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Stable Isotope Probing pp 137–149Cite as

Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2046))

Abstract

Quantitative stable isotope probing (qSIP) measures rates of taxon-specific element assimilation in intact microbial communities, utilizing substrates labeled with a heavy isotope.

The laboratory protocol for qSIP is nearly identical to that for conventional stable isotope probing, with two key additions: (1) in qSIP, qPCR measurements are conducted on each density fraction recovered after isopycnic separation, and (2) in qSIP, multiple density fractions are sequenced spanning the entire range of densities over which nucleic acids were recovered. qSIP goes beyond identifying taxa assimilating a substrate, as it also allows for measuring that assimilation for each taxon within a given microbial community. Here, we describe an analysis process necessary to determine atom fraction excess of a heavy stable isotope added to an environmental sample for a given taxon’s DNA.

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Acknowledgments

This research was supported by the National Science Foundation (grants EAR-1124078 and DEB-1321792), and by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program (grants to NAU and as part of the LLNL Soil Microbiome Scientific Focus Area).

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Authors and Affiliations

  1. Department of Biological Sciences, Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA

    Brianna K. Finley, Michaela Hayer, Alicia M. Purcell, Benjamin J. Koch, Egbert Schwartz & Bruce A. Hungate

  2. Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA

    Rebecca L. Mau

  3. Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA

    Natasja C. van Gestel

Authors
  1. Brianna K. Finley
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  2. Michaela Hayer
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  3. Rebecca L. Mau
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  4. Alicia M. Purcell
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  5. Benjamin J. Koch
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  6. Natasja C. van Gestel
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  7. Egbert Schwartz
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  8. Bruce A. Hungate
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Corresponding author

Correspondence to Brianna K. Finley .

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Editors and Affiliations

  1. School of Biological Sciences, University of Southampton, Southampton, UK

    Marc G. Dumont

  2. School of Biological Sciences, University of Southampton, Southampton, UK

    Marcela Hernández García

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Finley, B.K. et al. (2019). Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing. In: Dumont, M., Hernández García, M. (eds) Stable Isotope Probing. Methods in Molecular Biology, vol 2046. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9721-3_11

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  • DOI: https://doi.org/10.1007/978-1-4939-9721-3_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9720-6

  • Online ISBN: 978-1-4939-9721-3

  • eBook Packages: Springer Protocols

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