Quantitative microbial ecology through stable isotope probing

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

doi:10.7287/peerj.preprints.1282v1

Quantitative microbial ecology through stable isotope probing

Bruce A Hungate ^1,2, Rebecca L Mau¹, Egbert Schwartz^1,2, J Gregory Caporaso^1,2,3, Paul Dijkstra^1,2, Natasja van Gestel¹, Benjamin J Koch¹, Cindy M Liu^4,5,6, Theresa A McHugh¹, Jane C Marks^1,2, Ember M Morrissey¹, Lance B Price^7,8

1 Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States

2 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States

3 Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA

4 School of Medicine, Department of Pathology, The Johns Hopkins University, Baltimore, MD, United States

5 Pathogen Genomics Division, Center for Microbiomics and Human Health, Translational Genomics Research Center, Flagstaff, AZ, USA

6 Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States

7 Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, United States

8 Pathogen Genomics Division, Center for Food Microbiology and Environmental Health, Translational Genomics Institute, Flagstaff, AZ, USA

DOI: 10.7287/peerj.preprints.1282v1

Published: 2015-08-04
Accepted: 2015-08-04

Subject Areas: Ecology, Ecosystem Science, Microbiology, Molecular Biology
Keywords: stable isotope probing, oxygen-18, biodiversity, 18O-H2O, soil carbon cycle, ecosystem functioning, microbial ecology

Copyright: © 2015 Hungate et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Cite this article: Hungate BA, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, McHugh TA, Marks JC, Morrissey EM, Price LB. 2015. Quantitative microbial ecology through stable isotope probing. PeerJ PrePrints 3:e1282v1 https://doi.org/10.7287/peerj.preprints.1282v1

Abstract

Bacteria grow and transform elements at different rates, 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 determining the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers. 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 non-labeled 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 demonstrate qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variation in ¹⁸O and ¹³C composition after exposure to ¹⁸O-H₂O or ¹³C-glucose. Addition of glucose increased assimilation of ¹⁸O into DNA from ¹⁸O-H₂O. However, the increase in ¹⁸O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because glucose addition indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.

Author Comment

This manuscript is under review in the journal, Applied and Environmental Microbiology.

Supplemental Information

QIIME code for bioinformatics and statistical results from the bioinformatics procedures

This file contains the code used in QIIME to analyze the sequencing data, including all steps used in that analysis. This file also contains a table (Table S1), which summarizes results from the bioinformatics statistics.

DOI: 10.7287/peerj.preprints.1282v1/supp-1

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