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

Brianna K. Finley, Michaela Hayer, Rebecca L. Mau, Alicia M. Purcell, Benjamin J. Koch, Natasja C. van Gestel, Egbert Schwartz, Bruce A. Hungate

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Scopus citations


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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages13
StatePublished - 2019

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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