The Mass of Microbes in Deep African Mines Lead Lives of Quiet Desperation

The Witwatersrand Basin in southern Africa, one of the oldest geological formations on Earth, began as a shallow sea about 3 billion years ago. The Basin is home to extensive gold and diamond mining operations, where humans have dug some of the deepest mines in the world.

These deep mines have been a boon to scientists as well. The mining companies drill boreholes into surrounding pristine rock, which intersect with fractures filled with groundwater. Scientists can analyze this water to probe the limits of deep life and to learn how microbes make a living when trapped kilometers beneath the surface.

DCO Deep Energy and Deep Life Community members Thomas Kieft (New Mexico Institute of Mining and Technology, USA), Verena Heuer (University of Bremen, Germany), Esta van Heerden (University of the Free State, South Africa), Barbara Sherwood Lollar (University of Toronto, Canada), and Maggie C.Y. Lau and Tullis Onstott (both at Princeton University, USA) investigated the organic matter in fracture waters to find clues to how microbes live in these ancient rocks. The researchers sampled from mine boreholes reaching just over 3.4 kilometers deep and characterized the dissolved organic matter within. Their results paint a picture of isolated microbial communities eking out a living using dissolved hydrogen gas (H2) and inorganic carbon released by the rocks, with little or no input of organic carbon from the surface. The researchers report their findings in a new paper in the journal Organic Geochemistry [1].

“The study supports the hypothesis that there are hydrogen-driven microbial ecosystems in the deep subsurface, independent of the surface world,” said Kieft, who serves on the DCO Steering Committee for Deep Life.

The researchers sampled water from multiple boreholes within two gold mining regions and a handful of diamond mines, with depths ranging from 578 to 3,413 meters. In previous studies, researchers had examined these same deep groundwaters for microbial communities, inorganic carbon compounds, isotopes and age, but no one had looked at dissolved organic matter.

To accumulate enough material for their analyses, however, the researchers had to carry seven-liter glass columns of resin, a material that collects traces of organic carbon in the water, and set them up in the mines. They filtered tens of liters of groundwater underground and then carried the columns back to the lab. There, they released the carbon from the resin and concentrated and freeze-dried the newly released compounds for testing. Along with Cliff Walters and Meytal Higgins at ExxonMobil Research and Engineering Company in Annandale, New Jersey and Catherine Clewett at West Texas A & M University in Canyon, Texas, the researchers used numerous analytical techniques to separate and identify the different organic carbon components in the deep samples.

Compared to the surface groundwater, which is rich in plant and soil compounds whose carbon originally came from photosynthesis, the dissolved organic matter in the deep mine waters primarily came from microbial cells. “There’s a bunch of stuff missing in this very, very deep groundwater, when it’s compared to surface waters,” said Kieft. The shallower wells had minor inputs of surface carbon, but deeper down, the water held just simple metabolites and remnants of cell membrane and protein. The researchers did not detect any hydrocarbons from the rocks, suggesting that the microbes primarily live on inorganic carbon dissolved in the groundwater, H2 generated from radiolysis, and methane generated when that H2 reacts with the dissolved inorganic carbon.

“There’s an internal deep carbon cycle that’s going on here within the microbial communities,” said Kieft. “Carbon is derived from the subsurface itself.”

Some deep fracture water microbial communities may have been isolated for 1 million to 100 million years, though this estimate is based on the average age of the groundwater, which may be a mix of younger water (<10,000 years) and much older water (2 billion years) released from fluid inclusions in the rock.

For their next project at this ancient region, Kieft and Onstott, who also serves on the Deep Energy Scientific Steering Committee, plan to investigate the H2 generated by subsurface water-rock reactions and its role in microbial metabolism. The mines experience frequent earthquakes, both from natural causes and from blasting. Johanna Lippmann-Pipke of the Federal Institute for Geosciences and Natural Resources in Germany has shown that those earthquakes cause a burst of H2 to be released, which might trigger a flurry of microbial activity. The researchers plan to monitor the microbial communities to see if they are more active after a quake, and to see if these H2 pulses are helping to keep this isolated community alive in their 4-kilometer deep “Walden Pond.”


Thomas Kieft holds up the manifold that that they inserted into the borehole to collect groundwater more than a kilometer deep in the Beatrix gold mine in South Africa. Credit: DCO-supported “Carbon Cycling in the Deep Crustal Biosphere,” University of the Free State, January, 2011
Mike Pullin stands next to the columns of resin used to trap the organic carbon from hundreds of liters of deep groundwater. Credit: Tom Kieft

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