Over two decades ago, a U.S. scientist with a grant from the National Aeronautics and Space Administration (NASA) invited Mexican evolutionary microbiologist Valeria Souza Saldívar to help study a remote mountain-valley oasis in the northern Mexican municipality of Cuatro Ciénegas.

NASA’s interest was piqued by the presence in the valley’s spring-fed wetlands of live stromatolites, microbial reefs that are among the world’s oldest known fossils but are now rarely found living. The space agency believed the Cuatro Ciénegas valley, located in the mountains of Coahuila state, could aid efforts to determine whether there is life on Mars, since the microorganisms inhabiting the desert oasis show extraordinary adaptability.

But scientists had no idea that when it comes to microbes, the valley’s wetlands would turn out to be what Souza describes as “the most diverse place on earth.” In her ensuing 22 years of research—conducted in partnership with her husband, fellow microbiologist Luis Eguiarte—she explored the extent of that diversity.

An expert in the molecular evolution of microorganisms, she learned that the turquoise, spring-fed desert pools offered a glimpse of early life on Earth, when the planet was devoid of many nutrients. But the National Autonomous University of Mexico (UNAM) researcher also saw how this highly unusual ecosystem is increasingly threatened by large-scale farming.

Agricultural operations, most of which grow alfalfa for use as cattle fodder, now claim nearly 90% of the region’s groundwater resources, causing a drying of the extraordinary desert pools. A study done a decade ago by Conagua, Mexico’s National Water Commission, showed that farming at the time was already consuming water at nearly twice the region’s recharge rate.

What worries Souza, other scientists and environmental advocates is the possibility that the continued unsustainable use of water by commercial farming operations have weakened and could completely disrupt the local water cycle.

Souza life’s work has been to understand why there are so many fauna and flora species in the world. For over 20 years she pursued that goal in Cuatro Ciénegas, periodically shuttling there from Mexico City, where she teaches and has a lab at UNAM.

Cuatro Ciénegas sheds light on the question of species diversity because its wetlands have been so isolated that its microorganisms have remained in an “ancient state” for over 200 million years. The result is a living laboratory containing what is believed to be the widest array of such microorganisms on the planet.

The desert-bracketed wetlands are believed to have been part of a shallow sea in the Precambrian era that, due to powerful tectonic activity, wound up as an oasis in a mountain valley 740 meters (2,400 feet) above sea level. Former marine sediment and ancient microbes inhabiting it underpin the ecosystem, whose 200 natural springs form a hydrological complex of lagoons, pools, streams and marshes nurtured by a deep aquifer in a nearby mountain—Sierra de San Marcos y Pinos.

Bacteria have managed to survive thanks to water that rises at least 20 kilometers (12 miles) from deep, magma-warmed water tables and cycles back down. The bacteria rise and descend in the water cycle, too. Souza describes the land underlying the wetlands as a “giant body whose heart is the magma.” She adds: “The heart pumps hot water up to the wetlands, where it oxygenates. The wetlands are the body’s lungs. The cold oxygenated water then flows back down to the depths of the water table.”

Her work involves population-genetic approaches as well as microcosm studies to investigate gene transfer, patterns of diversity, and adaptations to specific environmental factors. She says her favored explanation of how life flourished on earth revolves around phosphorus. The crucial chemical element’s scarcity during the first three billion years of Earth’s existence enhanced metabolic diversification of early life, but inhibited the evolution of larger organisms that need more energy to grow, she says.

“The evolutionary theory that I believe most is that phosphorus was trapped in the rocks and needed to be released by erosion or a big bang,” Souza says. “So in the late Hadean [period], when water was already liquid, it’s possible a comet fell on the primitive planet’s bed of clay. On one hand, the impact liberated the phosphorus and, on the other hand, the comet contained a rich organic soup produced by interstellar dust. The mix possibly gave birth to life and the early diversification of life.”

She points out that in Cuatro Ciénegas, an extreme lack of phosphorus has persisted, so ancestral life, with its slow-growing ancient bacteria, marches on.

