By Ferris Jabr Credit Illustration by Brian Rea. Animation By Delcan & Co.
Ferris Jabr is a contributing writer at the magazine and the author of “Becoming Earth: How Our Planet Came to Life,” from which this article is adapted.
June 24, 2024 The New York Times
Earth’s crust teems with subterranean life that we are only now beginning to understand.
In the middle of North America, there is a portal to the deep recesses of Earth’s rocky interior. The portal’s mouth — a furrowed pit about half a mile wide — spirals 1,250 feet into the ground, exposing a marbled mosaic of young and ancient rock: gray bands of basalt, milky veins of quartz and shimmering constellations of gold. Beneath the pit, some 370 miles of tunnels twist through solid rock, extending more than 1.5 miles below the surface. For 126 years, this site in Lead, S.D., housed the Homestake Mine, the deepest and most productive gold mine on the continent.
In 2006, the Barrick Gold Corporation donated the mine to the state of South Dakota, which converted it into the largest subterranean laboratory in the United States, the Sanford Underground Research Facility. Although the lowest tunnels flooded after mining ceased, it is still possible to descend nearly a mile beneath the planet’s surface. Most of the scientists who do so are physicists conducting highly sensitive experiments that must be shielded from interfering cosmic rays. But a few biologists also venture into the underground labyrinth, typically seeking its dankest and dirtiest corners — places where obscure creatures extrude metal and transfigure rock.
On a bitingly cold December morning, I followed three young scientists and a group of Sanford employees into “the cage” — the bare metal elevator that would take us 4,850 feet into Earth’s crust. We wore neon vests, steel-toed boots and hard hats. Strapped to our belts were personal respirators, which would protect us from carbon monoxide in the event of a fire or explosion. The cage descended swiftly and surprisingly smoothly. Our idle chatter and laughter were just audible over the din of unspooling cables and whooshing air. After a controlled plummet of about 10 minutes, we reached the bottom of the facility.
Our two guides, both former miners, directed us into a pair of small linked rail cars and drove us through a series of narrow tunnels. Within 20 minutes, we had traded the relatively cool and well-ventilated region near the cage for an increasingly hot and muggy corridor. Whereas the surface world was snowy and well below freezing, a mile down it was about 90 degrees with nearly 100 percent humidity. Heat seemed to pulse through the rock surrounding us, and the air was thick and cloying; the smell of brimstone seeped into our nostrils. It felt as though we had entered hell’s foyer.
The rail cars stopped. We stepped out and walked a short distance to a large plastic spigot protruding from the rock. A pearly stream of water trickled from the wall near the faucet’s base, forming rivulets and pools. Wafting from the water was hydrogen sulfide — the source of the chamber’s odor. Kneeling, I realized that the water was teeming with a stringy white material similar to the skin of a poached egg. Caitlin Casar, a geobiologist, explained that the white fibers were microbes in the genus Thiothrix, which join together in long filaments and store sulfur in their cells, giving them a ghostly hue. Here we were, deep within Earth’s crust — a place where, without human intervention, there would be no light and little oxygen — yet life was literally gushing from rock. This particular ecological hot spot had earned the nickname Thiothrix Falls.
On a different level of the mine, we sloshed through mud and shin-high water, stepping carefully to avoid tripping on submerged rails and stray stones. Here and there, delicate white crystals, most likely gypsum or calcite, ornamented the ground and walls, glimmering like stars. We eventually reached another large spigot mired in what looked like wet clay, which varied in color from pale salmon to brick red. This, too, Casar explained, was the work of microbes — in this case a genus known as Gallionella, which thrives in iron-rich waters and excretes twisted metal spires. At Casar’s request, I filled a jug with water, scooped microbe-rich mud into plastic tubes and stored them in coolers, where they would await analysis.
Casar and her colleagues have visited the former Homestake Mine at least twice a year for many years. Every time they return, they encounter enigmatic microbes that have never been successfully grown in a laboratory and species that have not yet been named. Their studies are part of a collaborative effort whose leaders include Magdalena Osburn, a professor at Northwestern University and a prominent member of the relatively new field known as geomicrobiology.
Scientists like Osburn have shown that, contrary to long-held assumptions, Earth’s interior is not barren. In fact, a majority of the planet’s microbes, perhaps more than 90 percent, may live deep underground. These intraterrestrial microbes tend to be quite different from their counterparts on the surface. They are ancient and slow, reproducing infrequently and possibly living for millions of years. They often acquire energy in unusual ways, breathing rock instead of oxygen. And they seem capable of weathering geological cataclysms that would annihilate most creatures. Like the many tiny organisms in the ocean and atmosphere, the unique microbes within Earth’s crust do not simply inhabit their surroundings; they transform them. Subsurface microbes carve vast caverns, concentrate minerals and precious metals and regulate the global cycling of carbon and nutrients. Microbes may even have helped construct the continents, literally laying the groundwork for all other terrestrial life.
Like so much about Earth’s earliest history, exactly where and when life first emerged is not definitively known. At some point not long after our planet’s genesis, in some warm, wet pocket with the right chemistry and an adequate flow of free energy — a hot spring, an impact crater, a hydrothermal vent on the ocean floor — bits of Earth rearranged themselves into the first self-replicating entities, which eventually evolved into cells. Evidence from the fossil record and chemical analysis of the oldest rocks ever discovered indicate that microbial life existed at least 3.5 billion years ago and possibly as far back as 4.2 billion years ago.
