In a Fierce Desert, Microbe ‘Crusts’ Show How Life Tamed the Land
The landscape in Pan de Azúcar National Park in Chile’s Atacama Desert appears barren, but ancient, unusual communities of microbes grow in a thin crust across the terrain.
Zack Savitsky for Quanta Magazine
Introduction
In 2017, a team of scientists from Germany trekked to Chile to investigate how living organisms sculpt the face of the Earth. A local ranger guided them through Pan de Azúcar, a roughly 150-square-mile national park on the southern coast of the Atacama Desert, which is often described as the driest place on Earth. They found themselves in a flat, gravelly wasteland interrupted by occasional hills, where hairy cacti reached their arms toward a sky that never rained. The ground under their feet formed a checkerboard, with irregular patches of dark pebbles sitting between lighter ones as bleached as bone.
Initially, the black patches speckling the desert surface didn’t interest group leader Burkhard Büdel, a veteran biologist who had spent the last several decades scraping deserts on all seven continents for signs of life. Discolorations like these, known as desert varnish, are ubiquitous and routinely signify deposits of manganese or other minerals. Keep moving, he instructed his teammates.
But his graduate student Patrick Jung couldn’t get the checkerboard out of his head. Having spotted what looked like lichens on some of the dark pebbles, Jung suspected that something more might inhabit them. Eventually, he picked up a rock, dribbled some water on it from a bottle, and peered at it through his handheld magnifying lens. The face of the black stone erupted with green. The rubble had come alive.
Jung whipped a photosynthesis monitor out of his pack. One tap of its fluorescent blue sensor confirmed that something within the rocks was converting carbon dioxide to oxygen. After Jung’s colleagues, Büdel included, replicated the experiment, they all danced with excitement under the desert sun. Then they lay down on their bellies, eyes fixed on the microbial carpet living in the dust. All around them, the dark patches repeated across the landscape, each one filled with its own microscopic universe.
Since 2019, Jung has led a project at the University of Applied Sciences in Kaiserslautern, Germany, dedicated to the study of the unusual community of microbes, now known as grit crust. His team has worked to understand the extreme adaptations that have allowed these microorganisms to inhabit a land so infamously hostile, where they are refreshed only occasionally by sips of fog. The answers they have uncovered offer clues about how life may have first found a grip on our planet’s surface billions of years ago.
Two months ago, the park ranger who first brought the German scientists to Pan de Azúcar guided me to the site of their discovery. Kneeling in one of the checkerboard’s black spaces, José Luis Gutiérrez Alvarado picked up a stone about the size of an earring stud. From his pocket he retrieved a magnifying jeweler’s loupe, a personal keepsake inscribed with the words “Los secretos de las rocas.” He held the loupe over the stone in his palm so that I could learn its secrets too.
The discovery of the grit crust transformed the desert for Gutiérrez Alvarado, who has patrolled it every day for the last decade. “It’s not only rocks, not only empty space,” he said, peering out over the patches of pebbles. “Everything is breathing now.”
The researcher Liesbeth van den Brink and the park ranger José Luis Gutiérrez Alvarado examine the “grit crust” microorganisms that inhabit pebbles on the desert floor. A jeweler’s loupe that Gutiérrez Alvarado carries provides magnification.
Zack Savitsky for Quanta Magazine
The Planet’s Living Skin
Driving through Pan de Azúcar with Gutiérrez Alvarado is like riding in a geological time machine. Ancient volcanic caverns from one epoch fade to rolling hills of eroded sand from another, and beyond them sits an occasional grassy quarry or cactus grove.
Between the hills peeks an outcropping of the mother bedrock, a heap of quartz spiced with different minerals. At its feet lie its progeny, smaller chunks that have broken off over millions of years. Below them sits a parade of progressively smaller rocks, all the way down to the earring-size grains that first captivated Jung. The pebbles, which litter the desert floor, are known locally as “maicillo” and in English as “grit.” The substrate is amply porous, offering plenty of cracks and corners for microbes to nuzzle into. Wedged into the crevices of each grade of rock are tiny thickets of green and black life.
During the 2017 expedition, Jung collected and dried samples of this grit and shipped them back to Germany. Then he threw himself into learning more about the microbes with such determination that he finished his doctorate in just two and a half years, with over 10 publications to show for it. From DNA samples, he deduced that the grit crust is composed of several hundred species of cyanobacteria, green algae and fungi — including several previously unknown lichen combinations. Meanwhile, his colleagues sliced the stones thin for imaging. The photos showed how individual fungal hyphae had drilled deep into the rocks, carving out networks of branching canals.
