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Microbiome Analysis pp 1–15Cite as

Characterizing the Deep Terrestrial Subsurface Microbiome

Part of the Methods in Molecular Biology book series (MIMB,volume 1849)

Abstract

A large portion of the earth’s biomass resides in the subsurface and recent studies have expanded our knowledge of indigenous microbial life. Advances in the field of metagenomics now allow analysis of microbial communities from low-biomass samples such as deep (>2.5 km) shale core samples. Here we present protocols for the best practices in contamination control, handling core material, extraction of nucleic acids, and low-input library preparation for subsequent metagenomic sequencing.

Key words

  • Deep life
  • Deep biosphere
  • Terrestrial subsurface
  • Contamination
  • Shale
  • Metagenomics
  • Low biomass

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Acknowledgments

Rebecca Daly, Kelly Wrighton and Michael Wilkins were partially supported by funding from the National Sciences Foundation Dimensions of Biodiversity (Award No. 1342701) and by the Marcellus Shale Energy and Environment Laboratory (MSEEL) funded by Department of Energy’s National Energy Technology laboratory (DOE-NETL) grant DE#FE0024297.

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Authors and Affiliations

  1. Department of Microbiology, The Ohio State University, Columbus, OH, USA

    Rebecca A. Daly, Kelly C. Wrighton & Michael J. Wilkins

Authors
  1. Rebecca A. Daly
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  2. Kelly C. Wrighton
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  3. Michael J. Wilkins
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Corresponding author

Correspondence to Rebecca A. Daly .

Editor information

Editors and Affiliations

  1. Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada

    Robert G. Beiko

  2. Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada

    Will Hsiao

  3. Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada

    Prof. Dr. John Parkinson

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Daly, R.A., Wrighton, K.C., Wilkins, M.J. (2018). Characterizing the Deep Terrestrial Subsurface Microbiome. In: Beiko, R., Hsiao, W., Parkinson, J. (eds) Microbiome Analysis. Methods in Molecular Biology, vol 1849. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8728-3_1

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  • DOI: https://doi.org/10.1007/978-1-4939-8728-3_1

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8726-9

  • Online ISBN: 978-1-4939-8728-3

  • eBook Packages: Springer Protocols

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