Michael Travisano, a University of Minnesota evolutionary biologist who first visited Cuatro Ciénegas 20 years ago and has collaborated with Souza, says it is easy to drive straight through the area without appreciating its unique conditions. “Yet a closer look reveals information about the origin of life on earth and gives us a better idea of what a microbial dominated landscape can look like, with no plants or animals,” Travisano says. “Otherwise, it is hard to imagine just microbes.”

Souza says that in 22 years of study, she and fellow researchers were able to develop a range of tools to explore the vital biochemical cycles she describes as “the clock of life”—and to gauge how the rich array of ancient microbial resources kept it all in motion.

“What was fascinating…is that there are always replacement parts for this clock of life,” she says. “If it fails, there will be zillions of other microbes that have the genes capable of doing the job needed for the elements of life to circulate and make life.”

Travisano points out that microbes have been the dominant form of life on earth for 4 billion years and are still everywhere, carrying out the key functions they always have, such as transforming atmospheric nitrogen into nitrogen in the soil. But in most places microbial diversity has been overrun by what Travisano describes as “obscuring layers” of flora and fauna, making microbes much harder to observe.

“In Cuatro Ciénegas you can study microbial lineages with more clarity because there are not nearly as many obscuring layers and you can really see the microbes,” he says. “Being able to have the microbes less obscured by the diversity of life gives us so much insight into the evolutionary history of microbes on earth and a better understanding of what microbes are doing now.”

Microbial research also has given Souza and her team insight into how life on Earth continues to evolve. “The communities of bacteria in Cuatro Ciénegas are very interesting because they are hyper-diverse and they all help each other out, cooperating and feeding as a community,” she says. “A competition model dominated 20th century ecology, but now we understand that entire communities co-evolve. So organisms both change the environment and have to keep up with adapting to it, which means everything is constantly evolving together.”

She and other microbiologists believe that by learning how bacteria survived in low-phosphorus conditions, scientists could develop new ways to fight pollution. That’s because microbes have already shown they can survive on substances commonly implicated in contamination—heavy metals and carbon dioxide, for instance.

With scientific investigation of Cuatro Ciénegas still in its relatively early stages, Souza and other scientists warn that encroaching, water-intensive agriculture could destroy the wetland ecosystem and, in the process, undermine the microbial research. Souza has made a point of sharing her knowledge with local residents of Cuatro Ciénegas, encouraging them to understand and protect their unique environment from the unsustainable water demands of farm operations in the region. She has done so in ways ranging from appearances at public meetings to quiet one-on-one mentorship of youngsters.

Héctor Arocha, who was born and raised in the community, remembers meeting Souza in the 1990s when he was 14 years old. He says that after he told her he wanted to know more about her findings, she invited him to accompany her on a dawn expedition to a portion of the Cuatro Ciénegas wetlands called Churince lagoon.

Today, Arocha is director of Genesis 4C, an educational center focused on biodiversity and endemism in the Cuatro Ciénegas valley, which the Mexican government has designated as a Natural Protected Area. “Cuatro Ciénegas is a fragile place that holds the secrets to the origin of life, so the whole world should be concerned with making sure it is protected,” Arocha says. “We urgently need help from the federal government to avoid the wetlands being drained.”

Souza estimates the wetlands will dry up in the next five years if canal transport of their spring water outside the valley and unsustainable water use by alfalfa farmers are not controlled. “The bacteria would be fine, as they have been for three billion years, surviving five global extinctions and three ice ages,” she says. But as water levels fall, she adds, microorganisms will become less accessible for study in wetlands, and endemic species will face increasing danger. Among the latter are the Coahuilan box turtle (Terrapene coahuila), which requires the moisture of the wetlands to lay its eggs.

“Cuatro Ciénegas offers us the model of the ancient sea, when everything was in order,” Souza observes. “It is like looking at the original clock of life and when you understand that original state, and how the mechanism of cogs works, you can also understand that it can break.”

