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To Hell and Back

In the hot, radioactive world miles below us, microbe hunters encounter bizarre bugs that eat and breathe geologic ingredients like iron, manganese, and sulfur and, gasp, maybe our ancestors

By Kevin Krajick and Louise Aronson
Jul 1, 1999 5:00 AMNov 12, 2019 4:27 AM


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Braving100-degree temperatures two miles down in South Africa’s East Driefonteingold mine, geologist T. C. Onstott sheds his shirt to collect microbe sampleswith biologist Duane Moser. Scientists once thought life could not be sustainedso far underground, but Onstott says evidence now suggests “microbes have beenhere for 2 billion years.”

Four scientists wearing coveralls and hard hats shuffle warily into asteel cage the size of a closet, cramming themselves against a dozenminers. The doors clang shut, and the bottom seems to drop out as theelevator plunges hundreds of stories down into the darkness--No. 5Shaft in South Africa's East Driefontein gold mine. Within moments theair becomes oppressive--hot and curiously thick. This is one of thedeepest excavations in the world, burrowing more than two miles towardthe center of Earth. At the bottom of the mine, radioactivity and heatfrom the planet's core raise the temperature of the stone in thetunnels to a searing 120 degrees Fahrenheit, and the atmosphericpressure is double that on the surface. Oxygen rarely exists naturallyso far underground, and only a constant rush of forced air from thesurface disperses poisonous methane and hydrogen seeping from the rock.Pumped-in jets of water help keep workers from slowly cooking to death.

Oxygendoes not exist naturally so far underground, and only a constant rushof forced air from the surface disperses poisonous methane and hydrogenseeping from the rock. Pumped-in jets of water help keep workers fromcooking to death.

As the elevator plummets, a miner turns onhis headlamp, revealing beads of sweat popping out on the face ofgeologist T. C. Onstott. The Princeton University professor is notscared. He pulls a water bottle from his knapsack and takes a long,slow swig. To him, the heat and claustrophobia are merely aggravation.Real worry here centers on what are euphemistically referred to asseismic events. So much rock gets dragged out of the mine each day thatthe earth around it resettles frequently. The resulting quakes spurrock bursts—high-pressure cave-ins that kill.

Day-to-day workin this hellhole requires a toughness and adaptability that few peoplecan muster. But there are life-forms deep in the mine that are eventougher: bizarre tiny creatures that Onstott and his colleagues havecome to study. “If it’s not too bad for me down there, it’s probablynot too bad for the bugs,” he says with a laugh.

The EastDriefontein mine is located some 45 miles from Johannesburgin South Africa’s Gauteng Province. In the SeSotho language, Gauteng means “place ofgold.”

Not long ago, the very idea of finding life at such depths wasconsidered less likely than discovering it on other planets. Life wasthought to peter out a little past the depth of a grave. A billionbacteria may exist in a pinch of topsoil, but biologists found that thenumbers dropped to the millions, then the thousands, then the hundredsper sample as they dug down farther from the sun, air, and sources offood. Then in the last decade, researchers digging deeper and using newanalysis techniques were astonished to find hordes of unknown microbes.

Isolated from the surface for eons, these organisms have beenliving in environments presumed impossible—oil wells, aquifers, anddeep rock. Some even thrive in radioactive stone or at temperatures of200 degrees. And far from depending on organic matter from the surfaceworld, the deepest-dwelling microbes both eat and breathe geologicingredients—like iron, manganese, and sulfur—and possibly hydrogen. Intheir wake they may leave massive deposits of metals—including copperand gold—as well as natural gases such as methane. More than 11,000 newstrains of these subterranean bacteria have been cultured, but only afew have been studied and named. Some researchers now speculate thatthe mass of life below Earth’s crust may equal or exceed the mass oflife on the surface. A few bold scientists even ponder whether thecreatures from the deep could be our ancestors. Their discovery hasalso revived hopes of finding life beneath the surface of barrenplanets like Mars.

Some microbes thrive in radioactive stone orat temperatures of 200 degrees

Onstott, a calm, lanky man who smiles easily, has adapted readily tothe strange world below his feet. As a child, he walked in awe throughthe Carlsbad Caverns in New Mexico. As a graduate student in the 1970s,he studied rocks from South Africa’s diamond mines. Then in 1994 heexperienced his first serious encounter with deep life when he workedwith a group of scientists from the U.S. Department of Energy whoanalyzed samples taken from a 1.7-mile-deep exploratory natural-gaswell dug near Washington, D.C., by Texaco.

