In the deep subsoil that plunges into the Earth for miles, microscopic organisms inhabit vast pores and veins in the bedrock. Subterranean microorganisms, or microbes, constitute up to half of all living material on the planet and support the existence of all life forms in the food chain. They are essential to achieving an environmentally sustainable future and can alter the chemical composition of minerals, break down pollutants and change the composition of groundwater.
Although the importance of bacteria and archaea is undeniable, the only evidence of their existence deep underground comes from traces of biological matter seeping through mine walls, cave streams, and pits. drilling that taps into aquifers.
Many scientists have assumed that the composition of microbial communities in the deep subsoil is primarily shaped by local environmental pressures on microbial survival such as temperature, acidity, and oxygen concentration. This process, environmental selection, can take years, even millennia, to bring about significant changes at the community level in slow-growing communities like the basement.
Now, with data collected nearly 5,000 feet underground, Stanford University researchers have shown that deep underground microbial communities can change within days, and that the changes can be driven by geological activity – not only by environmental pressures. The results were published last month in Proceedings of the National Academy of Sciences (PNAS).
“In the deep underground, we can no longer understand that environmental selection is the dominant driver of community dynamics – it could simply be a change in flow or a movement of groundwater through the crevices and cracks in the subsoil that determines what we observe,” said study lead author Yuran Zhang, PhD ’20, who conducted the research as an energy resources engineering doctoral student.
Like reading a random page of someone’s 1,000-word biography, previous studies of deep underground microbes have offered only glimpses of the chronicles of their existence. By collecting water samples from multiple geothermal wells every week for 10 months, Stanford researchers have shown how these populations can change over space and time, demonstrating the first evidence for geologic activity as a driver. of change in the microbial community – and therefore of evolution.
“There is previous research on the composition of microbial communities in the deep subsoil, but it almost always uses samples from a single time point,” said geomicrobiologist Anne Dekas, the study’s lead author and assistant professor. of earth system science. “Having a 10-month time series — especially at a weekly resolution — is a really different perspective that allowed us to ask different questions about how and why these communities change over time.”
Dekas said that while microbial ecologists might have guessed geologic activity was at play, she was surprised by the scale of community changes that occurred after a shift in the flow pattern.
Boreholes and test specimens
The technique used in the study involved processing samples from a flow test performed at the Sanford Underground Research Facility (SURF), formerly Homestake Gold Mine, in South Dakota. Zhang said the experience of going from a drill sample to a lab full of test tubes with a PCR machine on campus was “like connecting two totally different worlds,” referring to how this work unites people. distinct fields of microbial ecology and geothermal engineering. .
By analyzing the properties of the water samples, the researchers identified fingerprints of microbial DNA. Each of the 132 water samples yielded tens of thousands of unique sequencing identifiers. This data was used to show that when geological activity occurs, it can quickly mix disparate biological communities – and from locations not previously known to be connected.
“One of the additional insights from this microbiology study is that we saw populations of microbes that moved not just directly from place to place, but as a result of the network between the two,” the author said. lead author of the study, Roland Horne, Professor Thomas Davies Barrow of Earth Sciences. “It’s so important from a reservoir perspective because it reveals something that isn’t revealed by normal geothermal analysis methods.”
Geology meets biology
The level of data collected by current geothermal techniques is equivalent to having access only to highways cut off from the secondary roads that will lead you to your home. Studying populations of microorganisms opens up the possibility of mapping the complex complexities of deep underground in greater detail, Horne said.
Being able to use biology as a tool can also provide insight into the deep underground as a frontier for geological storage, such as nuclear waste and carbon sequestration. But combining biology and geology requires a fundamental knowledge of both subjects.
“On the underground geothermal project, I realized that reservoir engineers or geologists or geophysicists are generally not familiar with microbiology,” said Zhang, who was co-advised by Horne and Dekas. “There is common knowledge about geochemistry, but not so much about geomicrobiology.”
This work might even have meaning beyond terrestrial disciplines: if some of the oldest lifeforms in the Earth’s deep subsoil can change and diversify due to geological activity, perhaps we can have similar expectations for the origin and diversification of life on other tectonic lands. planetary bodies.
“What we observe could potentially connect to the early history of life evolution,” Zhang said. “If geological activity is a driver of early life formation or diversification, then perhaps we should be looking for extraterrestrial life on geologically active planets.”
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Horne is also a senior fellow at the Precourt Institute for Energy and an affiliate at the Stanford Woods Institute for the Environment. Adam Hawkins, who worked on the project as a postdoctoral fellow at Stanford and currently works at Cornell University, is co-author of the paper. Other co-authors are from Lawrence Berkeley National Laboratory and Black Hills State University.
The study was funded in part by the US Department of Energy and Stanford’s TomKat Center for Sustainable Energy.