Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities

Authors

  • Bernhard Knierim,

    1. Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA.
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    • Contributed equally to this work.

  • Birgit Luef,

    1. Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA.
    2. Department of Earth and Planetary Science
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    • Contributed equally to this work.

  • Paul Wilmes,

    1. Department of Earth and Planetary Science
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    • Present address: Centre de Recherche Public – Gabriel Lippmann, and Luxembourg Center for Systems Biomedicine, University of Luxembourg, Belvaux, Grand-Duchy of Luxembourg.

  • Richard I. Webb,

    1. Centre for Microscopy and Microanalysis (CMM), The University of Queensland, St. Lucia, Queensland, Australia.
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  • Manfred Auer,

    1. Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA.
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  • Luis R. Comolli,

    Corresponding author
    1. Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA.
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  • Jillian F. Banfield

    Corresponding author
    1. Department of Earth and Planetary Science
    2. Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA.
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  • Author contributions: B.K., B.L., P.W., R.I.W., M.A., L.R.C. and J.F.B. designed the research; B.K., B.L., P.W. and R.I.W. developed and performed the CARD-FISH; B.L. and L.R.C. cultured Caulobacter crescentus and B.L. prepared AMD biofilm samples; B.K., P.W. and R.I.W. prepared the resin samples and B.K. carried out the resin section transmission electron microscopy; B.L. and L.R.C. prepared the cryogenic samples and did the cryogenic electron microscopy; B.L. performed the electron dose calibration and optimization; B.K., B.L. and P.W. performed the fluorescence microscopy and confocal laser scanning microscopy; B.K., B.L. and L.R.C. prepared the figures; B.K., B.L., L.R.C. and J.F.B. prepared the manuscript. All authors contributed to the manuscript.

E-mail lrcomolli@lbl.gov; Tel. 510 643 2155; Fax 510 643 9980;

E-mail jbanfield@berkeley.edu; Tel. 510 486 6437; Fax 510 486 6488.

Summary

Transmission electron microscopy (TEM) can provide ultrastructural information for cells in microbial community samples and phylogenetic information can be recovered via molecular surveys. Here we report an approach to link these data sets by coupling fluorescence in situ hybridization (FISH) with either conventional biological or cryogenic TEM. The method could fundamentally improve our understanding of the organization and functioning of microbial communities in natural systems.

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