Providing the deepestdrilling samples the biologists had seen, the hole bottoms out in ashale deposit, the remains of a long-buried lake bed. The well was abust for Texaco, but Onstott and his colleagues found otherriches—previously unknown anaerobic bacteria spread out as thinly asjust one per gram of rock, hanging on amid extreme salinity and 167degree temperatures.

The scientists who studied the wellconstructed a geologic history showing that the shale could have hostedbacteria as early as 160 million years ago—before flowering plantsfirst began growing on Earth. “The bacteria probably filtered in withgroundwater,” Onstott says.They took up residence in rock pores, andimpermeable sediment layers formed over them, blocking new migrationand the flow of nutrients. Then, about 80 million years ago, whendinosaurs were still walking around upstairs, the pore entries hadgotten too small for even the smallest bacteria to squeeze in or out.Onstott says the bacteria must have been trapped in their tiny tombssince that time. Amid such harsh conditions, cells become livingfossils, taking hundreds, even tens of thousands, of years to divide.Scientists named one strain discovered in the Texaco well Bacillusinfernus—bacterium from hell.

Even with advances in drillingtechniques, it is difficult to obtain samples from wells that have notbeen contaminated by air or water from the surface. Onstott decided hehad to find a way to visit the microbes himself. The mine he chose toexplore is part of a sprawling man-made underworld started on a Sundaymorning in 1886 when an Australian prospector found a gold-rich outcropon the present site of Johannesburg. Like a nose peeping out of thecovers, that outcrop was just the start; since then, three-quarters ofthe gold ever mined has come out of the region. The most recent shaftat East Driefontein took 15 years to excavate—and that was just thevertical hole.

In amakeshift lab, microbiologist Svetlana Kotelnikova uses an anaerobic chamber tohandle mine rocks. Some samples turned out to contain methane-eating microbes.

For his journey into this biosphere, Onstott rounded up an all-starcrew of microbiologists. They included: Bill Ghiorse, who led someEnvironmental Protection Agency research into subsurface bacteria thateat toxic waste; Duane Moser, a lab wizard and avid spelunker; SvetlanaKotelnikova, a Russian scientist working in Sweden; Mary DeFlaun ofEnvirogen; and Jim Fredrickson, who has isolated many deep-bacteriacultures while working at the Pacific Northwest National Laboratory.

AtEast Driefontein, Onstott and his teammates would spend three monthsgathering samples at a depth where no microbe hunters had venturedbefore: the Number Five shaft bottoms out at 11,222 feet. On thisscouting mission, the elevator comes to a grinding halt at 6,120 feetand the researchers walk through a short tunnel to a second elevatorthat takes them to the mine’s newest and deepest diggings. A faintsmell of ammonium-nitrate explosive hangs in the air during the secondelevator descent. At the bottom, two escort miners, Marius Coleske andRaj Nair, direct the group to a miniature train for a half-mile ridethrough the dark as a giant air pipe roars overhead. Everyone sweatsfreely from every pore, even the miners. “I couldn’t believe how muchfluid I lost,” Onstott says later. “My boots were full of sweat. Icould feel it slosh up against my shins at every step. I had to keepemptying the perspiration out of my gloves.”


Biologistsfound a wide variety of bacteria in a sample of mine-fissure water.

Theorganisms of the deep biosphere are amazingly well-adapted to the tough livingconditions of their world. Normal surface protozoans, which eat bacteria, canbe ten times the size of their prey. Far underground—where available foodamounts to as little as 1 percent or less of that found on thesurface—protozoans might be nearly the size of their victims. The bacteria thatlive much farther down are themselves much smaller than their relatives on thesurface and rarely have the fancy buds, appendages, or spiral shapes ofmicrobes in the soil. Most are efficient, resistant spheres and rods.

Sedimentaryrocks near the earth’s surface contain interconnected spaces for water toinfiltrate and bacteria to grow and move, plus the remains of dead plants andalgae once at the surface—the apparent food of many organisms. This isfirst-come, first-served dining. Those in upper layers grab the most digestiblecompounds, leaving lower ones fighting for leftovers, including waste and decayproducts from those above. Pore spaces that shelter subsurface microbes areconstricted to the vanishing point in metamorphic rocks buried over eons byfurther sedimentation, volcanic eruptions, or massive folding of Earth’s crust.And dense crystalline material formed by melting—basic igneous rock—offerslittle housing or dining. But igneous rock is brittle, and within a fewthousand feet of the surface, it develops water-filled fracture systems throughwhich groundwater-hosted nutrients and microbes can travel. Fluids may take tensof thousands of years to get somewhere, and in these narrow corridors, lifetakes hold. —K. K.