Patrick Jung, a researcher now at the University of Applied Sciences in Kaiserslautern, Germany, discovered the grit crust community in Pan de Azúcar in 2017.
Courtesy of Patrick Jung
At first glance, the grit crust could seem like a routine example of what researchers call a biological soil crust, or “biocrust” — a community of coexisting bacteria, fungi, algae and other microorganisms that caps the soil in coherent sheets. Around 12% of Earth’s land is covered by biocrusts. Ecologists often refer to these colonies as the planet’s “living skin.”
Over the last century, scientists have identified biocrusts around the globe and worked to understand their role in shaping ecosystems. They’ve learned that the crusts anchor soil grains in place and provide the organisms growing in that soil with essential nutrients such as carbon, nitrogen and phosphorus. In 2012, Büdel and his colleagues estimated that biocrusts soak up and recycle around 7% of all the carbon and nearly half of all the nitrogen that is chemically “fixed” by terrestrial vegetation. The role of the biocrusts in procuring digestible nitrogen is particularly critical in arid deserts: Elsewhere, lightning can often convert atmospheric nitrogen to nitrates, but in the deserts, electrical storms are rare.
The biocrust creates “little oases of fertility,” said Jayne Belnap, an ecologist at the U.S. Geological Survey who helped to standardize the term “biocrust” in 2001. “That area is going to be [like] popsicles for the soil organisms. They’re sugar addicts just like all the rest of us.”
But the microbial community in Pan de Azúcar isn’t just any old biocrust. While traditional biocrusts drape themselves over the top layer of fine soil particles, and other kinds of organisms sprout directly on top of individual boulders, “the grit is in between — it’s a transition zone,” said Liesbeth van den Brink, an ecology researcher at the University of Tübingen who now lives just outside Pan de Azúcar with Gutiérrez Alvarado. In grit crust, the stones provide the structure, but the microbes colonize them in a coherent sheet — like a thin layer of resin grouting together a rock garden.
Because the organisms are so intimately associated with the rocky substrate, the grit crusts embody “the collision of the abiotic with the biotic,” said Rómulo Oses, a biologist at the University of Atacama. “At this interface, you will see a lot of answers.”
The grit crusts of Pan de Azúcar have compelled scientists to expand their conception of what biocrusts are, where microbes can survive, and how microbial communities shape the environment around them. They are opening the door for reconsiderations of how Earth and life coevolved over epochs.
In the park, various species of cactus are nourished by a fog that regularly seeps in from the coast.
Zack Savitsky for Quanta Magazine
Sipping on Fog
Pan de Azúcar is desolate, but it’s far from lifeless. Bordering the Pacific Ocean near sea level, the park is much more temperate than the Atacama’s elevated hyper-arid core. Still, it receives at most 12 millimeters of rain per year, and the solar radiation levels are often blisteringly high.
On the way to the park’s sole food truck, where Gutiérrez Alvarado, van den Brink and I can stop for a local seafood empanada, we take a detour. Gutiérrez Alvarado stops to check on one of his weather-monitoring devices, which is enclosed in barbed wire and fastened down with rocks in the desert. Next to it, he points out a roughly cow-size depression in the ground where a guanaco, a wild relative of the llama, recently took a dust bath. Gutiérrez Alvarado and the other rangers recently counted 83 guanacos living in the park.
“How do they survive here?” van den Brink marveled. “How does anything survive here?”
The answer is the distinctive thick fog that rolls up the Chilean coastline, a weather phenomenon known locally as the camanchaca. With so little rainfall, all life in Pan de Azúcar ultimately depends on whatever moisture the fog carries. The guanaco, for example, relies on sips of water that is trapped by mosses clinging to cacti, which grow in soil fertilized by grit crust.
The humans in the park are no different. On a ridge overlooking the coast sit four mesh panels the size of garage doors, which Gutiérrez Alvarado and the other rangers set up as fog collectors. Enough water condenses on them every day to supply a sink at one of the park’s few toilets. The fog is so thick that it once nearly caused Gutiérrez Alvarado to drive straight off a cliff face into the ocean; only a tiny sign on the ground reminded him to turn left at the last moment.
A series of mesh panels catches the dense desert fog known as camanchaca. Runoff from the panels supplies water to a public sink.
Zack Savitsky for Quanta Magazine
Most of that water, however, is out of reach for the grit crust organisms. For much of the day, the stones get so hot that a boundary layer of roastingly hot air forms over them, preventing the microbes from soaking up the moisture. The microorganisms have learned to wait out the heat of the day in a dehydrated, dormant state. But at night, there’s no sunlight for them to use for photosynthesis. So the microbes have at most a few hours after sunrise to drink the water that has condensed as fog or dew.
