characteristic; it’s usually seen only in insects. Indeed, this was a clue that led some scientists to believe it might be the missing link between the two closely related arthropod groups. Of the handful of species known around the world, Iliffe has discovered about half of them.

Tom Iliffe/Texas A&M Galveston

Metacirolana mayana

These aspirin-size cave scavengers feed on whatever they can get their claws on — usually smaller crustaceans. During one of his expeditions in the Bahamas, Iliffe and his team dropped a chicken leg onto the floor of one of the caves, only to find it replaced by a writhing swarm of hundreds of isopods the next day. 

Fernando Alvarez/Instituto de Biologia, UNAM
Mexican Blind Brotula

Typhliasina pearsei

A fish species that inhabits the brackish and freshwater layers of the Yucatan’s caves, the albino, sightless brotula grows no longer than an iPhone. And unlike most other fish, it gives birth to live young.  

Tom Iliffe/Texas A&M Galveston

[This article originally appeared in print as "Cave Man."]

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