LEVEL 1:(TAN COLOR) The topsection of rock at the mine is andesite, pressing down into layers of quartziteshale and quartzite.LEVEL 2:(BLUE COLOR)Aquifersscattered in thick layers of dolomite, trap water that works its way from thesurface through fissures. LEVEL 3:(BROWN COLOR)In the lowerdepths of the mine, the shaft and tunnels were blasted through hard layers ofandesite.LEVEL 4:(BLACK COLOR)The microbehunters struck pay dirt in the carbon leader, a gold reef nestled in a mass ofancient quartzite.A WORLD OFBURIED TREASURE:The East Driefontein gold mine plumbs mineral-rich reefsangling down the buried slope of a 2.9-billion-year-old sea bottom. The microbehunters venture by elevator to a rail tunnel that becomes a crawl space as theynear their objective: the carbon leader. This seam of pebbly conglomerate is richwith gold, as well as bacteria that feast on minerals in the rock.

The train stops at a dark hole in the wall: the stope, or miningface. Coleske leads the way. The passage dips down at a steep angle; inmany sections the ceiling is only 3 feet high, forcing everyone tocrab-walk on hands and feet. Sharp-edged rubble coats the floor, andwater from cooling hoses used to spray the rock sluices through.

Thestope swarms with miners, their headlamps piercing a murk of watervapor and dust. Drills, saws, and jackhammers roar so loudly that handsignals must be used. Amid the pandemonium, the scientists find theirobjective: a black coal-like vein laced with round stones and sparklyfilaments. This mineral-rich seam is dubbed the carbon leader. Often nomore than a finger wide, sandwiched in a mass of ancient quartzite, thecarbon leader is heavily laced with uranium and holds anextraordinarily precious treasure: gold.

No one is certain howthe carbon leader formed. It could be the remains of either algae thatsettled on an ancient sea bottom or oil that shot through a crackunderground. In any case, the rock formation is loaded with carboncompounds potentially nutritious to microbes.

Strong evidencethat microbes could survive in an even more austere environment wasuncovered in 1995, when a team working at the Department of Energy’sHanford Reservation in Washington State found rock-eating organismsthat get their sustenance from elemental-mineral energy sources. Themicrobes were taken from groundwater sitting in igneous basalt 4,500feet down. In the lab, microbiologist Todd Stevens of Pacific NorthwestNational Laboratory showed that basalt may react with groundwater torelease hydrogen. The microbes combine the hydrogen with carbon dioxidein the water to make organic compounds. Their main waste product ismethane—a natural gas long thought to be formed near the surface byswamp-dwelling microbes, and in the depths of the Earth bynonbiological chemical reactions.

Coleskeshouts: “There’s no supports. Pull a piece and the wall might come in!”

But eating is only half the equation. Like us, some bacteria mustrespire—combine food with some other substance to release energy. Ourrespiratory agent is oxygen, a by-product of plant photosynthesis.Oxygen is rare below ground, and microbiologists have found subsurfaceorganisms that breathe an astounding variety of alternatives: ferriciron, sulfate, nitrate, nitrite, uranium, and carbon dioxide. On a 1996visit to another South African mine, microbiologists Jim Fredricksonand Tom Kieft discovered a heat-resistant bacterium that inhales iron,nitrate, manganese, sulfur, chromium, cobalt, or oxygen.

AtEast Driefontein, Onstott planned to gather more samples to test ahypothesis that some deep bacteria extract energy from elementsreleased as by-products of the natural radioactivity of the rocks. Now,crouched before the carbon leader, he reaches out and touches the seamwith a Geiger counter. The instrument lights up, and he grins. DuaneMoser starts to pull a chisel from his backpack to take a sample whenColeske slides over and shouts in his ear: “There’s no supports. Pull apiece and the wall might come in!” Suddenly, a drill starts upsomewhere, shaking the place like an earthquake. Rock fragmentsricochet off helmets. The researchers move on, looking for a saferspot. A few hundred feet down, they come upon a newly blasted sectionof tunnel where miners are shoving steel hydraulic jacks against theceiling. “Good!” hollers Onstott. “Means it’s fresh.”

Moserpulls out a ball peen hammer and a sterilized chisel and pounds at thecrumbly ore. Working the chisel in, he outlines a fist-size piece andpries it loose. As it falls, Onstott deftly catches it in a plasticsandwich bag. Moser takes a few minutes to catch his breath, thenstarts again. He loosens a foot-long piece a finger’s length deep andgingerly tips it into a sterile plastic bag that Onstott holds open.

