Life Thrives Within the Earth’s Crust
Life Thrives Within the Earth’s Crust

Life Thrives Within the Earth’s Crust

From journeys into mines to explorations of volcanoes on the ocean floor, deep voyages reveal the richness of the planet’s deep biosphere.

Oct 1, 2018
Catherine Offord


About a 20-minute drive north of the industrial town of Timmins, Ontario, the ground gives way to a gaping pit stretching more than 100 meters across. This pit is the most recognizable feature of Kidd Creek Mine, the deepest copper and zinc mine in the world. Below the Earth’s surface, a maze of underground tunnels and shafts pierces 3 kilometers of ancient volcanic rock. Were it not for a huge ventilation system keeping the passages cool, the air temperature at this depth would be 34 °C (93 °F).

It’s here that Barbara Sherwood Lollar, a hydrogeologist at the University of Toronto, journeys into the planet’s crust to hunt for signs of life. “You get into a small truck or vehicle and go down a long, winding roadway that corkscrews down into the Earth,” she tells The Scientist. By the time she and her fellow passengers clamber out into the corridors at the end of the roadway, “we are literally walking along what was the ocean floor 2.7 billion years ago,” she says. “It’s an utterly fascinating and magical place to visit.”


Unlike miners, who navigate these tunnels in search of metal ores, Sherwood Lollar and her colleagues are on the lookout for pools of salty water. “These aren’t waters you’d pump into your cottage and drink or spread on your crops,” Sherwood Lollar says. “These are waters that have been in contact with the rock for long geochemical timescales—they’re full of dissolved cations and anions that they’ve leached out of the minerals.” So full, in fact, that they give off a distinctive, musty odor. “As we’re walking along these tunnels, if I get a whiff of that stenchy smell, then we head in that direction.”

Where there’s water, there’s the potential for life. In 2006, Sherwood Lollar was part of a team led by Tullis Onstott at Princeton University that discovered an anaerobic, sulfate-reducing bacterium thriving in the sulfate-rich fracture waters of Mponeng gold mine in South Africa, 2.8 kilometers underground.1 A few years later, a different group described a diverse microbial community living at a similar depth in the Earth’s crust, accessed via a borehole drilled into the ground in Finland.2 With the recent discovery of 2-billion-year-old, hydrogen- and sulfate-rich water seeping out of the rock in Kidd Mine, Sherwood Lollar and her colleagues are hoping they might again find life.3

Before the rise of the land plants, deep biomass could have outweighed life on the surface by an order of magnitude.

These expeditions are just one part of a rapidly expanding field of research focused on documenting microbial and even eukaryotic life dwelling hundreds of meters deep in the Earth’s crust—the vast sheath of rock encasing the planet’s mantle. Researchers are now exploring this living underworld, or deep biosphere, not only in the ancient, slow-changing continental crust beneath our feet, but in the thinner, more dynamic oceanic crust under the seafloor. (See illustration on page 32.) Such habitats have become more accessible thanks to the last two decades’ expansion of scientific drilling projects—whereby researchers haul up cores of rock to study on the surface—as well as a growing number of expeditions into the Earth via mines or cracks in the ocean floor.

Studies of these dark—and often anoxic and hot—environments are challenging scientists to rethink the limits of life, at the same time highlighting how little we know about the world beneath our feet. “It’s a really good field if you don’t mind not knowing all the answers,” says Jason Sylvan, a geomicrobiologist at Texas A&M University. “For some people, that freaks them out. For me, a field is more exciting when you can ask really big questions.”

Researchers Explore the Deep Biosphere

Most research into the deep biosphere has been conducted using samples retrieved from less than a kilometer below the surface of the Earth. But a handful of boreholes and other manmade excavations at both continental and oceanic sites extend much deeper into the Earth’s crust.

Numbers 1-10: West to East.

