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

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages137-149
Number of pages13
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Molecular Biology
Volume2046
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fingerprint

Isotopes
DNA
Nucleic Acids

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Finley, B. K., Hayer, M., Mau, R. L., Purcell, A. M., Koch, B. J., van Gestel, N. C., ... Hungate, B. A. (2019). Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing. In Methods in Molecular Biology (pp. 137-149). (Methods in Molecular Biology; Vol. 2046). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9721-3_11

Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing. / Finley, Brianna K.; Hayer, Michaela; Mau, Rebecca L.; Purcell, Alicia M.; Koch, Benjamin J.; van Gestel, Natasja C.; Schwartz, Egbert; Hungate, Bruce A.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 137-149 (Methods in Molecular Biology; Vol. 2046).

Research output: Chapter in Book/Report/Conference proceedingChapter

Finley, BK, Hayer, M, Mau, RL, Purcell, AM, Koch, BJ, van Gestel, NC, Schwartz, E & Hungate, BA 2019, Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 2046, Humana Press Inc., pp. 137-149. https://doi.org/10.1007/978-1-4939-9721-3_11
Finley BK, Hayer M, Mau RL, Purcell AM, Koch BJ, van Gestel NC et al. Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing. In Methods in Molecular Biology. Humana Press Inc. 2019. p. 137-149. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9721-3_11
Finley, Brianna K. ; Hayer, Michaela ; Mau, Rebecca L. ; Purcell, Alicia M. ; Koch, Benjamin J. ; van Gestel, Natasja C. ; Schwartz, Egbert ; Hungate, Bruce A. / Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing. Methods in Molecular Biology. Humana Press Inc., 2019. pp. 137-149 (Methods in Molecular Biology).
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