Hydraulic Fluids Hospitable for Microbes

For the first time, scientists analyzed the genetic material of surface microbes that are colonizing the deep subsurface, where they are adapting and thriving.

For the first time, scientists reconstructed the genetic material from microbes in shale formations (represented here) being drilled for natural gas.

The Science

Hydraulic fracturing (“fracking”) is the industry standard for removing hydrocarbons from shale formations, which provide one-third of natural gas energy resources worldwide. The biogeochemical changes that this process induces in the deep subsurface are poorly understood. In a study, researchers, for the first time, reconstructed the genetic material, or genomes, from microbes in shale formations that are being drilled for natural gas. Coupled with information on the microbe’s metabolism, the data shed considerable light on the impacts to microbial communities in the deep subsurface, as well as on the sustainability of energy extraction through this approach.

The Impact

Microbial metabolism and growth in hydrocarbon reservoirs have both positive and negative impacts on energy recovery, but little is known about the structure, function, and activity of microorganisms in hydraulically fractured shale. This study provides evidence that microbes degrade chemical additives and can induce corrosion and formation of the gas methane, which benefits recovery efforts. Scientists could use these findings to develop strategies to reduce the risk of fracking-related environmental contamination and to improve long-term sustainability of energy extraction.


Hydraulic fracturing uses high-pressure injection of fresh water and chemical additives deep into the earth to generate extensive fractures in the shale matrix, thereby releasing hydrocarbons trapped in tiny pore spaces. A recent study—led by researchers from The Ohio State University, Department of Energy’s (DOE) Environmental Molecular Sciences Laboratory (EMSL), DOE Joint Genome Institute (JGI), and University of Maine—found that along with these fluids, microbes from the surface are also being injected and colonizing the deep subsurface, 2.5 kilometers (1.5 miles) underground. To find out how this process may be affecting resident microbial community structure, function, and activity, the research team conducted metagenomic and metabolite analyses on input and produced fluids from gas wells for up to a year after hydraulic fracturing at two Appalachian basin shales: the Marcellus and Utica/Point Pleasant formations. The researchers used several nuclear magnetic resonance instruments at EMSL and high-throughput DNA sequencing technologies at JGI, both of which are DOE Office of Science user facilities. By reconstructing the genomes of microbes in fractured shale, researchers discovered remarkable adaptations by microorganisms to survive the extreme chemical conditions produced by fracking. For example, microbes in fractured shales commonly consume injected chemical additives and produce an amino acid derivative called glycine betaine, which protects against high salinity by balancing the osmotic difference between the cell's surroundings and the internal cytoplasm. Glycine betaine is then taken up and used as a source of energy by other microbes, which, in turn, release metabolites that support methane-producing bacteria known to enhance energy recovery. On the other hand, salt-loving bacterial strains that synthesize glycine betaine also produce hydrogen sulfide, which contributes to equipment corrosion, risks environmental contamination, and decreases profits. Additional analysis revealed the majority of archaeal and bacterial genomes reconstructed from fluid samples showed evidence of acquired immunity against viruses, which actively infect other microbes vulnerable to fracking-related environmental stressors. Taken together, these findings illustrate the role of microbial communities resident in oil-bearing shales and begin to reveal a wide range of factors supporting long-term microbial persistence and adaptation to extreme environmental conditions in hydraulically fractured shales.


BER PM Contacts
Paul Bayer, SC-23.1, 301-903-5324
Dan Drell, SC-23.2, 301-903-4742

PI Contacts
Rebecca A. Daly
The Ohio State University

David Hoyt
DOE Environmental Molecular Sciences Laboratory

Susannah Tringe
DOE Joint Genome Institute


This work was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research (BER), and used resources at DOE’s Joint Genome Institute and Environmental Molecular Sciences Laboratory (EMSL), which are DOE Office of Science user facilities. Both facilities are sponsored by BER and operated under contracts DE-AC02-05CH11231 (JGI) and DE-AC05-76RLO1830 (EMSL). Additional funding was provided by the National Science Foundation’s Dimensions of Biodiversity (award 1342701).


R.A. Daly, M.A. Borton, M.J. Wilkins, D.W. Hoyt, D.J. Kountz, R.A. Wolfe, S.A. Welch, D.N. Marcus, R.V. Trexler, J.D. MacRae, J.A. Krzycki, D.R. Cole, P.J. Mouser, and K.C. Wrighton, “Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.” Nature Microbiology 1, 16146 (2016). [DOI: 10.1038/nmicrobiol.2016.146]

Related Links

EMSL highlight: Hydraulic Fluids Hospitable for Microbes

JGI science highlight: Microbial Metabolism Impacts Sustainability of Fracking Efforts

Highlight Categories

Program: BER , BSSD , CESD

Performer: University , DOE Laboratory , SC User Facilities , BER User Facilities , EMSL , JGI

Additional: Collaborations , Non-DOE Interagency Collaboration