1Hole 1256D,
East Pacific Ocean
1.5 kmResearchers reported evidence of microbially produced sulfides at this site in 2011.
2Kidd Creek Mine,
3.0 kmIn billions-of-years-old water samples, researchers found sulfate produced by interactions between water and rock, suggesting that any microbes living there would have an easily available food source.
3Hole 504B, Costa Rica Rift2.1 kmAnalysis of carbon isotopes in the 1990s suggested microbial activity, while a more recent analysis of data collected from an observatory in a shallower hole about a kilometer away revealed sulfur-oxidizing bacteria.
4Hole U1309D,
Atlantis Massif
1.4 kmIn 2010, researchers reported the presence of a community of bacteria surviving at depths of more than 1.3 kilometers, apparently surviving by degrading hydrocarbons and fixing carbon and nitrogen in the absence of oxygen.
5KTB Boreholes,
9.1 kmTemperatures at the base of the deepest well at this site reach 265°C—the most hyperthermophilic organisms known on anywhere on the planet can only survive to 113°C—and life has not yet been reported here.
6St1 Otaniemi,
9.1 kmTemperatures at the base of the deepest well at this site reach 265°C—the most hyperthermophilic organisms known on anywhere on the planet can only survive to 113°C—and life has not yet been reported here.
7Mponeng gold mine,
South Africa
3.9 kmIn the mid-2000s, researchers identified a new species of sulfate-reducing bacteria, Candidatus Desulforudis audaxviator, that seems to be endemic to deep habitats.
8Kola superdeep borehole,
12.3 kmResearchers reported finding water and microscopic fossils of single-celled organisms more than 6 kilometers below the surface.
9Hole 735B Southwest,
Indian Ridge
1.5 kmIn 2011, an isotope analysis of samples revealed evidence that seawater sulfate was being chemically reduced by microbes.
10Hole C0020A,
Japan Sea
2.5 kmEarly results indicate a slow-growing microbial community able to metabolize a range of carbon and nitrogen compounds more than 2 km below the seafloor.

Holes in the ground

A desire to explore the deep biosphere has led Julie Huber, a microbial oceanographer at Woods Hole Oceanographic Institution in Massachusetts, to some of the remotest places on Earth. Huber is interested in the huge volumes of water swilling around between rock particles in the oceanic crust, and the extent and diversity of microbial life within them. One way to access that water is via expensive drilling projects, many organized by the International Ocean Discovery Program (IODP), that bore through marine sediments to the crust. In 2013, this approach revealed bacteria living in 3.5-million-year-old basalt rock underneath the Pacific Ocean.4

The other way, Huber explains, “is to find where that water is naturally leaking out through the seafloor, and then try to capture it just as it’s coming out.” For that purpose, Huber has not only worked with teams of engineers to guide remotely operated vehicles down to the bottom of the ocean, she’s also joined the ranks of scientists who have taken the plunge with Alvin, a three-person submersible research vehicle owned by the US Navy that can dive down as far as 4,500 meters. “Claustrophobic people don’t do well in there,” Huber acknowledges—adding that anyone planning to dive is invited to try sitting in the sub before it leaves the boat deck to avoid “a full-on panic being launched into the ocean.”

Mines offer researchers direct access to the deep biosphere, kilometers into the Earth’s continental crust. Scientists have now used several of these sites, from Kidd Creek Mine in Ontario (left) to gold mines in South Africa (right), to search for underground life.

These technologies allow Huber to collect samples of the fluids seeping, or sometimes exploding, out of the oceanic crust from underwater volcanoes and hydrothermal vents. In the early 2000s, she and her colleagues used 16S rRNA gene sequencing to analyze subseafloor microbial diversity following multiple eruptions of Axial Seamount, an underwater volcano about 480 kilometers west of Oregon and nearly 1.5 kilometers under the water’s surface. Compared to background seawater, samples collected at the vent site revealed multiple unique bacterial5 and archaeal6 taxa that appeared to have been blasted out of the crust, pointing to a diverse microbial community thriving below the seafloor. More recently, Huber’s group carried out a detailed survey at the world’s deepest hydrothermal vent field—a site known as Piccard, after Swiss deep-sea adventurer Jacques Piccard—and turned up thousands of vent-specific microbial taxa in fluids exiting the crust at temperatures of up to 108 °C (226 °F).7

Such findings are becoming typical of this young research field. To date, studies of crustal sites all over the world—both oceanic and continental—have documented all sorts of organisms getting by in environments that, until recently, were deemed inhospitable, with some theoretical estimates now suggesting life might survive at least 10 kilometers into the crust. And the deep biosphere doesn’t just comprise bacteria and archaea, as once thought; researchers now know that the subsurface contains various fungal species,8 and even the occasional animal. Following the 2011 discovery of nematode worms in a South African gold mine, an intensive two-year survey turned up members of four invertebrate phyla—flatworms, rotifers, segmented worms, and arthropods—living 1.4 kilometers below the Earth’s surface.9



Jules Verne enthralls readers with a story of underground seas and prehistoric animals in his subterranean sci-fi, Journey to the Center of the Earth.


Geologist Edson Bastin and microbiologist Frank Greer of the University of Chicago report finding sulfate-reducing bacteria in samples retrieved from 300- million-year-old oil deposits that were buried hundreds of meters underground. The results are dismissed as surface contamination.


Microbiologist Claude Zobell describes aerobic bacteria in cores more than 50 centimeters long taken from deep-sea marine sediments off the coast of California, leading to speculation about life below the seabed.


