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Untargeted Soil Metabolomics Using Liquid Chromatography–Mass Spectrometry and Gas Chromatography–Mass Spectrometry

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Microbial Metabolomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1859))

Abstract

The molecular composition of soil organic matter (SOM) sets the foundation for terrestrial microbial community structures and carbon cycling dynamics. However, the specific chemical constituents of SOM are underexplored. In this chapter we present a protocol for the extraction of small molecule metabolites from soil followed by compound detection and identification using liquid chromatography–mass spectrometry and gas chromatography–mass spectrometry. There are options within the protocol to assess either the extracellular pool of metabolites or the total pool (including intracellular) and either polar or nonpolar metabolites, depending on the reader’s research interests. These methods can be followed individually for a more targeted analysis or all methods can be combined to obtain a more comprehensive understanding of SOM metabolite composition (such as amino acids, nucleobases, organic acids, fatty acids, carbohydrates, secondary metabolites, and antibiotics).

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Author information

Authors and Affiliations

  1. DOE Joint Genome Institute, Walnut Creek, CA, USA

    Trent R. Northen

  2. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Tami L. Swenson & Trent R. Northen

Authors
  1. Tami L. Swenson
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  2. Trent R. Northen
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Corresponding author

Correspondence to Trent R. Northen .

Editor information

Editors and Affiliations

  1. Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA

    Edward E.K. Baidoo

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© 2019 Springer Science+Business Media, LLC, part of Springer Nature

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Swenson, T.L., Northen, T.R. (2019). Untargeted Soil Metabolomics Using Liquid Chromatography–Mass Spectrometry and Gas Chromatography–Mass Spectrometry. In: Baidoo, E. (eds) Microbial Metabolomics. Methods in Molecular Biology, vol 1859. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8757-3_4

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  • DOI: https://doi.org/10.1007/978-1-4939-8757-3_4

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8756-6

  • Online ISBN: 978-1-4939-8757-3

  • eBook Packages: Springer Protocols

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