In recognition of her pioneering analysis of Cuatro Ciénegas’ microbial communities, Souza was made an International Honorary Member of the American Academy of Arts and Sciences in 2019. She also has been asked to bring her expertise to bear on ecosystems elsewhere—among them that of Ohuira, a Pacific coast bay in the Mexican state of Sinaloa.

There, coastal waters have been fouled by agricultural runoff containing nitrogen-based fertilizers, urban sewage and fuel pollution from vessels. Studies conducted during 2016 and 2017 detected low oxygen levels in the water; a weak plankton population unable to sustain the food chain; limited diversity and growth; and heavy metals in local shrimp, crab and fish.

Repairing nitrogen cycle

QB4 the Planet, a Mexican firm that advises companies on environmental restoration, is coordinating a project for a Swiss-German fertilizer company that is building three plants at Ohuira Bay and funding work to restore the area’s ecosystem. Tricia Montel, QB4’s cofounder and director, says her company turned to Souza to build consortia of bacteria and use them to help drive the process.

Souza and her team collected bacteria in the Cuatro Ciénegas oasis and in Ohuira Bay mangrove stands and are growing them together in a lab. Selected for their role in the nitrogen cycle, the bacteria will be used in conjunction with Arundo reeds planted in drainage canals at hundreds of artificial dam sites to remove nitrogen from farm runoff.

The Arundo will help slow the flow of water and suck up the excess nutrients, Souza says, and the microbes, which will be in the roots of the reeds, will dispose of the nitrogen. “The nitrogen cycle is what we think is broken in Ohuira,” she says. “The consortia are bacteria that can live together and work together in order to move the excess nitrogen in the water to the atmosphere. So the idea is that the mix of plants … and the microbes will do the trick of cleaning the water before it reaches the ocean.”

Souza is confident microbial strategies can help restore the bay’s water quality, but she says such problems will reoccur if agricultural practices are not overhauled. “By extracting fossil fuels and using carbon from oil to fix nitrogen, rather than fixing nitrogen naturally with bacteria, we are injecting more carbon and more nitrogen into the ecosystem and the clock of life has jammed,” she says. “We broke the balance that existed for 3.5 billion years in 50 years.”

Souza also has been invited to aid ecosystem-monitoring in Chile’s Magellan Straits. She is directing a project there to analyze microorganisms collected periodically on land and in the sea in different areas of the Francisco Coloane Coastal and Marine Protected Area. The goal is to create an ongoing means of tracking the largely pristine region’s ecological health in the face of rising global temperatures and strong solar radiation due to ozone depletion in the atmosphere above Antarctica.

Working with the Center for Study of the Quaternary Period (Cequa), an independent Chilean research center in the Patagonian city of Punta Arenas, her team will scrutinize microbes found on everything from penguins to bird feathers to seabed sediment and algae at varying water depths.

Microbes as monitor

Microorganisms are the project’s focus because their life and reproductive cycle are so short that they are a more efficient gauge than larger species. “The outer layers of microorganisms are very sensitive to environmental changes so they will rapidly show any adaptation if there is a change in water temperatures or effects from increased penetration of radiation,” says Paola Acuña, Cequa’s executive director.

Says Souza: “The Ohuira project is really hands-on bioengineering, while Francisco Coloane is an observation deck to understand what we are breaking in a place where human intervention doesn’t look evident.”

Acuña says Souza was chosen to lead the work on the strength of her research at Cuatro Ciénegas. “Souza is transferring her knowledge from the orange planet to the blue planet,” she says. “We are measuring the impact of climate change in situ on the entire ecosystem.”

Souza believes that insights gained from Cuatro Ciénegas can spur wide-ranging problem solving in the future. “We have a responsibility to use knowledge gained from Cuatro Ciénegas for humanity’s benefit,” she says. “We can find the cure for cancer and every antibiotic. The potential is huge. We have the mother of all golden eggs. Cuatro Ciénegas should be the world’s biotechnology hub.”