Ocean explorer Jacques Piccard discovers animal life at the deepest known point in the ocean, Challenger Deep in the Mariana Trench, nearly 11 kilometers beneath the surface of the water.


US Department of Energy engineers using drilling equipment designed to avoid surface contamination discover microbes living 500 meters underground around a nuclear processing facility near the Savannah River in South Carolina.


Astrophysicist Thomas Gold publishes an influential, controversial paper entitled “The Deep, Hot Biosphere,” arguing that subsurface biomass is comparable in volume to surface biomass, and that life may have originated underground.


Researchers discover a bacterium in fracture waters in a South African gold mine, 2.8 kilometers underground. Subsequent work shows it has no close relatives on the surface.


An ocean drilling program retrieves microbe-containing basalt, providing the first conclusive evidence of life in the oceanic crust.


Japanese researchers announce plans to drill all the way through the Earth’s crust to the mantle. The project, slated to start by 2030, is partly aimed to help answer the lingering question of how deep underground life can survive.

Unsurprisingly, as researchers explore these unusual habitats, they’re finding a number of organisms that were until recently unknown to science. The discovery of “extremophile” archaea species in the last decade has led scientists to rethink the entire domain’s phylogeny. (See “Archaea Family Tree Blossoms, Thanks to Genomics,” The Scientist, June 2018.) And while many of the bacteria and archaea discovered in the deep biosphere have analogs or close relatives on the surface, some are unlike anything found anywhere else.

One example is Candidatus Desulforudis audaxviator, first found by Onstott’s team in Mponeng gold mine in 2006. (“Audax viator,” which translates from Latin to “bold traveler,” is a reference to a line in Jules Verne’s Journey to the Center of the Earth.) Researchers have since identified bacteria resembling this species in other sites a kilometer or more into the crust, but haven’t yet found any close relatives in surface communities. Another bacterial species, unearthed more than 1,000 meters down in the Henderson molybdenum mine in Colorado, shows faint phylogenetic links to members of the phylum Nitrospirae, but is otherwise unlike anything on the surface.10

A key area of research now is understanding how such life survives. Devoid of sunlight, “these systems are typically energy-poor,” says Sherwood Lollar. Compared to surface communities, microbes in the deep biosphere are thought to be relatively slow-growing and sparsely distributed, she adds. While surface soil may contain in excess of 10 billion microbes per gram, oceanic crust usually contains around 10,000 cells per gram, and continental crust—where water is unsurprisingly in shorter supply—holds fewer than 1,000 cells per gram.

Click to watch a video about some of the deepest holes scientists have drilled into the Earth's crust.

Working with such low-biomass samples presents a challenge of its own, but researchers are using a combination of techniques, including metagenomic analyses and incubation of subsurface rocks or fluids with different potential food sources in the lab, to probe the function of subsurface microbes. Such studies are revealing genes for metabolic enzymes that suggest these organisms can gain energy from a suite of sources—particularly hydrogen and other molecules that are released by chemical reactions between water and rock. When geomicrobiologist Lotta Purkamo of the University of St Andrews and her colleagues characterized the ecosystem of a 600-meter-deep borehole in northern Finland, for example, they found evidence of metabolic pathways based on reducing or oxidizing sulfate, nitrate, methane, ammonia, and iron, as well as fixation reactions involving carbon.11

Additionally, thanks to metatranscriptomic analyses, “we’re learning that these organisms have a lot of potential metabolisms that they could be expressing,” says Huber, who recently carried out this sort of assay on the Axial Seamount community.12 “But depending on the conditions and the geological setting, just a small subset of those genes are being used.” Such results hint at flexible and opportunistic lifestyles, she adds, where microbes make use of whatever they can, whenever they can.

These findings are chipping away at some of the big questions about the diversity and uniqueness of life in the deep biosphere. But the insights afforded by a single drill core or fluid sample can be frustratingly fleeting, says University of Bergen geobiologist Steffen Jørgensen. One sample “doesn’t give us any understanding of the dynamics of the system and how it evolves over time,” he says. For a longer-term view of life deep in the Earth, researchers are taking their experiments underground.  

The fourth dimension

Last summer, Jørgensen stepped out of a helicopter onto a tiny basalt island about 30 kilometers from the south coast of Iceland. Too rocky to access by boat, the island of Surtsey is the tip of a huge mound of magma blown out of the seafloor by an under-water volcanic eruption that went on for nearly four years in the mid-1960s. This newly formed oceanic crust “gives us a huge advantage,” Jørgensen says. “We can actually drill into what is a marine system, but from land.”

