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Quantitative stable isotope probing with H 2 18 O to measure taxon‐specific microbial growth
Author(s) -
Purcell Alicia M.,
Dijkstra Paul,
Finley Brianna,
Hayer Michaela,
Koch Benjamin J.,
Mau Rebecca L.,
Morrissey Ember,
Papp Katerina,
Schwartz Egbert,
Stone Bram W.,
Hungate Bruce A.
Publication year - 2020
Publication title -
soil science society of america journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.836
H-Index - 168
eISSN - 1435-0661
pISSN - 0361-5995
DOI - 10.1002/saj2.20159
Subject(s) - taxon , stable isotope probing , stable isotope ratio , soil water , microorganism , isotope , biology , environmental chemistry , microbial population biology , isopycnic , ecology , botany , chemistry , bacteria , centrifugation , paleontology , biochemistry , physics , quantum mechanics
Microorganisms in soil assimilate, transform, and mineralize soil C to support growth. There are an estimated 2.6 × 10 29 microbial cells containing 26 Pg C in soils worldwide. Consequently, quantifying microbial growth in soil is critical for determining the degree to which microorganisms contribute to the global C cycle. Measuring taxonspecific microbial growth enables understanding of the contribution of microbial taxa to elemental transformations across ecosystems and their susceptibility to environmental perturbations. These measurements in soil have largely been lacking due to inadequate methods. Quantitative stable isotope probing (qSIP) with H 2 18 O is used to measure taxon‐specific growth of microbial taxa in soil, an improvement compared with traditional stable isotope probing (SIP). In qSIP, DNA extracted from both a labeled ( 18 O‐enriched water) and an unlabeled treatment is separated into numerous density fractions by isopycnic centrifugation, and target genes are quantified and sequenced in each fraction. The taxon‐specific DNA density shift and ultimately the isotopic composition ( 18 O enrichment) is calculated for each taxon. Here we discuss methods and illustrate the procedure for quantifying microbial taxon‐specific growth in soil with qSIP using heavy isotope enriched H 2 18 O.