Jung and colleagues tested just how little water the microbes need to start photosynthesizing. The ideal serving was 0.25 millimeters of water — lower than the requirement of any other known biocrust. Once dampened, the microbes start photosynthesizing faster than any community the researchers have ever seen.
“There is a way for these organisms to live long and prosper despite the fact that they’re in a hyper-arid area,” Belnap said. That resourcefulness hugely extends the terrain that biocrusts can occupy beyond what scientists had thought. Although grit crust has been found only in Pan de Azúcar so far, researchers suspect it may also grow in other regions of the Atacama and possibly in the deserts of southern Africa.
“The grit crust is setting a new threshold for conditions that make life possible,” Jung said.
Yet just as the desert has conditioned these microbes, the microbes literally shape the desert. Because of all the organisms colonizing the tiny rocks, when the grit crusts get wet and the cells rehydrate themselves, the volume of each grit stone increases by around 25%. As the desert fog rolls in and out, the grit stones swell and shrink. These regular contractions, along with the acids secreted by the microbes during photosynthesis, have a “biological weathering” effect — breaking rocks down to pebbles, and from pebbles to grit.
Van den Brink points out cactus lichens, which trap droplets of fog water that are sipped by the park’s wildlife.
Zack Savitsky for Quanta Magazine
While all biocrusts perform some degree of weathering, the larger grains of the grit crust are especially suited for it. The process reveals the full potential of microbes to impact their environment. A microbial skin can glue together pebbles, break them down into soil and fertilize that soil with essential nutrients. In effect, the crust can “terraform” the desert.
The power of the microbes was on full display after a disaster in 2015. Two years before Jung set foot in Pan de Azúcar, a rare flash flood ravaged the area. In just two days, the region received many years’ worth of rain. The resulting floods caused at least 31 deaths in neighboring towns.
The desert, however, burst with life. Over the following months, the dirt gave rise to a miraculous display of wildflowers — a “desierto florido.” How the plants awakened from a decades-long rest with such zest has perplexed soil biologists. But again, the key may be in the crust.
Fernando D. Alfaro, a microbial ecologist at Major University in Chile, tests that hypothesis by unleashing his own tiny floods upon the desert. He pours gallons of bottled water onto square-meter plots of desert soil. The plots that are covered in biocrust retain water for much longer, and some have managed to sprout plants in just a few weeks.
“For many years, [biocrusts] are preparing the system and the substrate to respond very fast to this input of rains,” Alfaro said. “These flower events depend on these tiny communities of microbes.”
Jung, too, has witnessed the microbes’ resilience. At 11 sites around Pan de Azúcar, he selected neighboring black and white splotches and measured their biological activity. Then he collected the top layer of grit, sterilized it in a pressure cooker, and placed it back on the ground. Within a year, the once-black areas became dark again as the microorganisms started recolonizing the sterile plots — far more quickly than usually occurs with the lichens and other microbes in biocrusts. Remote sensing data taken during the past decade has shown that 89% of the park’s surface is covered in the checkerboard pattern. Within that colonized area, about a quarter of the black-and-white design shifted over the last eight years — a surprisingly quick reaction time for the usually sluggish microbes.
Tiny Conquerors of the Land
The grit crust plays an important role in the local ecosystem, but its scientific allure doesn’t stop there. Ancient, stable and unearthly, this environment also draws the attention of astrobiologists.
For decades, scientists have used sections of the Atacama Desert as terrestrial analogues for Mars. The extreme radiation, infrequent precipitation, barren landscape and wild temperature fluctuations make the desert distinctively otherworldly. (Gutiérrez Alvarado, however, maintains that the most alien thing about Pan de Azúcar are his fellow park rangers — “definitely they are Martians,” he said, cracking a smile.)
Researchers are using Atacama biocrusts to construct a library of chemical signatures that could guide the search for microbial life on Mars. But the biocrust organisms also open a window into life on a slightly less foreign planet: the early Earth.
Fossil evidence suggests that microbes were living near deep-sea hydrothermal vents around 3.5 billion years ago. When and how life conquered the land, however, is less clear. The terrain on the continents was harder, sharper and far more forbidding than it is today.
“You wouldn’t have had nicely developed soil like you do now,” said Ariel Anbar, a geochemist at Arizona State University. “Plants that depend on there having been many generations of plants before to create an environment that’s hospitable — they would have had a tough time.”
Pebbles filled with grit crust microbes form a patchy black layer that covers much of the ground in Pan de Azúcar.