Using equipment flown to Surtsey by helicopter, Jørgensen and a large team of engineers drilled down into the basalt. They didn’t just remove cores from the island; rather, the researchers set up a mini observatory to take in situ measurements of the deep biosphere. Into a 190-meter-deep hole in the rock, the team installed a series of 10-meter-long aluminum tubes, several with a number of small slits to allow fluids to trickle through from the surrounding rock. Then, into the tubes the team lowered a cable with various bits of equipment—temperature and pressure loggers, and microbial incubators—attached at specific intervals, until the equipment lined up with the slits. Since then, the instruments in the observatory have been collecting data from the oceanic crust, and next summer, Jørgensen and his colleagues will go back to see what they’ve found.

The Surtsey installation is now one of a handful of deep observatories around the world and part of a larger effort to establish long-term studies in both oceanic and continental crust. Such sites offer a window into the activity of the deep biosphere, as well as an opportunity to collect time-series data that are critical to understand how that biosphere changes over time. “It’s the only way that we can . . . make observations that are more than ‘I went to this place, one time in the history of the world, and I grabbed a bunch of rocks, and here’s what I saw,’” says Sylvan.

Journey to the Center of the Earth

The recent expansion of large-scale scientific drilling programs, combined with intensified efforts to take advantage of existing portals into the crust, has led to an explosion of research on the deep biosphere.

Deep-sea, manned submersibles and remotely operated vehicles collect fluid samples that exit natural points of access to the oceanic crust, such as underwater volcanoes or hydrothermal vents. These samples contain microbes living in the crust beneath.

Drilling holes into the Earth’s crust allows retrieval of rock and sediment cores reaching kilometers below the surface. The holes can then be filled with monitoring equipment to make long-term measurements of the deep biosphere.

Deep mines provide access points for researchers to journey into the Earth’s continental crust, from where they can drill even deeper into the ground or search for microbes living in water seeping directly out of the rock.
See full infographic: WEB | PDF

Oceanic CrustContinental Crust
Thickness6–10 kilometers30–50 kilometers
AreaAbout 60 percent of Earth’s surfaceAbout 40 percent of Earth’s surface
Rarely more than 200 million yearsUp to 4 billion years
Water ContentHighLow

Data coming out of long-term studies of the deep biosphere paint a dynamic picture. This July, a team that included Onstott and Sherwood Lollar published metagenomic, metatranscriptomic, and metaproteomic analyses of data collected over a period of two and a half years at a depth of 1,339 meters from a borehole drilled into South Africa’s Beatrix gold mine.13 Over the course of the study, the microbial community structure shifted in concert with natural fluctuations in the groundwater’s geochemistry—in particular, the availability of electron-accepting compounds such as nitrates and sulfates.

Meanwhile, Huber’s group published an analysis of data gathered over two years from two so-called CORK (circulation obviation retrofit kits) observatories installed in the oceanic crust below North Pond, a site on the Mid-Atlantic Ridge, through which circulates well-oxygenated and—at less than 15 °C (59 °F)—relatively cold water.14 Metagenomics showed that the microbial communities, which were substantially different from those of warmer and anoxic environments, went through substantial shifts over time—with one phylum dominating one month, and another taking over the next—despite only minor fluctuations in the water’s geochemistry.

Such underground observatories can also act as in situ laboratories. By incubating rocks inside these sites for years at a time, researchers can study how microbial communities colonize new material in their natural environments rather than in the lab, and how the mineralogical composition of the crust influences who grows where.15 The sites might even reveal subsurface dynamics on much longer timescales, by helping scientists identify signs of ancient life. To date, many of the clues about deep microbial communities throughout geological history come from what look like fossilized or mineralized remains of bacteria and archaea on rocks retrieved from the crust. But given how little researchers know about the processes of mineralization in the deep subsurface, the authenticity of at least some of these remains is in question.

“It’s quite difficult to tell whether you’re actually looking at a fossil of an organism that lived in the deep biosphere billions of years ago,” explains University of Edinburgh geobiologist Sean McMahon. “Not only is it difficult in general to recognize fossil bacteria, which look very much like minerals at that size scale, it’s difficult to show, if it really is a fossil bacterium, that the organism lived below the surface at the time it was living billions of years ago.”

It’s a really good field if you don’t mind not knowing all the answers.

—Jason Sylvan, Texas A&M University

To get a better grip on the long-term dynamics of the deep biosphere, groups such as McMahon’s are trying to recreate deep mineralization in the lab. They do this by inoculating rocks with bacteria, McMahon explains, then tweaking physical and chemical conditions to trigger fossilization. “The idea is to try and find the sweet spot where the microbes are able to live happily, but you only have to change a small thing for them to become entombed in minerals and fossilized,” he says.

