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

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.

doi:10.1111/1462-2920.14467

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

Journal Article · 01 December 2018 · Environmental Microbiology

DOI:https://doi.org/10.1111/1462-2920.14467· OSTI ID:1496791

^[1]; Daly, Rebecca A. ^[1]; O'Banion, Bridget ^[2]; Hoyt, David W. ^[3]; Marcus, Daniel N. ^[4]; Welch, Susan ^[5]; Hastings, Sybille S. ^[4]; Meulia, Tea ^[6]; Wolfe, Richard A. ^[1]; Booker, Anne E. ^[4]; Sharma, Shikha ^[7]; Cole, David R. ^[5]; Wunch, Kenneth ^[8]; Moore, Joseph D. ^[8]; Darrah, Thomas H. ^[5]; Wilkins, Michael J. ^[1]; Wrighton, Kelly C. ^[1]

Soil and Crop Sciences, Colorado State UniversityFort CollinsCOUSA
Department of MicrobiologyUniversity of TennesseeKnoxvilleTNUSA
EMSL, Pacific Northwest National LabRichlandWAUSA
Depatment of MicrobiologyThe Ohio State UniversityColumbusOHUSA
School of Earth SciencesThe Ohio State UniversityColumbusOHUSA
Molecular and Cellular Imaging Center, The Ohio State University Wooster OH USA
Department of Geology and GeographyWest Virginia University Morgantown WV USA
DowDuPont Industrial Biosciences Wilmington DE USA

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.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1496791

Report Number(s):: PNNL-SA-138432

Journal Information:: Environmental Microbiology, Vol. 20, Issue 12; ISSN 1462-2912

Publisher:: Wiley

Country of Publication:: United States

Language:: English

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