Saving Mexico’s Lost World

Microbes have lived in Cuatro Ciénegas for 500 million years. They’ve survived countless cataclysms and extinctions. But can they survive us?

“Sorry,” Valeria Souza says, threading her battered Ford Expedition through ruts of pale, packed dirt and stands of spiky ocotillo cacti. Long spines rake a fresh set of racing stripes in the truck’s silver paint. She jolts past knee-high boulders and wheel-deep potholes. “Sorry!” she says again, as her head careens against the side of the truck.

Souza rolls to a stop at a warm, sulfurous, blue-green pool that is partially hidden behind a low concrete wall of rushes and sedges. The water’s surface is as still and clear as glass. The pool—called La Becerra—was once a tourist attraction, one of four shimmering lakes that brought health-seekers and holidaymakers to this butterfly-shaped basin near the town of Cuatro Ciénegas in north-central Mexico. Spanish for “four marshes,” Cuatro Ciénegas was once a lush desert oasis, where water bubbled up through the basin’s limestone floor to create springs, streams, and shimmering blue-green ponds, or pozas, that dotted the arid landscape and nurtured complex microbial communities unlike anything else seen on Earth.

Today, La Becerra has withered to a shadow of its former self. Its sands are littered with derelict toilets, overturned white plastic chairs, and sun-bleached cans of Tecate. It has been closed to tourists since 2008, when Souza, a microbiologist based in Mexico City, convinced the Mexican billionaire Carlos Slim to purchase and protect a large plot of land that included La Becerra and several other pozas.

Souza hops out of the Ford. Round and diminutive, with a flyaway pouf of brown curl, she looks at the pool and shakes her head. “I have never seen the water this low. Never,” she says, pointing to the dark brown high-water mark on the cement nearly a foot above the present water level.

In the shallows, finger-sized striped silver fish, unique to these pools, flick their tails as they search for algae. Tangles of climbing milkweed and spiny lotebrush clot the marsh’s edges. Tiny, cream-colored snails dot the shoreline. This lagoon was once home to five species of aquatic box turtles, 17 types of fishes, 145 bird species, and the strange microbes for which Souza and her team of ecologists and microbiologists have come searching today. Many of these species are found nowhere else on Earth. “This is our Galápagos,” Souza says. “And now look what we’ve done to it.”

Over the past 50 years, irrigation canals feeding distant alfalfa fields have drained the aquifer that lies beneath the pozas. Prickly pears and sand have already reclaimed 90 percent of the surface water, including the basin’s largest lagoon, Churince, which dried up in 2016. The farms’ unslakeable thirst has transformed the remaining pozas from vast lakes more than a kilometer in diameter into glorified puddles.

Souza leans against an orange gate locked open over a manmade river that races away from La Becerra. “We don’t need these channels,” she yells over the rushing water. A vulture circles overhead, updrafts carrying it ever higher. “They are draining the heart of Cuatro Ciénegas.”

But La Becerra hasn’t dried up, not yet—and Souza is doing battle with some of the strongest political forces in her native Mexico in order to keep it that way.

The American and the snorkel

Souza has been wild about microbes since she was 10 years old, when, in 1969, she received a Time-Life encyclopedia for Christmas. On the cover was an image of a DNA strand, a double helix coiling like one of Souza’s brown curls. The illustration captured the young girl’s imagination: “This image could explain everything I knew and loved,” she says.

By the time Souza started university, she had distilled her interests into a single, if complex, question: How could so many species exist on a single planet? Souza received bachelor’s, master’s, and doctoral degrees in ecology and genetics from the Institute of Ecology at the National Autonomous University of Mexico, or UNAM, studying how the domestication of runner beans (legumes also known as butter beans) affects the diversity of their associated soil microbes. The work wasn’t splashy or sexy, but it enabled Souza to explore basic questions about why some species live in one place and not another, and why some environments can support a broad range of organisms while others contain precious few.

