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Title: Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales

Abstract

Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth’s surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilus strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.

Authors:
 [1]; ORCiD logo [2]; ORCiD logo [3];  [1];  [4];  [2];  [2];  [2];  [5];  [4];  [4];  [1];  [6];  [6]; ORCiD logo [4];  [5];  [2];  [7];  [1]
  1. The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Science Lab.
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. The Ohio State Univ., Columbus, OH (United States). The School of Earth Sciences
  5. Univ. of New Hampshire, Durham, NH (United States). Dept. of Civil and Environmental Engineering
  6. West Virginia Univ., Morgantown, WV (United States). Dept. of Geology and Geography
  7. The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology. The School of Earth Sciences
Publication Date:
Research Org.:
West Virginia Univ., Morgantown, WV (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States); The Ohio State Univ., Columbus, OH (United States)
Sponsoring Org.:
USDOE Office of Fossil Energy (FE); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Science Foundation (NSF)
OSTI Identifier:
1491839
Grant/Contract Number:  
FE0024297; AC02-05CH11231; AC05-76RL01830; 1342701
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 115; Journal Issue: 28; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; hydraulic fracturing; metaproteomics; Stickland reaction; methanogenesis; metagenomics

Citation Formats

Borton, Mikayla A., Hoyt, David W., Roux, Simon, Daly, Rebecca A., Welch, Susan A., Nicora, Carrie D., Purvine, Samuel, Eder, Elizabeth K., Hanson, Andrea J., Sheets, Julie M., Morgan, David M., Wolfe, Richard A., Sharma, Shikha, Carr, Timothy R., Cole, David R., Mouser, Paula J., Lipton, Mary S., Wilkins, Michael J., and Wrighton, Kelly C. Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. United States: N. p., 2018. Web. doi:10.1073/pnas.1800155115.
Borton, Mikayla A., Hoyt, David W., Roux, Simon, Daly, Rebecca A., Welch, Susan A., Nicora, Carrie D., Purvine, Samuel, Eder, Elizabeth K., Hanson, Andrea J., Sheets, Julie M., Morgan, David M., Wolfe, Richard A., Sharma, Shikha, Carr, Timothy R., Cole, David R., Mouser, Paula J., Lipton, Mary S., Wilkins, Michael J., & Wrighton, Kelly C. Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. United States. doi:10.1073/pnas.1800155115.
Borton, Mikayla A., Hoyt, David W., Roux, Simon, Daly, Rebecca A., Welch, Susan A., Nicora, Carrie D., Purvine, Samuel, Eder, Elizabeth K., Hanson, Andrea J., Sheets, Julie M., Morgan, David M., Wolfe, Richard A., Sharma, Shikha, Carr, Timothy R., Cole, David R., Mouser, Paula J., Lipton, Mary S., Wilkins, Michael J., and Wrighton, Kelly C. Mon . "Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales". United States. doi:10.1073/pnas.1800155115. https://www.osti.gov/servlets/purl/1491839.
@article{osti_1491839,
title = {Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales},
author = {Borton, Mikayla A. and Hoyt, David W. and Roux, Simon and Daly, Rebecca A. and Welch, Susan A. and Nicora, Carrie D. and Purvine, Samuel and Eder, Elizabeth K. and Hanson, Andrea J. and Sheets, Julie M. and Morgan, David M. and Wolfe, Richard A. and Sharma, Shikha and Carr, Timothy R. and Cole, David R. and Mouser, Paula J. and Lipton, Mary S. and Wilkins, Michael J. and Wrighton, Kelly C.},
abstractNote = {Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth’s surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilus strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.},
doi = {10.1073/pnas.1800155115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 28,
volume = 115,
place = {United States},
year = {2018},
month = {6}
}

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Works referenced in this record:

Search and clustering orders of magnitude faster than BLAST
journal, August 2010


Evolution and classification of the CRISPR�Cas systems
journal, May 2011

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