How Injected Microbes Persist in Hydraulically Fractured Shale

Scientists use laboratory and field studies to reveal the importance of an amino acid as an energy source and protectant for microbial community’s deep underground.

The Science

A boon to natural gas production, hydraulic fracturing or fracking introduces surface microbes thousands of feet below the Earth’s surface. How do they survive? Could they be harnessed to increase energy output? Scientists brought these microbes into the laboratory and found that the amino acid glycine betaine serves as an osmoprotectant and as an energy source for a specific community of microorganisms that become adapted to life in fractured shale.

The Impact

Sixty percent of U.S. natural gas comes from hydraulically fractured shales. These shales are located primarily in Ohio, West Virginia, and Pennsylvania. As engineers inject water and chemical additives into the ground, microbes hitch a ride. The microbes in this new fractured-shale ecosystem can affect the efficiency of gas and oil production, increase methane formation, corrode equipment, and “sour” the field. A greater understanding of the metabolism of these microbes will help scientists develop strategies to manage them and possibly increase their production.


Researchers at The Ohio State University, the University of New Hampshire, and West Virginia University worked with colleagues at the Pacific Northwest National Laboratory; EMSL, the Environmental Molecular Sciences Laboratory; and the Joint Genome Institute (JGI). Both EMSL and JGI are Office of Science user facilities within the Department of Energy and sponsored by the Office of Biological and Environmental Research. The team recreated a shale microbial community in the laboratory, which allowed them to measure microbial activity and fluid chemistry under temperature and pressure conditions similar to those underground. They confirmed their results by comparing the laboratory-recreated communities with more than 40 real-world samples from five fracturing wells in the Appalachian Basin. Fusing metagenomics sequencing data from JGI with proteomic and metabolomics data from EMSL gave researchers unique insights into chemical transformations being controlled by the microorganisms. Based on these data, the team used regression-based modeling to identify key indicators of microbial activity and predict conditions underground. By scaling results from the laboratory to the field, they discovered mechanisms behind critical biogeochemical reactions, including ways to increase gas production. This knowledge could be harnessed to increase energy yields and improve management practices in hydraulically fractured shales. Such knowledge can also be applied to protein-rich microbial ecosystems like soils to predict emission of potent gasses.

Principal Investigator(s)

Kelly Wrighton
The Ohio State University

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This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research), including support of the Environmental Molecular Sciences Laboratory and the Joint Genome Institute, both DOE Office of Science User Facilities.


M.A. Borton, D.W. Hoyt, S. Roux, R.A. Daly, S.A. Welch, C.D. Nicora, S. Purvine, E.K. Eder, A.J. Hanson, J.M. Sheets, D.M. Morgan, R.A. Wolfe, S. Sharma, T.R. Carr, D.R. Cole, P.J. Mouser, M.S. Lipton, M.J. Wilkins, and K.C. Wrighton. “Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.Proceedings of the National Academy of Sciences USA 115(28), E6585-E6594 (2018). [DOI:10.1073/pnas.1800155115]