Organized microbial ‘workforces’ keep Earth’s underground biosphere running
Underground ecosystems consistently assemble into functional microbial guilds
image:
Prof. Magdalena Osburn removes a sample during a site visit.
view moreCredit: Sanford Underground Research Facility
By studying life deep inside a former gold mine, a Northwestern University-led team of scientists uncovered evidence that Earth’s hidden biosphere operates less like a random collection of microbes and more like an organized workforce.
In one of the most comprehensive long-term studies of deep underground microbial life to date, the researchers tracked how microbial communities shifted across six sites over four years. From site to site, the ecosystems were incredibly different from one another but largely stable through time.
They discovered these underground ecosystems consistently assemble into functional guilds. While stable microbes maintain core processes, more responsive microbes capitalize on new opportunities as they arise. Together, these populations create a division of labor that helps underground ecosystems survive in one of Earth’s most extreme and energy-starved environments.
By identifying how these hidden microbial communities organize and function, scientists could improve understanding of Earth’s biogeochemistry, including the global carbon cycle. The work also could offer clues into how life survives in similarly harsh environments elsewhere in the solar system.
The study will be published on Wednesday (June 3) in the Journal of Geophysical Research – Biogeosciences. The paper is a part of a special issue dedicated to the life and work of Jan Amend, a geobiochemistry pioneer who passed away in March 2024.
“Within the goldmine, we sampled six spots, ranging from 250 meters deep to 1500 meters deep,” said Northwestern’s Magdalena Osburn, who led the study. “We thought we might see some subtle variation with depth but assumed the microbial communities should be broadly similar. That’s not what we found at all. We found that each site is its own little microcosm, and they looked very little like other sites — even nearby sites. We thought it would be like sampling different spots in the same forest, but it was more like sampling different islands in the same ocean.”
An expert on geobiology, Osburn is an associate professor of Earth and planetary science at Northwestern’s Weinberg College of Arts and Sciences.
A goldmine of life
Hosting roughly 20% of Earth’s microbial life, the deep underground is one of the planet’s largest ecosystems. But, because the deep underground is difficult to access and study over long periods of time, this vast ecosystem remains among the least understood.
To access this mysterious subterranean world, Osburn and her team used the former Homestake Mine in Lead, South Dakota. Established in 1876 during the Black Hills Gold Rush, the mine was once the largest and deepest gold mine in the Western Hemisphere. Now the Sanford Underground Research Facility (SURF), the deep underground laboratory hosts a number of research experiments across a range of disciplines. In 2015, Osburn established six experimental sites, collectively called the Deep Mine Microbial Observatory (DeMMO), throughout SURF.
By boring holes into rocks inside the mine, Osburn and her team capture fracture fluids, comprising water and dissolved gases. Some of these fluids are up to 10,000 years old and teeming with microbial life that is otherwise isolated and ignored. In 2023, Osburn published a study focused on eight fluid samples collected during one visit. In the new study, Osburn wanted to see how these communities changed over time.
“This was a real gap in the literature that we thought we could fill,” she said. “Most microbial samples from the subsurface are from one point in time. We wanted to see what happened if we made a time series.”
Between 2015 and 2019, Osburn’s team repeatedly sampled microorganisms and monitored the chemistry flowing through multiple underground sites at DeMMO. Then, they took the samples back to Osburn’s lab at Northwestern. There, she and her team sequenced specific genetic markers, ultimately identifying which microbes were present in each sample.
Stable crews and responsive teams
The scientists found that each sample site hosted a distinct microbial community shaped by local chemistry and geology. Surprisingly, they did not find a universal microbiome shared across all sites. Instead, each underground environment maintained its own stable microbial community.
“Because deep underground environments share extreme conditions, including darkness, isolation and limited energy, we thought we’d find a common set of specially adapted microbes,” Osburn said. “But effectively, we found there is not a core microbiome anywhere in this mine. We did not expect that.”
The team found that each underground community was organized around two broad groups of microbes. A stable group remained consistently present over time, forming the ecological backbone of the ecosystem. These microbes quietly sustain life underground by recycling carbon and surviving on extremely limited resources.
The second group behaved more dynamically. These microbes fluctuated over time, consuming various chemicals, including sulfur, nitrogen and iron, as they became available underground.
“The core community has a low and slow metabolism,” Osburn said. “Then this other community of organisms is poised to respond to pulses of nutrients when they become available. Earthquakes, for example, can trigger chemical changes that release a supply of nutrients, but those don’t happen often.”
The new findings suggest that life in extreme environments may not require specific organisms to thrive. Instead, deep underground ecosystems may be structured more around shared functions rather than shared species.
“I have a friend who says, ‘Every town needs a plumber,’” Osburn said. “These sites reflect that idea. Each one is filled with different types of microbes, but all have a ‘plumber.’”
Understanding biological consequences
This work offers a new lens for evaluating how human activity may affect the underground environment. As industry increasingly looks below ground for carbon storage and geothermal energy extraction, understanding the microbial systems living there is critically important. Because these communities help drive chemical reactions involving carbon, sulfur, nitrogen and metals, disturbing them could alter underground chemistry in unexpected ways.
“If we give microbes chemicals that they can metabolize, they will wake up,” Osburn said. “We’ve identified populations that are poised to use iron, sulfur and nitrogen, and they are just waiting for the opportunity. If they wake up, they could start corroding our metals in infrastructure and wells. Understanding these microbial communities could help us better predict and manage the biological consequences of engineering the deep subsurface.”
The study, “Microbial ecology of the heterogeneous terrestrial deep biosphere over 4 years in the Deep Mine Microbial Observatory (DeMMO),” was supported by NASA, the David and Lucille Packard Foundation and the Canadian Institute for Advanced Research.
Prof. Magdalena Osburn collects fracture fluids, composed of water and dissolved gases.
Credit
Sanford Underground Research Facility
Exterior view of the former goldmine turned laboratory.
Credit
Sanford Underground Research Facility
Journal
Journal of Geophysical Research Biogeosciences
Method of Research
Experimental study
Subject of Research
Cells
Article Title
Microbial ecology of the heterogeneous terrestrial deep biosphere over 4 years in the Deep Mine Microbial Observatory (DeMMO)
Article Publication Date
3-Jun-2026
