Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing
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 wordsAtom percent excess Quantitative stable isotope probing (qSIP) Microbial element cycling Quantitative microbial ecology
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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