While at the Institute of Ecology, she met her husband, fellow UNAM microbiologist Luis Eguiarte, who was studying agave genetics. The match seemed ludicrous at first. Eguiarte was Souza’s opposite in every way: He was tall and lean, while she was stocky and barely reached his shoulder. He was soft-spoken, solitary, practical; Souza was gregarious, passionate, and brimming with wild ideas. But their mutual curiosity about the natural world and shared humor (hers punctuated with a gravelly chuckle, his with a quiet smile) helped smooth the rough edges. “She is a dreamer,” Eguiarte says. “She thinks things that I don’t. I often have to bring her back to Earth.”

The couple married in 1991. Not long after their I-dos, the pair took an extended postdoc in the lab of famed microbiologist Richard Lenski at the University of California, Irvine. Lenski, now at Michigan State University, is most famous for running a decades-long, continuous study of the evolution of the bacterium Escherichia coli. Souza’s work studying microorganisms in the Lenski lab launched her along on the inquiry that would consume her career: How did life on this blue planet become so diverse? “It’s the one question I want to answer,” she says.

In 1994, Souza and Eguiarte returned to UNAM, this time as professors in the Institute of Ecology. And then, four years later, an American wearing heavy lug boots stomped down the tile floors of the Institute of Ecology and pounded on Souza’s door.

Wendell Minckley was an intense, white-maned, bushy bearded limnologist from Arizona State University. He had first visited Cuatro Ciénegas in 1958 to study an unusual box turtle that a colleague had discovered in the pozas there. Box turtles are aquatic animals but this particular species (Terraplene coahuila) lived in the middle of the Mexican desert. Over countless trips spanning more than four decades, Minckley studied the groundwater there and the creatures that lived in it, many of which were more likely to be found in an ocean than a freshwater pond. They were remnants, he came to believe, of an incredibly ancient ocean system that had somehow survived into the present.

Souza and Eguiarte had heard of Minkley’s work, and were aware that Cuatro Ciénegas had, thanks to his efforts, recently been named a Protected Natural Area. They didn’t understand, however, the area’s relevance to their own work on microbial ecology and evolution. But Minckley did. He had received a grant from NASA to study the microbes of Cuatro Ciénegas in order to explore life’s evolution in unusual environments, especially those with different chemical properties. He persuaded the skeptical couple to accompany him to the pools, and several days later, the trio pulled up to La Beccera. Minckley handed Souza a snorkel and told her to go for a swim.

She waded into the water—warm as bathwater, clear as glacial run-off—and put on her mask. When she surfaced, ten minutes later, Minckley was waiting on the sand. “What did you see?” he asked.

“A snail, and all of these fishes and turtles,” she said in amazement. How could so many species thrive in a small pond in the middle of the desert?

Minckley explained that he had come to believe that the ancestors of those snails, fish, and turtles had lived in an ancient ocean, where they subsisted on sulfur bacteria from hydrothermal vents. The pozas, he theorized, were fed by the underground remnants of that 500-million-year-old ocean, trapped by the rise of the Sierra Madre mountains. While the rest of the world’s ocean creatures—from the tiniest microbes to the largest marine mammals—evolved to rely on phosphorus as their energy currency, the species in this desert oasis stayed the same, subsisting at the base level of the ecosystem on the same primordial, sulfur-eating bacteria that nourished them hundreds of millions of years ago. But Minckley hadn’t yet found a way to determine the creatures’ marine origin—and he believed that Eguiarte and Souza, with their expertise in evolution and genetics, could help. “It is your job,” Minckley said, “to figure out how these snails survived for so long.”

Souza and Eguiarte didn’t hesitate in accepting the challenge.

The couple began by collecting samples from the bottom of Churince, the largest of the pozas. It was wide, covering more than a square kilometer, but shallow, and even Souza, standing just over five feet, was too tall to gather samples without disturbing the lagoon’s bottom and contaminating the sensitive microbes they sought to collect. Armed with only a small boogieboard, the couple sent their 8-year-old daughter, María—the youngest of their two children—to collect samples of water and mud. From this simple transect, the team found a profusion of bacterial diversity—56 of the 87 major bacterial families, more than anywhere else on Earth. In other microbial hotspots, scientists have documented far fewer species—48 bacterial families along the entire 2,500-mile length of China’s Pearl River.

At the Pozas Azules pool on the east side of the basin, the UNAM team found similar diversity: hundreds of thousands of different microbial species packed into thin layers that form giant, rocky domes beneath the surface. In one small section of dome, Souza says, “there was more diversity than in all sediment collected in the Pearl River.”

