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

doi:10.1007/978-1-4939-9721-3_11

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

Biological Sciences

Research output: Chapter in Book/Report/Conference proceeding › Chapter

6 Scopus citations

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 language	English (US)
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	137-149
Number of pages	13
DOIs	https://doi.org/10.1007/978-1-4939-9721-3_11
State	Published - 2019

Publication series

Name	Methods in Molecular Biology
Volume	2046
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

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

ASJC Scopus subject areas

Molecular Biology
Genetics

Access to Document

10.1007/978-1-4939-9721-3_11

Cite this

Finley, B. K., Hayer, M., Mau, R. L., Purcell, A. M., Koch, B. J., van Gestel, N. C., Schwartz, E., & 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

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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{\textquoteright}s DNA.",

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

note = "Funding Information: 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). Publisher Copyright: {\textcopyright} Springer Science+Business Media, LLC, part of Springer Nature 2019.",

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doi = "10.1007/978-1-4939-9721-3_11",

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AU - Hayer, Michaela

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AU - Purcell, Alicia M.

AU - Koch, Benjamin J.

AU - van Gestel, Natasja C.

AU - Schwartz, Egbert

AU - Hungate, Bruce A.

N1 - Funding Information: 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). Publisher Copyright: © Springer Science+Business Media, LLC, part of Springer Nature 2019.

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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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KW - Microbial element cycling

KW - Quantitative microbial ecology

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

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