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Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific

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† ‡ Department of Earth and Planetary Science and Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, United States
§ Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
BioSciences Division and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
Cite this: ACS Chem. Biol. 2013, 8, 8, 1755–1763
Publication Date (Web):May 28, 2013
Copyright © 2013 American Chemical Society

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    The fractionation of hydrogen stable isotopes during lipid biosynthesis is larger in autotrophic than in heterotrophic microorganisms, possibly due to selective incorporation of hydrogen from water into NAD(P)H, resulting in D-depleted lipids. An analogous fractionation should occur during amino acid biosynthesis. Whereas these effects are traditionally measured using gas-phase isotope ratio on 1H-1H and 1H-2H, using an electrospray mass spectrometry-based technique on the original biomolecular structure and fitting of isotopic patterns we measured the hydrogen isotope compositions of proteins from an acidophilic microbial community with organism specificity and compared values with those for lipids. We showed that lipids were isotopically light by −260 ‰ relative to water in the growth solution; alternatively protein isotopic composition averaged −370 ‰. This difference suggests that steps in addition to NAD(P)H formation contribute to D/H fractionation. Further, autotrophic bacteria sharing 94% 16S rRNA gene sequence identity displayed statistically significant differences in protein hydrogen isotope fractionation, suggesting different metabolic traits consistent with distinct ecological niches or incorrectly annotated gene function. In addition, it was found that heterotrophic, archaeal members of the community had isotopically light protein (−323 ‰) relative to growth water and were significantly different from coexisting bacteria. This could be attributed to metabolite transfer from autotrophs and unknown aspects of fractionation associated with iron reduction. Differential fractionation of hydrogen stable isotopes into metabolites and proteins may reveal trophic levels of members of microbial communities. The approach developed here provided insights into the metabolic characteristics of organisms in natural communities and may be applied to analyze other systems.

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