When Souza and Eguiarte sequenced the genomes of their samples, they found something equally astonishing: the Cuatro Ciénegas microbes were not only wildly diverse, but many were also entirely new to science. One bacterium in particular had an unusual way of coping with the pools’ lack of phosphorus. Instead of using phosphorus to build the backbones of their fatty membranes, these microbes used sulfur. No one had seen a similarly constructed cell membrane before—nor, 25 years later, has anyone seen it since. They dubbed the new bacterium Bacillus coahuilensis.

In 2006, Souza and Eguiarte published their findings. The Bacillus coahuilensis bacterium’s closest relatives were not other desert dwellers, they reported, but rather marine bacteria found in the Gulf of Mexico, the Sea of Korea, and the Yellow Sea’s tidal flats. Follow-up analyses found that viruses from Cuatro Ciénegas were also closely related to marine viruses. These microbes, the scientists concluded, had separated from other lineages as much as 680 million years ago.  

“It was just as Minckley predicted,” Souza says. Minckley had died in 2001, but these analyses confirmed his hunch that the underground aquifer held the remnants of the Proto-Pacific Ocean, and that the microbes there had survived intact over a half-billion years of the Earth’s history, from life’s first wobbly steps onto land through the cataclysmic end of the dinosaurs. The ecosystem there was an ancient relic of an era when life existed just as single cells.

It was a literal lost world. Which made it all the more important to protect.

Death by Alfalfa

Before Minckley and the UNAM team parted ways in 1998, Minckley urged Souza and Eguiarte to waste no time getting to work. The valley was drying up, and Minckley feared that it might vanish completely within the next few decades. Over their next several treks north from Mexico City to Coahuila, Souza, and Eguiarte realized that Minckley had been overly optimistic. Every time they returned, large pozas had shrunk further, while some small pozas had disappeared completely.

The death of Cuatro Ciénegas began in the 1960s, when new, long-distance irrigation channels were built to transport the basin’s water to far-flung alfalfa fields more than 80 kilometers south. By the late 1990s, the water diversions began to take their toll, drying up Cuatro Ciénegas’s local rivers and pozas. The strain on the aquifer grew worse in 2000, when alfalfa farmers in nearby Laguna de Coahuila drained the area dry while irrigating their fields and were unable to supply feed for the region’s large ranches and for Lala, Mexico’s largest milk producer. The Mexican government relocated the farmers to Cuatro Ciénegas, where they sank deep wells that tapped the aquifer connected to Souza’s pozas.

Alarmed, the team plunged into their research, now even more critical, knowing that the pozas might soon be gone. Souza also called or wrote every government official, dignitary, and journalist she could find to tell them of the exceptional, irreplaceable resource that they would soon lose. “Cuatro Ciénegas is beautiful, and it is going to die,” she told them.

But her efforts were met with official denial. Conagua, Mexico’s federal water agency, maintained that the subterranean aquifer wasn’t connected to the pozas, nor were the pozas connected to each other. If farmers and ranchers tapped the groundwater at the southern end of Cuatro Ciénegas, Conagua argued, it shouldn’t affect the town or the pozas. Souza was furious. She traveled from corporate headquarters to government office, slapping down glossy snapshots on the large desks of executives showing dead turtles and fish in the drying pozas, and presenting them with genetic data showing similar microbial signatures from pozas around the valley, indicating an underground connection. Conagua continued to insist there was plenty of water to go around. “Conagua just couldn’t stand up to the ranchers. They didn’t have the power,” she says.

In 2002, however, the agency, worn down by Souza’s agitating, cautiously proposed limiting the amount of water that could leave through the irrigation canals. In a rage, incensed local ranchers sunk 250 deep wells to access the basin’s unregulated deep aquifer. Conagua backed off.

In 2006, the duo brought a delegation of dignitaries, including American scientists, high-level Mexican officials, and an international team from National Geographic, to Cuatro Ciénegas to plead the case for the pozas’ conservation. As Souza, Eguiarte, and the delegates drove through the town, hundreds of townspeople turned out to protest Souza’s work. Children lined the streets carrying hand-lettered signs: “Conservation is killing my future.”