Underground observation stations such as the one at Surtsey will soon be able to complement this research, says Jørgensen. “By having the observatory, we can hopefully clarify whether these [fossil-like] structures can be produced abiotically, or if we only see them where there’s microbes present,” he says. “It is a very difficult question to get to the bottom of.”

The Icelandic island of Surtsey (left) was created by a four-year volcanic eruption in the 1960s.
Researchers have now installed a deep observatory into a hole they drilled to monitor life in the deep marine biosphere.

Missing pieces

Despite the infancy of research into the deep biosphere, it’s clear to many in the field that science has long held a warped view of what constitutes life in our universe. Researchers are far from agreeing on the extent of this underworld—one 1990s paper controversially suggested that deep life constituted 50 percent of the Earth’s current biomass,16 though most estimates are now below 15 percent. Before the rise of land plants around 400 million years ago, though, deep biomass could have outweighed life on the surface by an order of magnitude, according to calculations published this summer by McMahon and the University of Aberdeen’s John Parnell.17

However much life exists below the Earth’s surface, its mere presence is forcing a reevaluation of biological normalcy, not only on Earth but deep within other planets such as Mars. After all, in the Earth’s crust, “we had made an assumption that there was no life,” notes Purkamo, who has also been affiliated with St Andrews’s Centre for Exoplanet Science. “And then, tada!”

Findings from the underground frontier are also pushing scientists to consider how subsurface microbes—and the reactions they carry out—influence global processes occurring above the surface. “I’m quite sure that people don’t really think about that,” notes Jørgensen. “That they’re walking on this enormous biosphere that could have a really significant impact on how the system works.” The same goes for attempts to understand physical and biological evolution throughout the planet’s history. “When we think about how life on Earth has changed over time, and how it’s interacted with the chemistry of rocks, sediments, groundwater, oceans, atmosphere, we shouldn’t be thinking just about charismatic animals and plants,” says McMahon. “We should be thinking about this huge quantity of microorganisms, most of which are living on the surfaces of mineral grains and interacting with them.”

That’s exactly the view today’s deep biosphere researchers are trying to expand, and to most in the field, it’s an exciting journey. “It’s like: Damn, there’s so much we do not know about what is happening down there,” says Huber, whose team is currently exploring the deep biosphere at an active underwater volcano known as Loihi, about 35 kilometers off the coast of Hawaii’s Big Island. “And what a privilege to be able to ask these questions and to do this type of science and try to figure it out.” 


  1. L.-H. Lin et al., “Long-term sustainability of a high-energy, low-diversity crustal biome,” Science, 314:479–82, 2006.
  2. M. Itävaara et al., “Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield,” FEMS Micro Ecol, 77:295–309, 2011.
  3. L. Li et al., “Sulfur mass-independent fractionation in subsurface fracture waters indicates a long-standing sulfur cycle in Precambrian rocks,” Nat Commun, 7:13252, 2016.
  4. M.A. Lever et al., “Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt,” Science, 339:1305–08, 2013.
  5. J.A. Huber et al., “Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption,” FEMS Microbiol Ecol, 43:393–409, 2003.  
  6. J.A. Huber et al., “Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat,” Appl Env Microbiol, 68:1585–94, 2002.
  7. J. Reveillaud et al., “Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise,” Env Microb, 18:1970–87, 2016.
  8. H. Drake et al., “Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures,” Nat Commun, 8:55, 2017.
  9. G. Borgonie et al., “Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa,” Nat Commun, 6:8952, 2015.
  10. J.W. Sahl et al., “Subsurface microbial diversity in deep-granitic-fracture water in Colorado,” Appl Environ Microbiol, 74:143–52, 2008.
  11. L. Purkamo et al., “Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater,” FEMS Microbiol Ecol, 94:fiy116, 2018.
  12. C.S. Fortunato, J.A. Huber, “Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent,” ISME, 10:1925–38, 2016.
  13. C. Magnabosco et al., “Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability,” FEMS Microbiol Ecol, 94:fiy089, 2018.
  14. B.J. Tully et al., “A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer,” ISME J, 12:1–16, 2018.
  15. A.R. Smith et al., “Deep crustal communities of the Juan de Fuca Ridge are governed by mineralogy,” Geomicrobiol J, 34:147–56, 2017.
  16. T. Gold, “The deep, hot biosphere,” PNAS, 89:6045–49, 1992.
  17. S. McMahon, J. Parnell, “The deep history of Earth’s biomass,” J Geol Soc, doi:10.1144/jgs2018-061, 2018.