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Sampling the Subsurface

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Hydrocarbon and Lipid Microbiology Protocols

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Abstract

Drilling and coring methods developed for sampling deep subsurface terrestrial environments have led to the discovery of active, diverse, indigenous microbial communities in a variety of subsurface habitats, including oil and natural gas reservoirs. The primary drilling and coring methods are hollow-stem augering, direct-push coring, cable-tool drilling, and rotary drilling. Rotary drilling is required for depths >300 m and for hard rock environments. The potential for chemical and microbiological contamination during drilling, coring, and sample handling is great, and so obtaining subsurface samples that are truly representative of the subsurface and that are suitable for geochemical and microbiological analyses requires specialized techniques. Solute and particulate tracers are used to quantify chemical and microbiological contamination, respectively. Cores are dissected to remove inner subcore material, in which tracer concentrations should be orders of magnitude lower than in the surrounding material. Samples are generally processed in an anaerobic chamber to avoid exposure of redox-sensitive chemical species and strictly anaerobic microbes to O2. Once drilled, boreholes can be further used to collect groundwater microbes, monitor subsurface chemistry and microbial processes, and enrich for microorganisms. While the methods described here have been successfully used in a variety of subsurface environments, including deep marine sediments, other approaches have also been used, e.g., sampling in deep mines, and still others are being developed.

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Authors and Affiliations

  1. New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA

    Thomas L. Kieft

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  1. Thomas L. Kieft
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Correspondence to Thomas L. Kieft .

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Editors and Affiliations

  1. University of Essex, School of Biological Sciences University of Essex, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

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Kieft, T.L. (2014). Sampling the Subsurface. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2014_27

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  • DOI: https://doi.org/10.1007/8623_2014_27

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