title: Quantitative microbial ecology through stable isotope probing.
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 (18)O and (13)C composition after exposure to [(18)O]water or [(13)C]glucose. The addition of glucose increased the assimilation of (18)O into DNA from [(18)O]water. However, the increase in (18)O 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.
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA Bruce.Hungate@nau.edu.
authors: Bruce A
authors: BA
authors: Hungate
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA.
authors: Rebecca L
authors: RL
authors: Mau
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
authors: Egbert
authors: E
authors: Schwartz
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA.
authors: J Gregory
authors: JG
authors: Caporaso
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
authors: Paul
authors: P
authors: Dijkstra
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA.
authors: Natasja
authors: N
authors: van Gestel
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA.
authors: Benjamin J
authors: BJ
authors: Koch
authors: Translational Genomics Research Center, Flagstaff, Arizona, USA Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
authors: Cindy M
authors: CM
authors: Liu
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA.
authors: Theresa A
authors: TA
authors: McHugh
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
authors: Jane C
authors: JC
authors: Marks
authors: Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA.
authors: Ember M
authors: EM
authors: Morrissey
authors: Translational Genomics Research Center, Flagstaff, Arizona, USA Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
authors: Lance B
authors: LB
authors: Price
mesh_terms: D001419:Bacteria / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D058448:Biota; D002499:Centrifugation, Density Gradient; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004783:Environmental Microbiology; D007553:Isotope Labeling / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial