Characterizing the Deep Terrestrial Subsurface Microbiome

  • Rebecca A. DalyEmail author
  • Kelly C. Wrighton
  • Michael J. Wilkins
Part of the Methods in Molecular Biology book series (MIMB, volume 1849)


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 



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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Rebecca A. Daly
    • 1
    Email author
  • Kelly C. Wrighton
    • 1
  • Michael J. Wilkins
    • 1
  1. 1.Department of MicrobiologyThe Ohio State UniversityColumbusUSA

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