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

Nature Microbiology volume 2, pages 1344–1349 (2017)Cite this article

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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.

Planktonic microorganisms control the biogeochemistry and productivity of marine ecosystems1. This global-scale influence is governed by the rate at which individual microorganisms access organic substrates from the water column, which in turn is dependent upon the spatial distribution of substrates and the capacity of cells to exploit microscale nutrient hotspots2. Seawater is surprisingly heterogeneous at the scale of individual microorganisms3, with nutrient hotspots on and around organic particles4, phytoplankton cells5 and zooplankton faecal pellets6. These microscale features of the water column represent important biogeochemical microenvironments where microbial activity and transformation rates considerably exceed background levels5,7. Consequently, the microbial behaviours involved in accessing and maintaining contact with these microenvironments can have profound implications for basin-scale chemical cycling, but have remained largely inaccessible by traditional oceanographic sampling approaches.

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Fig. 1: Fabrication of the in situ chemotaxis assay (ISCA) and laboratory tests.
Fig. 2: Field tests of the ISCA.

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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.

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Author notes

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

Authors and 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

Authors
  1. Bennett S. Lambert
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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.

Corresponding author

Correspondence to Roman Stocker.

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The authors declare no competing financial interests.

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Supplementary Information

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

Life Sciences Reporting Summary.

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.

Supplementary File 2

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

Supplementary Video 1

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

Supplementary Video 2

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

Supplementary Video 3

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

Supplementary Video 4

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

Supplementary Video 5

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

Supplementary Video 6

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

Supplementary Video 7

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

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Lambert, B.S., Raina, JB., Fernandez, V.I. et al. A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nat Microbiol 2, 1344–1349 (2017). https://doi.org/10.1038/s41564-017-0010-9

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