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Microbial DNA can reveal water’s underground origins

Stanford researchers have sequenced microbial communities in samples of reservoir fluids to identify where water traveled through underground networks and pathways.

water abstract
(Image credit: Ameen Fahmy/Unsplash)

Veins of water and oil percolate within Earth’s subsurface through rock fractures in the dark crevices beneath our feet. Hidden in the subsurface, the routes of these liquid networks are largely a mystery, pieced together in fragments using traditional well records and borehole imaging.

Now, using a new application of DNA sequencing, Stanford researchers have found a way to harness the unique microbial community profiles in these valuable fluids and identify the channels they traveled through, their connectivity and their origins more effectively than conventional methods.

“As geothermal scientists, we try to figure out where the fluids come and go,” said Roland Horne, a professor of energy resources engineering at the School of Earth, Energy & Environmental Sciences (Stanford Earth) and co-author of the work. “It’s like a subway system you don’t have a map of – you’re often searching in the dark trying to figure out what the underground plumbing looks like.”

These maps inform where to drill new wells and the size of the resources available – important data for groundwater management and energy exploitation like oil extraction and carbon sequestration.

In a study published Nov. 11 in Water Resources Research, Yuran Zhang, a doctoral student in the Department of Energy Resources Engineering and lead author on the paper, reveals that the key to understanding where the fluid comes from is actually in the fluid itself. In the process of traveling through crevices and rock, fluids curate a unique collection of microbes that create a revealing DNA barcode.

“The answer is just in there,” Zhang said. “There’s something pretty amazing about that.”

Into the mines

Traditional methods for identifying well connections and natural fractures – well logging and borehole imaging – have significant limitations. While they record the rock formations during drilling processes and create a detailed record of the geology of a particular location, they do not reach the large spaces between wells. Seismic data – the vibrations of the Earth – can describe a larger area, but with limited resolution, and chemical tracers are limited in numbers and therefore not effective for complex branching subsurface systems.

Analyzing the chemistry of these fluids is still useful to supplement the new technique, but Zhang’s method using the DNA of the microbial community produces more specific results.

“It’s like using the chemical composition of the human body to distinguish individuals from one another, as opposed to just using their fingerprint,” Zhang said.

To test this novel method, Zhang went underground. Once the largest and deepest gold mine in North America, the Sanford Underground Research Facility in Lead, South Dakota, now hosts researchers mining for answers instead.


The site along the mine drift at the Sanford Underground Research Facility in Lead, South Dakota. (Photo credit: Yuran Zhang)

Cavernous tunnels and mine shafts led Zhang to a newly developed field site boasting eight freshly drilled boreholes 4,850 feet (1,478 meters) below ground. Initially, the researchers had only intended to bring the cores back for analysis, not knowing the wealth of information that would spew from the holes themselves.

“In a natural field setting, you really don’t know what’s going to happen,” said Zhang, who is co-advised by both Horne and geomicrobiologist Anne Dekas. “We were just there when the unexpected happened – some of the wells started to produce water.”

The microbial key

Before heading underground, Zhang was inspired by a poster about the microbial communities in marine environments hanging outside of the office of Dekas, an assistant professor of Earth system science at Stanford Earth and a co-author on the study. Zhang was struck by the similar-looking barcodes in her own work, leading her to the idea to explore microbial DNA fingerprints within underground fractures.

“It’s well known that microbes are nearly everywhere,” Zhang said. “I was thinking if they are already happily living in the subsurface, why not try to take advantage of the information they contain?”

Dekas credits the interdepartmental collaboration entirely to Zhang for seeing the utility of molecular microbiology techniques to the field of subsurface engineering.

“She is an incredible connection between my world and Roland’s world,” Dekas said. “By combining fields, we can make progress that we couldn’t make before.”

Each water sample provided tens of thousands of sequencing reads – and each is unique. “Individual parts of rock have detectable signals, so using the startlingly large amount of DNA that’s already there you can sort of put a barcode on fluids,” said Horne, who is also a senior fellow at the Precourt Institute for Energy.

Two of the boreholes showed significant overlap in microbial families, indicating the flows were connected through a shared natural fracture in the rock. The researchers used the core logs and camera footage to confirm the connection.

Student working
Doctoral student Yuran Zhang working at the field site deep underground. (Photo courtesy of Yuran Zhang)

Knowledge of fluid pathways and connectivity has a number of applications, aside from simply providing a better understanding of the subsurface. Scientists can use this technique to predict the spread of contamination, assess artificial fracturing effects or determine the potential for leakages, for example, when studying carbon sequestration.

Dekas sees potential for taking this method back to the marine environment that first inspired it in order to assess fluid flow in the marine subsurface, such as through geothermal vents – openings on the seafloor that emit heated water.

“Because there are so few studies on subsurface microbiology, each new study is really meaningful,” Dekas said. “Now, in addition to learning about the microbes themselves, we can use the DNA to learn about the structure of the subsurface. This is an exciting application of these methods.”

Zhang’s work in the gold mine earned her an additional reward: co-recipient of the Henry J. Ramey Jr. Fellowship Award for outstanding research in the Department of Energy Resources Engineering.

Horne is also the Thomas Davies Barrows Professor and an affiliate of the Stanford Woods Institute for the Environment.

This research was supported by the TomKat Center for Sustainable Energy.

Media Contacts

Danielle T. Tucker
School of Earth, Energy & Environmental Sciences, 650-497-9541

Anne Dekas
School of Earth, Energy & Environmental Sciences, 650-736-1225 

Roland Horne
School of Earth, Energy & Environmental Sciences, 650-723-9595

Yuran Zhang
School of Earth, Energy & Environmental Sciences

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