Among all living creatures, the peculiar microbes that dwell deep within the planet’s crust today may most closely resemble some of the earliest single-celled organisms that ever existed. Collectively, these subsurface microbes make up an estimated 10 to 20 percent of the biomass — that is, all the living matter — on Earth. Yet until the mid-20th century, most scientists did not think subterranean life of any kind was plausible below a few meters.
The oldest scientific reports of subsurface life date only to the 1600s. In 1684, while traveling through central Slovenia, the naturalist Janez Vajkard Valvasor investigated rumors of a dragon living beneath a spring near Ljubljana. Local residents believed the dragon forced water to the surface every time it shifted its body. After heavy rains, they sometimes found baby dragons washed up on rocks nearby: slender and sinuous with blunted snouts, frilled throats and nearly translucent pink skin. It was not for another century that naturalists formally identified the creatures as aquatic salamanders that lived exclusively underground in water flowing through limestone caves. They are now known as olms.
In the early 20th century, scientists started to get glimpses of the true abundance of life deep underground. Around 1910, while trying to determine the source of methane gas in mines, German microbiologists isolated bacteria from coal samples collected 3,600 feet below the surface. In 1911, the Russian scientist V. L. Omelianski discovered viable bacteria preserved in permafrost alongside an unearthed mammoth. Not long after that, Charles B. Lipman, a soil microbiologist at the University of California, Berkeley, reported that he had revived ancient bacterial spores trapped in chunks of coal obtained from a Pennsylvania mine.
Although these early studies were tantalizing, many scientists remained skeptical because of the possibility that surface microbes had contaminated the samples. In subsequent decades, however, researchers continued to find microbes in rock and water obtained from mines and drill sites all over the world. By the 1980s, attitudes had started to shift. Studies of aquifers clearly indicated that bacteria populated groundwater, even thousands of feet below the surface. And scientists developed more rigorous methods for preventing the accidental introduction of surface microbes, such as disinfecting drill bits and tracking the movement of fluids through the crust to make sure surface water was not mingling with their samples.
Ultimately, the results of this research confirmed that, if anything, early proponents of a subterranean biosphere had been too conservative. Wherever scientists looked — within the continental crust, beneath the seafloor, under Antarctic ice — they found unique communities of microbes collectively containing thousands of unidentified species. In certain pockets of the crust, there appeared to be as few as one microbe per cubic centimeter, equivalent to a country with only one person every 400 miles. The underworld was real, but its inhabitants were much smaller and stranger than anyone had imagined.
In the 1990s, Thomas Gold, an astrophysicist at Cornell University, published a series of provocative claims about Earth’s inner microbial wilderness. Gold proposed that micro-organisms permeated the entire subsurface, living in fluid-filled pores between the grains in rocks. Although scientists had not yet found microbes farther than 1.86 miles underground, Gold suspected that they lived as deep as six miles and that the biomass within the crust was at least equal to, if not greater than, that on the surface. He further suggested that at least some branches of life may have originated in the planet’s interior; that other planets and moons might also harbor subterranean ecosystems; and that deep-dwelling microbes were likely to be the most common form of life throughout the cosmos.
By the early 2000s, scientists started devising new ways to plunge even farther into Earth’s crust. Mines were particularly promising because they provided access to the remote subsurface without requiring much additional drilling or infrastructure. Tullis Onstott, a professor of geosciences at Princeton University, and his colleagues traveled to ultradeep gold mines in South Africa and retrieved samples of groundwater from nearly two miles underground. Within some of the deepest samples, they found a single species: a baguette-shaped bacterium with a whiplike tail that endured temperatures up to 140 degrees and acquired energy from the chemical byproducts of radioactively decaying uranium embedded in its sunless home.
Onstott and his colleagues decided to name the microbe Desulforudis audaxviator, after a passage in Jules Verne’s “Journey to the Center of the Earth,” which reads “descende, Audax viator, et terrestre centrum attinges” — “descend, bold traveler, and you will attain the center of the Earth.” The water in which D. audaxviator was discovered had not been disturbed for tens of millions of years at a minimum, suggesting that a population of these daring microbial terranauts may have sustained itself for at least as long. “We do not normally think of rock as harboring life,” Onstott writes in his book “Deep Life.” “Like most geologists, I too have viewed rocks as inanimate entities.” But now, he continues, as a geomicrobiologist, he sees all rocks as little worlds unto themselves, composed of micro-organisms, “some of which may have been living in the rock since its formation hundreds of millions of years ago.”
Some communities of subsurface microbes may be even older. The Kidd Creek Mine in Ontario, Canada, is one of the largest and deepest mines in the world. Extending about 1.86 miles below ground, it contains rich veins of copper, silver and zinc that formed nearly three billion years ago on the ocean floor. In 2013, the University of Toronto geologist Barbara Sherwood Lollar published a study demonstrating that some parcels of water in the Kidd Creek Mine have been isolated from the surface for more than a billion years, making it the oldest water ever discovered on Earth. Transparent when first collected, the iron-rich water turns a pale orange when exposed to oxygen; it has the consistency of maple sap, contains at least twice as much salt as modern seawater and, in Sherwood Lollar’s judgment, “tastes terrible.” In 2019, Sherwood Lollar, Magdalena Osburn and several colleagues confirmed that just like much younger fluids circulating through the pores and fissures in rock a few thousand feet below the surface, the billion-year-old water miles deep in Kidd Creek Mine is also populated by micro-organisms. Although some of these microbial communities are likely a few hundred million years old at most, it is possible that others have continuously inhabited the deep crust for an eon or more. (Click here for the full article from The New York Times)
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