Quantitative microbial ecology through stable isotope probing

Bruce A Hungate, Rebecca L. Mau, Egbert Schwartz, James G Caporaso, Paul Dijkstra, Natasja van Gestel, Benjamin J. Koch, Cindy M. Liu, Theresa A. McHugh, Jane C Marks, Ember M. Morrissey, Lance B. Price

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in 18O and 13C composition after exposure to [18O]water or [13C]glucose. The addition of glucose increased the assimilation of 18O into DNA from [18O]water. However, the increase in 18O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.

Original languageEnglish (US)
Pages (from-to)7570-7581
Number of pages12
JournalApplied and Environmental Microbiology
Volume81
Issue number21
DOIs
StatePublished - 2015

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microbial ecology
Ecology
Isotopes
stable isotopes
stable isotope
isotope labeling
isotope
glucose
assimilation (physiology)
isotopes
tracer
DNA
bacterium
Glucose
Bacteria
bacteria
soil bacteria
nucleic acid
Soil
Isopycnic Centrifugation

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology

Cite this

Quantitative microbial ecology through stable isotope probing. / Hungate, Bruce A; Mau, Rebecca L.; Schwartz, Egbert; Caporaso, James G; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa A.; Marks, Jane C; Morrissey, Ember M.; Price, Lance B.

In: Applied and Environmental Microbiology, Vol. 81, No. 21, 2015, p. 7570-7581.

Research output: Contribution to journalArticle

Hungate, Bruce A ; Mau, Rebecca L. ; Schwartz, Egbert ; Caporaso, James G ; Dijkstra, Paul ; van Gestel, Natasja ; Koch, Benjamin J. ; Liu, Cindy M. ; McHugh, Theresa A. ; Marks, Jane C ; Morrissey, Ember M. ; Price, Lance B. / Quantitative microbial ecology through stable isotope probing. In: Applied and Environmental Microbiology. 2015 ; Vol. 81, No. 21. pp. 7570-7581.
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