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Title: Comparative genomics and physiology of the genus Methanohalophilus , a prevalent methanogen in hydraulically fractured shale

Abstract

Currently about 60% of natural gas production in the United States comes from the hydraulic fracturing of shale. This process inoculates and enriches for halotolerant microorganisms in shales overtime, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of these methanogens across shales, and report that members of the genus Methanohalophilus are recovered from every fractured shale play sampled by metagenomics. We provide the first genomic sequencing of 3 isolate genomes, as well as 2 metagenome assembled genomes. Utilizing 6 other previously sequenced genomes, we perform a comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with the constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same shale well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in the CRSIPR-Cas systems of Methanohalophilus, with genomes from geographically distinct hydraulically fractured shales sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic 47 methane production 48 in hydraulically fractured shales.

Authors:
ORCiD logo [1];  [1];  [2];  [3];  [4];  [5];  [4];  [6];  [1];  [4];  [7];  [5];  [8];  [8];  [5];  [1];  [1]
  1. Soil and Crop Sciences, Colorado State UniversityFort CollinsCOUSA
  2. Department of MicrobiologyUniversity of TennesseeKnoxvilleTNUSA
  3. EMSL, Pacific Northwest National LabRichlandWAUSA
  4. Depatment of MicrobiologyThe Ohio State UniversityColumbusOHUSA
  5. School of Earth SciencesThe Ohio State UniversityColumbusOHUSA
  6. Molecular and Cellular Imaging Center, The Ohio State University Wooster OH USA
  7. Department of Geology and GeographyWest Virginia University Morgantown WV USA
  8. DowDuPont Industrial Biosciences Wilmington DE USA
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1496791
Report Number(s):
PNNL-SA-138432
Journal ID: ISSN 1462-2912
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 20; Journal Issue: 12; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English

Citation Formats

Borton, Mikayla A., Daly, Rebecca A., O'Banion, Bridget, Hoyt, David W., Marcus, Daniel N., Welch, Susan, Hastings, Sybille S., Meulia, Tea, Wolfe, Richard A., Booker, Anne E., Sharma, Shikha, Cole, David R., Wunch, Kenneth, Moore, Joseph D., Darrah, Thomas H., Wilkins, Michael J., and Wrighton, Kelly C. Comparative genomics and physiology of the genus Methanohalophilus , a prevalent methanogen in hydraulically fractured shale. United States: N. p., 2018. Web. doi:10.1111/1462-2920.14467.
Borton, Mikayla A., Daly, Rebecca A., O'Banion, Bridget, Hoyt, David W., Marcus, Daniel N., Welch, Susan, Hastings, Sybille S., Meulia, Tea, Wolfe, Richard A., Booker, Anne E., Sharma, Shikha, Cole, David R., Wunch, Kenneth, Moore, Joseph D., Darrah, Thomas H., Wilkins, Michael J., & Wrighton, Kelly C. Comparative genomics and physiology of the genus Methanohalophilus , a prevalent methanogen in hydraulically fractured shale. United States. doi:10.1111/1462-2920.14467.
Borton, Mikayla A., Daly, Rebecca A., O'Banion, Bridget, Hoyt, David W., Marcus, Daniel N., Welch, Susan, Hastings, Sybille S., Meulia, Tea, Wolfe, Richard A., Booker, Anne E., Sharma, Shikha, Cole, David R., Wunch, Kenneth, Moore, Joseph D., Darrah, Thomas H., Wilkins, Michael J., and Wrighton, Kelly C. Sat . "Comparative genomics and physiology of the genus Methanohalophilus , a prevalent methanogen in hydraulically fractured shale". United States. doi:10.1111/1462-2920.14467.
@article{osti_1496791,
title = {Comparative genomics and physiology of the genus Methanohalophilus , a prevalent methanogen in hydraulically fractured shale},
author = {Borton, Mikayla A. and Daly, Rebecca A. and O'Banion, Bridget and Hoyt, David W. and Marcus, Daniel N. and Welch, Susan and Hastings, Sybille S. and Meulia, Tea and Wolfe, Richard A. and Booker, Anne E. and Sharma, Shikha and Cole, David R. and Wunch, Kenneth and Moore, Joseph D. and Darrah, Thomas H. and Wilkins, Michael J. and Wrighton, Kelly C.},
abstractNote = {Currently about 60% of natural gas production in the United States comes from the hydraulic fracturing of shale. This process inoculates and enriches for halotolerant microorganisms in shales overtime, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of these methanogens across shales, and report that members of the genus Methanohalophilus are recovered from every fractured shale play sampled by metagenomics. We provide the first genomic sequencing of 3 isolate genomes, as well as 2 metagenome assembled genomes. Utilizing 6 other previously sequenced genomes, we perform a comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with the constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same shale well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in the CRSIPR-Cas systems of Methanohalophilus, with genomes from geographically distinct hydraulically fractured shales sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic 47 methane production 48 in hydraulically fractured shales.},
doi = {10.1111/1462-2920.14467},
journal = {Environmental Microbiology},
issn = {1462-2912},
number = 12,
volume = 20,
place = {United States},
year = {2018},
month = {12}
}