Article

Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem

  • Nature Microbiology 1, Article number: 16130 (2016)
  • doi:10.1038/nmicrobiol.2016.130
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Abstract

Much remains unknown about what drives microbial community structure and diversity. Highly structured environments might offer clues. For example, it may be possible to identify metabolically similar species as groups of organisms that correlate spatially with the geochemical processes they carry out. Here, we use a 16S ribosomal RNA gene survey in a lake that has chemical gradients across its depth to identify groups of spatially correlated but phylogenetically diverse organisms. Some groups had distributions across depth that aligned with the distributions of metabolic processes predicted by a biogeochemical model, suggesting that these groups performed biogeochemical functions. A single-cell genetic assay showed, however, that the groups associated with one biogeochemical process, sulfate reduction, contained only a few organisms that have the genes required to reduce sulfate. These results raise the possibility that some of these spatially correlated groups are consortia of phylogenetically diverse and metabolically different microbes that cooperate to carry out geochemical functions.

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Acknowledgements

This material is based on work supported by the National Science Foundation Graduate Research Fellowship (grant no. 1122374) and by the US Department of Energy, Office of Science, Office of Biological and Environmental Research (award no. DE-SC0008743).

Author information

Author notes

    • Sarah P. Preheim
    •  & Scott W. Olesen

    These authors contributed equally to this work.

Affiliations

  1. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Sarah P. Preheim
    • , Scott W. Olesen
    • , Sarah J. Spencer
    •  & Eric J. Alm
  2. Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA

    • Sarah P. Preheim
  3. Qiagen Corp., 8000 Aarhus, Denmark

    • Arne Materna
  4. Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

    • Charuleka Varadharajan
  5. École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland

    • Matthew Blackburn
  6. Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Jonathan Friedman
  7. Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, PO Box 54224, Abu Dhabi, United Arab Emirates

    • Jorge Rodríguez
  8. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Harold Hemond

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Contributions

S.P.P., S.W.O., H.H. and E.J.A. designed the research. S.P.P., S.W.O., A.M., C.V., M.B. and S.J.S. performed the research. S.P.P., S.W.O., J.F. and J.R. contributed analytical tools. S.P.P., S.W.O. and J.R. analysed the data. S.P.P., S.W.O. and E.J.A. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Eric J. Alm.

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    Supplementary information

    Supplementary Text, Supplementary References, Supplementary Tables 1–6, Supplementary Figures 1–9