Zack Savitsky for Quanta Magazine
Before plants arrived, some researchers think, crusts of microbes could have helped prepare the land by transforming bare rock into fertilized soil. A biocrust well adapted to extreme conditions could take hold of a suitable substrate that held nutrients and was regularly moistened with fog. By gradually weathering the rocks and stabilizing the sediment as soil, it could alter the environment in a way that promoted the development of higher organisms.
“This biocrust of Pan de Azúcar represents this scenario,” Alfaro said. “It is like a primordial community to increase the development of soils and make more complex communities.”
The grit crust microbes in the Atacama today aren’t a perfect replica of the ones that may have prepared the early Earth. Such an ancient community likely would have been tuned for an oxygen-deficient environment and devoid of lichens, which are thought to have evolved only in the last 250 million years. But the researchers agree that modern grit crust communities can still serve as valuable analogues for what came eons before.
The idea that microbes could have primed the habitability of early Earth is not a new one. In the 1980s, the environmental scientists David Schwartzman at Howard University and Tyler Volk at New York University suggested that the biological weathering caused by early land life could have sequestered enough carbon dioxide from the atmosphere to cool the Earth’s surface into a range habitable for other creatures. “We have evidence of really intense weathering in the Archean,” Schwartzman said. “Presumably biocrusts played some role in that.”
But we don’t have to rely on assumptions. Over the past few decades, indirect evidence has surfaced for microbial communities on land during the Archean. Gregory Retallack, an emeritus professor at the University of Oregon, believes he has found evidence for communities resembling biocrusts in fossilized soils (or “paleosols”) as far back as 3.7 billion years ago — challenging the common assumption that life originated in the sea. “The evidence from paleosols is pretty clear that there were all sorts of things on land, even very early on,” he said. “You can see these microbial crust fabrics just with the naked eye.”
A team led by Christophe Thomazo, a geobiologist at the University of Burgundy, has found evidence that some modern biocrusts could have survived in the atmosphere of the early Earth during the Archean: Their microbes could have efficiently fixed gaseous nitrogen into ammonium and nitrate, delivering accessible nutrients to the emerging global ecosystem. The researchers also noticed that some of the isotopic carbon and nitrogen content of some desert biocrusts is like that of rocks from the Archean.
“There are signatures [in these biocrusts] that are compatible with Archean organic matter,” Thomazo said. He is “quite confident” that the planet’s first terrestrial residents were something akin to modern biocrusts.
Resilient but Fragile
During the drive out of the park, Gutiérrez Alvarado stops the car, gets out, and turns around. His car’s tire tracks have sliced sharply through the dense coverage of grit crust, leaving an array of microbial corpses in their wake. The crust is resilient, but it’s far from indestructible, and even human footprints can wipe out small chunks of it. That’s why the National Park Service has posted “Don’t bust the crust” signs across the western United States, urging hikers to stay on the paths to protect the breathing soil.
Gutiérrez Alvarado walks back to his car through the fog. The desert crust is highly sensitive to trampling by cars and hikers.
Zack Savitsky for Quanta Magazine
Gutiérrez Alvarado treasures the expanse of grit crust. As a ranger, his mission is to keep the park’s landscape and all that inhabits it safe from negligent visitors and invasive mining operations, he said. In a study published in April that he co-authored with Jung and van den Brink, he urged the Chilean national park management to consider biocrusts in their nature conservation plans.
“We need to justify why we close roads or close some trails so no one can go there,” Gutiérrez Alvarado said. “We don’t have laws, so the research is our backup.”
But biocrusts face an anthropogenic threat much worse than footprints: climate change.
In 2018, Belnap, Büdel and their colleagues published a study estimating how different biocrusts around the world would adapt to climate change and land-use intensification. Their models predicted that by the end of the century, the global coverage of biocrusts could diminish by 25% or more. Those reductions could make for less healthy soils and cause loose dust to settle onto snowpacks, trapping more heat and worsening the planet’s climate ills. “Then we will truly start to see the analogues with Mars,” van den Brink said.
However, the Atacama biocrusts stand out in this model. Under advanced climate scenarios, when most other crusts die off, the grit appears to flourish.
As the sun recedes, Gutiérrez Alvarado, van den Brink and I climb up a sandy mound for one last glimpse of the rolling hills being swallowed by fog. From the top, I can also admire the true expanse of the grit empire and its legions quietly claiming territory out to the horizon. I can’t help but think how all along, the rocks may have been keeping one more secret: that if microbes like these were the first to arrive, perhaps they’ll also be the last to go.
