Brief Communication

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities

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Abstract

Microbial interactions influence the productivity and biogeochemistry of the ocean, yet they occur in miniscule volumes that cannot be sampled by traditional oceanographic techniques. To investigate the behaviours of marine microorganisms at spatially relevant scales, we engineered an in situ chemotaxis assay (ISCA) based on microfluidic technology. Here, we describe the fabrication, testing and first field results of the ISCA, demonstrating its value in accessing the microbial behaviours that shape marine ecosystems.

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Acknowledgements

The authors thank A. Gavish and A. Vardi for supplying V. coralliilyticus YB2, A. Stahl and M. Ullrich for supplying M. adhaerens (HP15 ΔfliC) and C. Gao and F. Moser for assistance generating the fluorescent E. coli strain used in this study. This work was supported by the Gordon and Betty Moore Foundation through a grant (GBMF3801) to J.S., G.T., P.H. and R.S. J.B.R. was supported by Australian Research Council fellowship DE160100636.

Author information

Author notes

  1. Bennett S. Lambert and Jean-Baptiste Raina contributed equally to this work.

Affiliations

  1. Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

    • Bennett S. Lambert
    • , Vicente I. Fernandez
    •  & Roman Stocker
  2. Department of Civil, Environmental and Geomatic Engineering, Institute for Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland

    • Bennett S. Lambert
    • , Vicente I. Fernandez
    •  & Roman Stocker
  3. Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA

    • Bennett S. Lambert
  4. Climate Change Cluster, University of Technology Sydney, Ultimo, 2007, NSW, Australia

    • Jean-Baptiste Raina
    • , Nachshon Siboni
    •  & Justin R. Seymour
  5. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, 4072, QLD, Australia

    • Christian Rinke
    • , Francesco Rubino
    • , Philip Hugenholtz
    •  & Gene W. Tyson

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Contributions

B.S.L., J.-B.R., J.R.S. and R.S. designed the experiments. B.S.L., J.-B.R. and N.S. performed the experiments. B.S.L., J-B.R., V.I.F., F.R. and C.R. analysed the results. C.R., F.R., G.W.T. and P.H. generated and analysed sequencing data. B.S.L., J.-B.R., J.R.S. and R.S. wrote the manuscript. All authors edited the manuscript before submission.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Roman Stocker.

Electronic supplementary material

  1. 1.

    Supplementary Information

    Supplementary Notes 1–3 (incl. Supplementary Figures N1 and N2), Supplementary Figures 1–12 and Supplementary References.

  2. 2.

    Life Sciences Reporting Summary.

  3. 3.

    Supplementary File 1

    Computer-aided design (CAD) file for the ISCA mold; CAD file for the laboratory ISCA microcosm; CAD file for the ISCA field deployment enclosure.

  4. 4.

    Supplementary File 2

    Mathematical model of chemotaxis into an ISCA well implemented in COMSOL.

  5. 5.

    Supplementary Video 1

    Evolution of the chemoattractant concentration field as it diffuses from the ISCA well, as predicted by the mathematical model.

  6. 6.

    Supplementary Video 2

    Accumulation of bacteria into an ISCA well predicted by the mathematical model.

  7. 7.

    Supplementary Video 3

    Fluorescently labelled Vibrio coralliilyticus cells at middepth in an ISCA well containing 10% marine broth.

  8. 8.

    Supplementary Video 4

    Fluorescently labelled Vibrio coralliilyticus cells at middepth in an ISCA well containing filtered artificial seawater.

  9. 9.

    Supplementary Video 5

    Example of cell enumeration through image analysis in laboratory ISCA experiments, for Vibrio coralliilyticus.

  10. 10.

    Supplementary Video 6

    Example of cell enumeration through image analysis in laboratory ISCA experiments, for Escherichia coli.

  11. 11.

    Supplementary Video 7

    Example of cell enumeration through image analysis in laboratory ISCA experiments, for Marinobacter adhaerens.