Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities
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Natural microbial communities are extremely diverse and contain uncharacterized but functionally important small molecules. By coupling a deuterium (D) labeling technique to high mass accuracy untargeted liquid chromatography-electrospray ionization-mass spectrometry (LC–ESI–MS) metabolomic analysis, we found that natural acidophilic microbial biofilms dominated by bacteria of the genus Leptospirillum contained unusual lyso phosphatidylethanolamine (PE) lipids in high abundance (more than 10 nmol/mg of dry biomass). The unusual polar head group structure of these lipids is similar to lipids found in phylogenetically unrelated acidophilic chemoautolithotrophs and may be related to the affinity of these lipids for iron and calcium ions. Correlations of lyso phospholipid and proteome abundance patterns suggest a link between the lyso phospholipids and the UBA-type substrain of Leptospirillum group II. By combining untargeted metabolomics with D exchange we demonstrate the ability to identify cryptic but biologically functional small molecules in mixed microbial communities.
KeywordsDeuterium exchange Untargeted metabolomics Microbial community Lyso lipid
The authors thank Mr. T. Arman for access to the Richmond Mine, Mr. R. Caver for on-site assistance, the Banfield lab members for assistance with biofilm sampling in the field, Susan Spaulding for assistance with bioreactor operation and sample preparation, and John Hayes for valuable technical discussions. This research was funded by the US Department of Energy, Office of Biological and Environmental Research Carbon-Cycling Program (DE-SC0004665), the DOE Genomics:GTL Program grant number DE-FG02-05ER64134. PWs recent involvement was supported by a Luxembourg National Research Fund ATTRACT grant (FNR/A09/03).
Conflicts of interests
The authors declare no competing interests.
- Baran, R., Bowen, B. P., Bouskill, N. J., Brodie, E. L., Yannone, S. M., & Northen, T. R. (2010). Metabolite identification in Synechococcus sp. PCC 7002 using untargeted stable isotope assisted metabolite profiling. Analytical Chemistry, 82(21), 9034–9042.Google Scholar
- Cowie, B. R., Slater, G. F., Bernier, L., & Warren, L. A. (2009). Carbon isotope fractionation in phospholipid fatty acid biomarkers of bacteria and fungi native to an acid mine drainage lake. Organic Geochemistry, 40(9), 956–962.Google Scholar
- Denef, V. J., Kalnejais, L. H., Mueller, R. S., Wilmes, P., Baker, B. J., Thomas, B. C., et al. (2010). Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proceedings of the National Academy of Sciences of USA, 107(6), 2383–2390.CrossRefGoogle Scholar
- Goltsman, D. S. A., Denef, V. J., Singer, S. W., VerBerkmoes, N. C., Lefsrud, M., Mueller, R. S., et al. (2009). Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) bacteria in acid mine drainage biofilms. Applied and Environmental Microbiology, 75(13), 4599.PubMedCrossRefGoogle Scholar
- Han, X., & Gross, R. W. (2005). Shotgun lipidomics: Electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Bioorganic Chemistry, 24, 367–412.Google Scholar
- Jeans, C., Singer, S. W., Chan, C. S., VerBerkmoes, N. C., Shah, M., Hettich, R. L., et al. (2008). Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. The ISME Journal, 2(5), 542–550.PubMedCrossRefGoogle Scholar
- Mueller, R. S., Denef, V. J., Kalnejais, L. H., Suttle, K. B., Thomas, B. C., Wilmes, P., Smith, R. L., Nordstrom, D. K., McCleskey, R. B., Shah, M. B., VerBerkmoes, N. C., Hettich, R. L., & Banfield, J. F. (2010). Ecological distribution and population physiology defined by proteomics in a natural microbial community. Molecular Systems Biology, 6, 314.Google Scholar