Becausesurface microbes swept down by the ventilation system could confoundthe samples, Onstott wants to gauge how far they might penetrate therock. Using spray cans, he spritzes the rock with a mist of brightchartreuse latex spheres, each the size of a bacterium, and then withan orange-colored chemical tracer. Because cooling-water jets mightwork bugs farther into the rocks, he wants to simulate the process. Buthe cannot reach the rock with the hose. So, one by one, several minerstake off their helmets, fill them from a spigot, and pass them toOnstott to splash water on the spray-painted spot.

Precioussamples in hand, Onstott and his fellow scientists’ grim faces finallybreak into smiles. They climb slowly down the stope to another railroadtunnel and begin hiking out, pressing tight against the wall a coupleof times to avoid passing ore trains.

When life is encountered this deep and distant, one question must beasked: Did it all start in the proverbial scummy surface pool—or downin the groanings of Earth? Some evolutionary scientists argue thatsubsurface microbes had the best chance of survival on the Earth earlyin its history. Below ground they were safe from extreme radiation,asteroids, and other hazards. Respirers of iron and like substances mayhave evolved before oxygen existed on the surface. Deep methane-makingmicrobes could have come from a lineage stretching back even further.Wouldn’t oxygen breathers—including humans—have evolved from them?

Theimplications go beyond Earth. Planetary scientists long skeptical offinding extraterrestrial life are intrigued by the discovery of deepmicrobes. Early landing craft showed the surface of Mars to be barren.But a prime objective of future planetary landing missions is to drilldownward as fast and far as possible. Onstott and his colleagues havebeen asked to help design those probes.

At the moment, they havesomething less glamorous to accomplish. With bags of chunks from thecarbon leader, the group drives to a sheet-metal mine building. There,Moser puts the rocks into an airtight plastic tent filled with 98percent nitrogen and 2 percent hydrogen, to protect organisms thatmight be poisoned by our alien atmosphere. Using gloves fixed in thetent’s side, he sticks a piece of rock in a hydraulic vise and pumps afew times. Crack. It splits open neatly. With the vise, he pares therock into successively smaller pieces that had not been exposed on anyside to air. One pristine piece is ground into powder for conductingvarious tests on-site. Then the scientists take turns dropping otherrock pieces into jars and test tubes headed for various labs in theUnited States and Europe.

Thediscovery of deep microbes has made scientists less skeptical of findingextraterrestrial life.

Months later, they were in for a surprise:some stones appeared to house between 100,000 and one million microbesper gram. “That’s 100 times what we expected,” Onstott says. The team’strove also included mine-water samples containing rod-shaped microbessix times the size of many surface microbes. Some of the bugs breatheiron; some live on methane. Others might eat hydrogen freed whenradiation breaks down water molecules. Onstott and his colleagues evenspeculate that some of the deep microbes may have deposited thefiligree of gold in the East Driefontein mine.

After theirjourney into the mine, Onstott and his colleagues appear relieved to beout of the mine, far from the privations of the deep. While they huddlein the comfort of their makeshift lab, the sky darkens and a violentstorm cranks up. Rain cascades through a leak in the roof, and wind,heavy with the smell of wet trees and dirt, gusts through an open door.A “seismic event” shakes the building. No one seems to mind.


Thomas Gold

Deepmicroorganisms have long remained hidden because it is so difficult topenetrate Earth, much less gather biological samples there. The first inklingsof life far below the surface came in the 1920s, when a microbiologist and ageologist at the University of Chicago cultured anaerobic (non-oxygen-breathing)bacteria from Illinoisoil wells 2,000 feet deep. Skeptics said drills must have polluted samples withsurface organisms. The study went forgotten.

Ahalf-century later, biologists began finding microbes living, inconceivably, attemperatures of nearly 250 degrees in hot springs and ocean vents. That intrigued Thomas Gold, aCornell astrophysicist known for his rebellious theories. He proposed that ifmicrobes could live in superheated environments, they must be alive beneath thesurface in porous sections of rock. Gold made some calculations. Beneath thesurface, the temperature of rock increases 20 to 35 degrees per half-mile.Based on a maximum tolerable temperature of about 250 degrees, that would meanmicrobes could exist more than three miles down. Suppose, he said, that poresin rock account for about 3 percent of Earth’s upper crust and microbes occupy1 percent of those pores. Suck all those bugs out and they would cover thesurface of Earth with slime five feet thick—more than all the insects, plants,people, and everything else alive. Shutting our eyes to creatures of the deep,says Gold, is “surface chauvinism.” —K. K.

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