Which microorganisms flourish in the depths beneath us—in places like gold mines, aquifers, and deep ocean boreholes—and how do they compare to the microbiomes found on the Earth’s surface, both on land and in water? A groundbreaking global study has tackled this significant question, unveiling a remarkable level of microbial diversity in certain subsurface environments. This discovery highlights the potential for extensive, unexplored subsurface diversity that could lead to new compounds and medicines, improve our understanding of how cells adapt to low-energy settings, and enhance our search for life beyond Earth.
Which microorganisms thrive in the darkness beneath us—in gold mines, aquifers, and deep ocean boreholes—and how do these compare to the microbiomes found on the Earth’s surface, both on land and in water?
The initial global study to explore this vast question, conducted at the Marine Biological Laboratory (MBL) in Woods Hole, uncovers unexpectedly high levels of microbial diversity in some subsurface locations (reaching depths of up to 491 meters below the seafloor and 4375 meters underground).
This revelation indicates that there are significant, unexplored subsurface reservoirs of microbial diversity that could be beneficial for discovering new compounds and medicines, gain insights into how cells thrive in extremely low-energy conditions, and aid in the quest to find extraterrestrial life. The study, which is led by MBL Associate Scientist Emil Ruff, is published this week in Science Advances.
“It’s often thought that the deeper you go into the Earth’s crust, the less energy is available, leading to a decrease in the number of cells that can survive,” Ruff explains. “In contrast, areas with more energy, like tropical forests or coral reefs, support high levels of diversity due to abundant sunlight and warmth.
“However, we found that in certain subsurface environments, microbial diversity can match or even surpass diversity found at the surface. This is especially true for marine settings and microbes within the Archaea group,” he adds.
This comprehensive study, which took 8 years to finalize, is also one of the first to compare microbial diversity and community structure between marine and terrestrial environments.
“Consider plants and animals—very few species can adapt to both marine and terrestrial environments, with salmon being a rare exception,” Ruff points out. “This raises an interesting question: Are microbes similar in this regard?”
The answer is yes. The study discovered substantial differences in the composition of marine and terrestrial microbiomes, even though their diversity levels appeared comparable.
“This suggests a fundamental ecological principle,” Ruff states. “There exists a clear distinction between life forms in marine and terrestrial environments, not just at the surface, but also beneath it. The differing selective pressures in each realm lead to the evolution of distinct organisms that struggle to thrive in both habitats.”
Life in the Deep, Dark, Slow Lane
“Scientists first recognized the immense reservoir of microbes lying kilometers deep in rock and seafloor sediments in the mid-1990s,” says Ruff. Present estimates suggest that 50-80 percent of Earth’s microbial cells inhabit the subsurface, where energy availability can be drastically lower than that of sunlit surfaces.
To endure in the subsurface, “it is evolutionarily advantageous to minimize power and energy needs and optimize every metabolic process for maximum energy efficiency,” Ruff says. “Studying this could teach us how to operate efficiently even in resource-scarce situations.”
If Mars or other planets had liquid water at any point in their past—and there is evidence suggesting that Mars did—then the rocky ecosystems found 3 kilometers beneath its surface could resemble those on Earth, Ruff argues. “The energy levels would be very low; organisms would have long generation times. Comprehending deep life on Earth might serve as a model for exploring potential life on Mars and assessing its survival,” he explains.
How This Study Succeeded Where Others Could Not
While studies of microbial life in various Earth’s surface and subsurface environments are not new or overly rare, Ruff points out that previous data was challenging to synthesize due to varying research methodologies.
Conversely, this study initiated in 2016 when Ruff, as a postdoctoral researcher, attended a meeting for the Census of Deep Life—a pioneering effort to investigate subsurface microbial life co-led by MBL Distinguished Senior Scientist Mitchell Sogin. Research teams worldwide contributed subsurface samples to MBL, where scientists employed standardized procedures to analyze and sequence microbial DNA (conducted by MBL scientist Hilary Morrison). This approach provided, for the first time, a consistent dataset that enabled comparisons across over 1,000 samples from 50 different marine and terrestrial ecosystems, sparking Ruff’s interest in pursuing this large-scale analysis.
“For the first time, we were able to compare microbiomes directly, for instance, from sediments of the Great Lakes surface and those from two kilometers below the seafloor,” Ruff expresses. “This is where the importance of this synthesis paper becomes evident.”
Large-scale research like this relies on many collaborators, notably co-first author Isabella Hrabe de Angelis from the Max Planck Institute for Chemistry, whose bioinformatics expertise proved crucial. Many other scientists from the Marine Biological Laboratory (including Mitchell Sogin, Hilary Morrison, Anna Shipunova, and Aleksey Morozov) contributed to the research, alongside experts from various institutions including the University of South Alabama, Oregon State University, ETH Zurich, University of Tennessee-Knoxville, University of Minnesota-Duluth, Dauphin Island Sea Laboratory, University of Toulon, Queen Mary University of London, Université Savoie Mont-Blanc, Michigan State University, University of Georgia, Woods Hole Oceanographic Institution, University of Duisburg-Essen, University of California-San Francisco, and Arva Intelligence.
