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

  • Brianna K. FinleyEmail author
  • Michaela Hayer
  • Rebecca L. Mau
  • Alicia M. Purcell
  • Benjamin J. Koch
  • Natasja C. van Gestel
  • Egbert Schwartz
  • Bruce A. Hungate
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Atom percent excess Quantitative stable isotope probing (qSIP) Microbial element cycling Quantitative microbial ecology 

Notes

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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Copyright information

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

Authors and Affiliations

  • Brianna K. Finley
    • 1
    Email author
  • Michaela Hayer
    • 1
  • Rebecca L. Mau
    • 2
  • Alicia M. Purcell
    • 1
  • Benjamin J. Koch
    • 1
  • Natasja C. van Gestel
    • 3
  • Egbert Schwartz
    • 1
  • Bruce A. Hungate
    • 1
  1. 1.Department of Biological Sciences, Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffUSA
  2. 2.Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffUSA
  3. 3.Department of Biological SciencesTexas Tech UniversityLubbockUSA

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