ABOVE: Oases scattered around the Cuatro Ciénegas Basin in Northern Mexico are home to ancient microbial life.

Deep within Northern Mexico’s Chihuahuan Desert lies the Cuatro Ciénegas Basin, a butterfly-shape valley where small turquoise lagoons dot the landscape. These hidden oases possess conditions remarkably similar to those of the planet’s prehistoric past and house many organisms, including fish, diatoms, and bacteria, that cannot be found anywhere else on Earth. The aquatic system is also one of the few places where stromatolites—rock- or reeflike structures, built up by microbes, that once dominated the shores of ancient oceans—still live and grow, their surfaces made up of active microbial colonies.

The unusual features of the Cuatro Ciénegas Basin and its inhabitants have drawn many scientists to the area since it was first encountered by biologists in the late 1930s. Valeria Souza, a microbiologist at the National Autonomous University...

Since the early days of her work in Cuatro Ciénegas, Souza has been interested in the microbial communities that inhabit the basin. The nutrient composition of the lagoons is quite different from that found elsewhere in the world, Souza says, probably due to the inflow of water from deep aquifers under the mountain—which harbors ancient sediments and clay—at the center of the valley. With high levels of sulfur and very low concentrations of phosphorus, the water in Cuatro Ciénegas is much more similar to oceans of the Precambrian era, which ended approximately 542 million years ago, than to modern-day seas. Most of Earth’s contemporary life forms require more phosphorus in the environment to survive, so Souza and her colleagues were puzzled when they found a high level of microbial diversity in the area (PNAS, 103:6565–70, 2006). “This is probably [one of] the most diverse places on Earth,” Souza says. “And I’ve been trying to understand why.”

Given the prehistoric Earth–like conditions of the basin, Souza and her colleagues hypothesized that Cuatro Ciénegas may be a “lost world,” a safe haven where ancient organisms could persist and evolve in isolation from the rest of the planet. To test this theory, the researchers recently gathered soil, sediment, and water samples from ten sites in Churince, a 300-meter-long lagoon in the basin. They then extracted DNA and conducted 16S ribosomal sequencing, which revealed more than 5,000 species of bacteria and archaea.

The water in Cuatro Ciénegas is much more similar to oceans of the Precambrian era than to modern-day seas.

To uncover the evolutionary history of some of these organisms, the team zoomed in on one genus of bacteria, Bacillus. By comparing the sequences of approximately 2,500 species to those in two online databases, the team identified two lineages that were unique to Cuatro Ciénegas—one that appeared in sediment and another that was related to modern-day marine microbes (eLife, 7:e38278, 2018).

When the researchers dated the two groups using software that reconstructs evolutionary trees from molecular sequences, they discovered that the sediment lineage appeared approximately 650 million years ago—during the late Precambrian period—and that the marine one emerged around 160 million years ago, during the Late Jurassic. The researchers suggest that there were two events that led the lineages to set up shop in the basin: one, an abrupt change in the balance of nutrients at the end of the Precambrian era, and the other, the breakup of Pangea during the Jurassic.

“It’s odd to think that there is a place where there are organisms that have not been anywhere else for [this long],” says Frederick Cohan, a microbiologist at Wesleyan University who did not take part in the study but was a reviewer of the paper. “It’s like Jules Verne in a microscope,” he adds, referring to the author of Journey to the Center of the Earth, where fictional explorers descend into a volcano and discover prehistoric animals hidden below the surface. “And that just blows me away.”

“This idea of a lost world, where a certain environment is a niche for ancient microorganisms, is quite interesting,” says Brendan Burns, a microbiologist at the University of New South Wales in Australia who was not involved in this work. “I think it might take some more digging to see whether other areas like this can be found, to see how unique what they discovered really is.”

Souza and her colleagues believe that the extreme nutrient conditions in Cuatro Ciénegas—and possibly a heightened ability of native bacterial species to fight off invading microorganisms—may explain why these ancient microbial lineages never left the basin. Cohan agrees that the uniqueness of the environment is likely a key factor, but doubts that rivalry between species played a big role. “My understanding is that antagonism in bacteria is primarily against fairly close relatives,” Cohan says. “I think it would be difficult to imagine that this community is defended from everything that could come in.”

More research is needed to fully understand the history of these ancient bacterial communities. But for scientists who wish to continue investigating the Cuatro Ciénegas Basin, there is some bad news: the wetlands in the valley have shrunk by 90 percent over the last 50 years. The Churince lagoon dried up in 2017. “The last time we saw it with water was in 2016,” Souza says. When she and her colleagues returned to find the area bone dry in the fall of the following year, “we cried like crazy,” Souza recalls.

One of the primary causes of the desiccation is agriculture—specifically, farmers diverting water from the valley’s wetlands for their crops. To address this problem, Souza and her colleagues have started to engage the local community in conservation efforts. In 2011, for example, they set up a lab at the high school in the small city of Cuatro Ciénegas to educate students about the importance of the region—and have been taking them out into the field and getting them involved in collecting and analyzing samples. The efforts have resulted in positive change—for example, some irrigation systems in Cuatro Ciénegas have now been replaced with ones that use much smaller amounts of water—but Souza says their conservation work is far from complete.

“It’s sad to think that this basin has been there with those living organisms for [almost] a billion years,” says Cohan, “and yet with the short time of human disturbance, it [could] disappear.”

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