Later that day, in a small, hot room at the Cuatro Ciénegas town hall, Souza faced an angry gathering of 500 people. The regional government had assembled local ranchers, farmers, and townspeople to oppose Souza’s efforts to cut the irrigation channels’ flow. Souza was slated to speak last. Each group argued that saving Cuatro Ciénegas would destroy their livelihoods, which caused Souza to rethink her talk. She realized that the people opposing her efforts weren’t acting out of malice. They simply didn’t know what was at stake. Stepping up to the podium, Souza wiped her sweaty palms on her skirt and took a deep, steadying breath. “This is the most important place in the world,” she told the crowd. “It is going to die. But you can save it.”

Souza spoke with passion and determination, hands gesturing wildly, hair flying around her face. She told the story of how the microbes at Cuatro Ciénegas turned the world from a toxic wasteland to a verdant marvel, brimming with life. When she finished, silence enveloped the room. Then it disappeared beneath thunderous applause. “It was everything against us,” Souza says. “But I had two beautiful children and I had to show them how to battle for the future. You don’t just stare at doomsday. You do something about it.”

In the years that followed, that is what Souza did, devoting fully half of her time to conservation work. In the process, she has transformed some of her fiercest opponents into close friends. What could have been simply a means to an end—you can’t study vanished microbes—had become an act of love, a crusade to save her most sacred place. “She’s a force of nature,” says limnologist James Elser, who has worked with Souza and Eguiarte for nearly a decade. “Valeria is just what Cuatro Ciénegas needs. No one else could have had the same impact.”

She continued her research in the pozas. But she also visited schools and community organizations, building a state-of-the-art molecular biology lab at the local high school to allow students to study and appreciate the natural wonders in their own backyard. And slowly, her passion thawed even the iciest hearts and minds. After one school visit, a student—the daughter of an executive at dairy giant Lala—spoke to her father about Cuatro Ciénegas’ disappearing water. “What do I have to do?” he asked Souza in an email. She suggested that Lala switch their cattle feed from alfalfa to less-water-intensive fodder, such as corn, soybeans and barely. The company did. In 2007, Souza also persuaded a friend to lobby Carlos Slim to buy the parcel of land encompassing La Becerra, Churince, and other lagoons, to protect the land and their research.

But Slim’s purchase couldn’t protect the water beneath, and the basin continued to wither. By 2011, two-thirds of Churince had been replaced by parched sand and stands of sotol shrubs. By 2016, Churince was completely dry. Intermedia, another large lagoon several hundred meters to the northwest, followed a year later. Without an official change in water policy, neither Souza and Eguiarte’s discoveries nor Slim’s billions would save Cuatro Ciénegas. The byzantine nature of the laws governing Mexico’s water rights meant that every agency at every level of government could make the case that their hands were tied and they could do nothing. Locals are caught in the middle with Conagua’s use-it-or-lose-it policy around water. One townsperson explained that they want to save the pozas but they’re afraid to cut down their water usage for fear that, next year, Conagua won’t give them enough water.

“When it’s everyone’s problem, it’s no one’s responsibility,” says Gabriela Olmedo-Alvarez, a genetic engineer who works with Souza.

In 2018, Souza finally turned to the legal system. Bolstered by more than a decade of groundwork and goodwill, Souza teamed up with Pronatura Noreste, a Mexican NGO, to file an injunction asking a federal court to force Conagua to close a major irrigation canal draining the Churince and Intermedia lagoons. Though both pozas were dry, Souza hoped that halting the continuing drainage would allow them to recover. In November 2018, a federal judge agreed, and the valve was shut—though other canals, including the one at La Becerra, remain open. The ruling was upheld on March 14, 2019—just as Souza’s team pulled into town.

Mud and revival

The day dawns clear and cold. As the sun’s weak rays try to warm the pale sky, scientists transform the front walkway of a small hotel just outside Cuatro Ciénegas into a research staging area. Today they plan to visit Intermedia, the large poza that dried up two years earlier. Armed against the cold in a colorful array of sweaters and jackets, a crew of 20 microbiologists, most of them undergraduate and PhD students, chug coffee and haul gear under Eguiarte’s close supervision. Souza rushes around, passing out gloves and test tubes, coursing with nervous energy. “Do you have Gatorade? Two bottles? And don’t forget your munchies,” she says, the morning air turning her breath into tiny clouds. “Bring munchies! I don’t know how long we’ll be!”

