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Abstract

Most microbes in the biosphere remain unculturable1. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) can be used to study the genetic and metabolic properties of natural microbial communities2,3,4. However, in communities of high complexity, metagenomics fails to link specific microbes to specific ecological functions. To overcome this limitation, we developed a method to target microbial subpopulations by labeling DNA through stable isotope probing (SIP), followed by WGS sequencing. Metagenome analysis of microbes from Lake Washington in Seattle that oxidize single-carbon (C1) compounds shows specific sequence enrichments in response to different C1 substrates, revealing the ecological roles of individual phylotypes. We also demonstrate the utility of our approach by extracting a nearly complete genome of a novel methylotroph, Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This high-resolution, targeted metagenomics approach may be applicable to a wide variety of ecosystems.

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Acknowledgements

This research was supported by the National Science Foundation as part of the Microbial Observatories program (MCB-0604269). This work was performed, in part, under the auspices of the US Department of Energy's Office of Science Biological and Environmental Research Program, and by the University of California, Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract no. DE-AC02-05CH11231 and Los Alamos National Laboratory under contract no. DE-AC02-06NA25396. The sequencing for the project was provided through the US Department of Energy Community Sequencing Program (http://www.jgi.doe.gov/CSP/index.html).

Author information

Author notes

    • Alice C McHardy

    Present address: Computational Genomics and Epidemiology Group, Max Planck Institute for Computer Science, Campus E1 4, 66123 Saarbruecken, Germany.

Affiliations

  1. Department of Microbiology, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, Washington 98105, USA.

    • Marina G Kalyuzhnaya
    •  & Mary E Lidstrom
  2. Department of Chemical Engineering, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, Washington 98105, USA.

    • Samuel R Levine
    • , Mary E Lidstrom
    •  & Ludmila Chistoserdova
  3. Production Genomics Facility, DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400, Walnut Creek, California 94596, USA.

    • Alla Lapidus
    • , Natalia Ivanova
    • , Alex C Copeland
    • , Asaf Salamov
    • , Igor V Grigoriev
    • , Susannah G Tringe
    •  & Paul M Richardson
  4. Bioinformatics and Pattern Discovery Group, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA.

    • Alice C McHardy
    •  & Isidore Rigoutsos
  5. Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50A-1148, Berkeley, California 94720, USA.

    • Ernest Szeto
    •  & Victor M Markowitz
  6. Combimatrix Corporation, 6500 Harbour Heights Pkwy., Mukilteo, Washington 98275, USA.

    • Dominic Suciu
  7. DOE Joint Genome Institute, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico 87545, USA.

    • David C Bruce

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Contributions

M.G.K., M.E.L. and L.C. conceived the project. M.E.L. and L.C. coordinated project execution. M.G.K. collected samples, performed SIP, purified DNA for sequencing and performed microarray hybridizations. D.C.B. and P.M.R. oversaw library construction and sequencing. S.G.T. oversaw sequence assembly and analysis. A.C.C. and A.L. carried out assemblies. A.S. and I.V.G. conducted gene prediction and annotation. A.C.M. and I.R. carried out binning. E.S. and V.M.M. carried out data processing and loading into IMG/M. L.C. and N.I. carried out metabolic reconstruction. S.R.L. and M.G.K. performed species richness estimates. D.S. carried our microarray design. M.G.K., M.E.L. and L.C. wrote the initial draft of the paper; all other authors contributed.

Corresponding author

Correspondence to Ludmila Chistoserdova.

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DOI

https://doi.org/10.1038/nbt.1488