Brief Communication

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

Published online:


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.

  • Subscribe to Nature Microbiology for full access:



Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.


  1. 1.

    Azam, F. Microbial control of oceanic carbon flux: the plot thickens. Science 280, 694–696 (1998).

  2. 2.

    Azam, F. & Malfatti, F. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5, 782–791 (2007).

  3. 3.

    Blackburn, N., Fenchel, T. & Mitchell, J. Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria. Science 282, 2254–2256 (1998).

  4. 4.

    Kiørboe, T., Grossart, H.-P., Ploug, H. & Tang, K. Mechanisms and rates of bacterial colonization of sinking aggregates. Appl. Environ. Microbiol. 68, 3996–4006 (2002).

  5. 5.

    Smriga, S., Fernandez, V. I., Mitchell, J. G. & Stocker, R. Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria. Proc. Natl Acad. Sci. USA 113, 1576–1581 (2016).

  6. 6.

    Jefferson, T. T. Zooplankton fecal pellets, marine snow and sinking phytoplankton blooms. Aquat. Microb. Ecol. 27, 57–102 (2002).

  7. 7.

    Fenchel, T. Microbial behavior in a heterogeneous world. Science 296, 1068–1071 (2002).

  8. 8.

    Adler, J. & Dahl, M. A method for measuring the motility of bacteria and for comparing random and non-random motility. Microbiology 46, 161–173 (1967).

  9. 9.

    Ford, R. M., Phillips, B. R., Quinn, J. A. & Lauffenburger, D. A. Measurement of bacterial random motility and chemotaxis coefficients: I. Stopped-flow diffusion chamber assay. Biotechnol. Bioeng. 37, 647–660 (1991).

  10. 10.

    Hol, F. J. H. & Dekker, C. Zooming in to see the bigger picture: microfluidic and nanofabrication tools to study bacteria. Science 346, 1251821 (2014).

  11. 11.

    He, K. & Bauer, C. E. Chemosensory signaling systems that control bacterial survival. Trends Microbiol. 22, 389–398 (2014).

  12. 12.

    Stocker, R. & Seymour, J. R. Ecology and physics of bacterial chemotaxis in the ocean. Microbiol. Mol. Biol. Rev. 76, 792–812 (2012).

  13. 13.

    Garren, M. et al. A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals. ISME J. 8, 999–1007 (2014).

  14. 14.

    Lewus, P. & Ford, R. M. Quantification of random motility and chemotaxis bacterial transport coefficients using individual-cell and population-scale assays. Biotechnol. Bioeng. 75, 292–304 (2001).

  15. 15.

    Mesibov, R. & Adler, J. Chemotaxis toward amino acids in Escherichia coli. J. Bacteriol. 112, 315–326 (1972).

  16. 16.

    Ahmed, T. & Stocker, R. Experimental verification of the behavioral foundation of bacterial transport parameters using microfluidics. Biophys. J. 95, 4481–4493 (2008).

  17. 17.

    Ammerman, J. W., Fuhrman, J. A., Hagstrom, A. & Azam, F. Bacterioplankton growth in seawater: I. Growth kinetics and cellular characteristics in seawater cultures. Mar. Ecol. Prog. Ser. 18, 31–39 (1984).

  18. 18.

    Taylor, J. R. & Stocker, R. Trade-offs of chemotactic foraging in turbulent water. Science 338, 675–679 (2012).

  19. 19.

    Stocker, R., Seymour, J. R., Samadani, A., Hunt, D. E. & Polz, M. F. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc. Natl Acad. Sci. USA 105, 4209–4214 (2008).

  20. 20.

    Azam, F. & Long, R. A. Oceanography: sea snow microcosms. Nature 414, 495–498 (2001).

  21. 21.

    Rinke, C. et al. Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ 4, e2486 (2016).

  22. 22.

    Pedler, B. E., Aluwihare, L. I. & Azam, F. Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean. Proc. Natl Acad. Sci. USA 111, 7202–7207 (2014).

  23. 23.

    Sonnenschein, E. C. et al. Development of a genetic system for Marinobacter adhaerens HP15 involved in marine aggregate formation by interacting with diatom cells. J. Microbiol. Methods 87, 176–183 (2011).

  24. 24.

    Kelly, J. R. et al. Measuring the activity of BioBrick promoters using an in vivo reference standard. J. Biol. Engineer. (2017).

  25. 25.

    Temme, K. et al. Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Res. 40, 8773–8781 (2012).

  26. 26.

    Ahmed, T., Shimizu, T. S. & Stocker, R. Microfluidics for bacterial chemotaxis. Integ. Biol. 2, 604–629 (2010).

  27. 27.

    Marie, D., Partensky, F., Jacquet, S. & Vaulot, D. Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR green I. Appl. Environ. Microbiol. 63, 183–186 (1997).

  28. 28.

    Parks, D. H., Tyson, G. W., Hugenholtz, P. & Beiko, R. G. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30, 3123–3124 (2014).

  29. 29.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

  30. 30.

    Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

Download references


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.


  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


  1. Search for Bennett S. Lambert in:

  2. Search for Jean-Baptiste Raina in:

  3. Search for Vicente I. Fernandez in:

  4. Search for Christian Rinke in:

  5. Search for Nachshon Siboni in:

  6. Search for Francesco Rubino in:

  7. Search for Philip Hugenholtz in:

  8. Search for Gene W. Tyson in:

  9. Search for Justin R. Seymour in:

  10. Search for Roman Stocker in:


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.