When they arrive at Intermedia, it looks dead. No grasses edge the pond’s receded shoreline, only toothy sotol shrubs, most of them dried out, their water source gone. Trapped between vast, cloud-white dunas de yeso (gypsum dunes) and the menacing dark peaks of San Marcos, thousands of drivers on Mexico’s busy Highway 30 pass this ancient site each day with no knowledge of its matchless microbial heritage.  

Souza walks to the shoreline and ventures into the dried bed of the lagoon. Her shoes sink almost imperceptibly into the earth. “Mud!” she says.

Mud means water. Souza’s research has shown that the pozas’ rare microbes can lie dormant in sediment for years. What Eguiarte and Souza don’t know is whether the return of water to the basin will be enough to revive them and the rest of the dying ecosystem.

She plunges into the remnants of another small, nearby poza. “Mind the mud,” she warns the students following in her tracks—but several don’t, and they sink up to their knees in the quagmire. “You have been baptized by Cuatro Ciénegas,” she laughs, hauling them back onto dry land.

Within seconds, she returns to examining minutiae on the ground. Her team fans out to do the same, gypsum crust crunching beneath muddy boots. They chip chunks from the lakebed with sticks or fingernails, then line up before her so she can examine their haul.

“Those are just cyanos,” she says, observing a thin green layer of photosynthetic blue-green bacteria topping one sample. “We’re not impressed by cyanos.” Cyanos are beautiful, but they don’t belch out sulfur. Without that distinctive stench, Souza knows instantly that they’re not what she’s looking for.

For more than half an hour, though, cyanos are all that the team finds. Souza examines and discards sample after sample. Eguiarte stands slightly apart from the rest of the group, pinching small clumps of dark mud, taking a sniff, and then tossing it back with a shake of his head.

Then a young undergraduate visiting from Bogotá shyly approaches Souza cradling a thumb-sized chunk of mud in her palms. Souza picks it up between two fingers, holding it up to the light. She frowns and scrapes with her fingernail at several layers, each a slightly different shade of brown. Then she brings it to her nose and inhales. She breathes out and inhales again, more deeply: a faint but distinct odor of rotten eggs. Souza looks up with a whoop.

“We found it!” She raises a fist in victory. A cheer goes up in the group.

To Souza and Eguiarte, this is everything: Life, on the edge of this shallow, beleaguered pool. Eguiarte squats down and gazes into the mud, his salt-and-pepper beard and long, silvery mane making him look not unlike Charles Darwin, who pondered “warm little ponds” where he imagined life began. And in Cuatro Ciénegas, near the bleached bones of cattle and sheep, life begins again.

Estan recuperando,” Eguiarte says, with a quiet confidence. They are recovering.

This discovery is not an end to the pair’s conservation work, but a new beginning. Cuatro Ciénegas can recover, if only given the chance. Now they will continue to fight for that chance.

“It’s not finished yet,” Souza says, then pauses. After a deep breath, she mutters, almost to herself, “There’s hope.”

Carrie Arnold

Carrie Arnold is an award-winning, independent health and environment reporter from Virginia. Her work has been appeared in the New York Times, Scientific American, Nature, National Geographic, Smithsonian, and more.

You can find her on Instagram and Twitter at @edbites.

Miguel Ángel de la Cueva

Miguel Ángel de la Cueva

Miguel Ángel de la Cueva is a documentary photographer who focuses on the natural and cultural heritage of northern Mexico. He is an Associate Fellow of the International League of Conservation Photographers and he has covered Conservation stories for iLCP, National Geographic, Geo magazine, Mexico Desconocido and environmental organizations like The Nature Conservancy, Conservation International, Wildcoast, Niparajá-WWF among others. Ángel de la Cueva has published two books: Oasis de Piedra, which won a Silver Medal Award in ExpoBook America NY 2006 in the Nature Category and La Giganta y Guadalupe, which helped to advance the creation of a New Biosphere Reserve in Baja California Sur, México.

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