U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

Microbial Metabolism Impacts Sustainability of Fracking Efforts
Published: September 05, 2016
Posted: October 12, 2016

Oil and gas well site in the Appalachian Basin similar to the well sites where researchers conducted metagenomic and metabolite analyses on hydraulic fluids. [Image courtesy of the Marcellus Shale Energy and Environment Laboratory]

Through hydraulic fluids, surface microbes are colonizing the deep subsurface where they are adapting and thriving.

The Science
Hydraulic fracturing (“fracking”) is the industry standard for extracting hydrocarbons from shale formations, which provide one-third of natural gas energy resources worldwide. Poorly understood, however, are the biogeochemical changes that this process induces in the deep subsurface. In a recent study, researchers, for the first time, were able to reconstruct microbial genomes from shale formations that are being drilled for natural gas. Coupled with microbial metabolic information, 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 are known to 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 for microbial degradation of chemical additives and the potential for microbially induced corrosion and formation of biogenic methane. These findings could be used 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 km underground. To find out how this process may be impacting 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 first 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, which are DOE Office of Science user facilities. Both facilities are sponsored by BER and operated under contract numbers DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). Additional funding was provided by the National Science Foundation’s Dimensions of Biodiversity (award number 1342701).

Daly, R. A., 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. 2016. “Microbial Metabolisms in a 2.5-KM-Deep Ecosystem Created by Hydraulic Fracturing in Shales,” Nature Microbiology, DOI: 10.1038/nmicrobiol.2016.146. (Reference link)

Related Links
EMSL Highlight
JGI Highlight

Topic Areas:

  • Research Area: Subsurface Biogeochemical Research
  • Research Area: DOE Environmental Molecular Sciences Laboratory (EMSL)
  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: DOE Joint Genome Institute (JGI)

Division: SC-23.1 Climate and Environmental Sciences Division, BER,SC-23.2 Biological Systems Science Division, BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

May 10, 2019
Quantifying Decision Uncertainty in Water Management via a Coupled Agent-Based Model
Considering risk perception can improve the representation of human decision-making processes in age [more...]

May 09, 2019
Projecting Global Urban Area Growth Through 2100 Based on Historical Time Series Data and Future Scenarios
Study provides country-specific urban area growth models and the first dataset on country-level urba [more...]

May 05, 2019
Calibrating Building Energy Demand Models to Refine Long-Term Energy Planning
A new, flexible calibration approach improved model accuracy in capturing year-to-year changes in bu [more...]

May 03, 2019
Calibration and Uncertainty Analysis of Demeter for Better Downscaling of Global Land Use and Land Cover Projections
Researchers improved the Demeter model’s performance by calibrating key parameters and establi [more...]

Apr 22, 2019
Representation of U.S. Warm Temperature Extremes in Global Climate Model Ensembles
Representation of warm temperature events varies considerably among global climate models, which has [more...]

List all highlights (possible long download time)