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  • Review Article
  • Published:

Going local: technologies for exploring bacterial microenvironments

Nature Reviews Microbiology volume 11, pages 337–348 (2013)Cite this article

Subjects

Key Points

  • Microorganisms are social creatures that reside in complex communities in which spatial organization affects microbial behaviour. Recently, new approaches and creative experimental designs have been used to study previously unexplored aspects of bacterial behaviour in spatially structured populations.

  • Microfluidic devices, hydrogels and multiphoton lithography provide platforms for confining small numbers of bacteria and assessing their responses to environmental signals, chemical gradients and neighbouring cells. These technologies have provided new insights into bacterial behaviours, including antibiotic resistance and quorum sensing.

  • High-throughput microscale techniques, including the use of lipid–silica containers and droplet microfluidics, have been applied to the study of single cells. Together with single-cell genomics, these techniques have improved our understanding of the physiology and behaviour of individual cells.

  • New analytical techniques, including scanning electrochemical microscopy and imaging mass spectrometry, have provided insights into the chemical nature of the microenvironments surrounding single cells and microcolonies.

  • Although a single-species population has been traditionally viewed as a uniform group of cells, these technologies have revealed that such populations display a high degree of phenotypic heterogeneity, which has major implications for our understanding of bacterial behaviour. By combining cell confinement techniques with these analytical methods, we have the opportunity to gain insights into previously unexplored aspects of the phenotypic heterogeneity of microbial populations.

Abstract

Microorganisms lead social lives and use coordinated chemical and physical interactions to establish complex communities. Mechanistic insights into these interactions have revealed that there are remarkably intricate systems for coordinating microbial behaviour, but little is known about how these interactions proceed in the spatially organized communities that are found in nature. This Review describes the technologies available for spatially organizing small microbial communities and the analytical methods for characterizing the chemical environment surrounding these communities. Together, these complementary technologies have provided novel insights into the impact of spatial organization on both microbial behaviour and the development of phenotypic heterogeneity within microbial communities.

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Figure 1: Microfluidic devices, hydrogels and optical trapping for the study of bacterial interactions in spatially organized communities.
Figure 2: Bacterial lobster traps.
Figure 3: Small-volume confinement.
Figure 4: Production of droplets for confining, sorting and spatially arranging bacteria.
Figure 5: Detecting metabolic activity in spatially organized populations.

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References

  1. Hall-Stoodley, L. & Stoodley, P. Biofilm formation and dispersal and the transmission of human pathogens. Trends Microbiol. 13, 7–10 (2005).

    Article  CAS  PubMed  Google Scholar 

  2. Lyons, M. M., Ward, J. E., Gaff, H., Drake, J. M. & Dobbs, F. C. Theory of island biogeography on a microscopic scale: organic aggregates as islands for aquatic pathogens. Aquat. Microb. Ecol. 60, 1–13 (2010).

    Article  Google Scholar 

  3. Stoodley, P. et al. Growth and detachment of cell clusters from mature mixed-species biofilms. Appl. Environ. Microbiol. 67, 5608–5613 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Yildiz, F. H. Processes controlling the transmission of bacterial pathogens in the environment. Res. Microbiol. 158, 195–202 (2007).

    Article  PubMed  Google Scholar 

  5. Pamp, S., Sternberg, C. & Tolker-Nielsen, T. Insight into the microbial multicellular lifestyle via flow-cell technology and confocal microscopy. Cytometry A 75A, 90–103 (2009). This comprehensive review describes the utility of flow cells and provides a summary of biofilm flow cell studies.

  6. Nielsen, A. T., Tolker-Nielsen, T., Barken, K. B. & Molin, S. Role of commensal relationships on the spatial structure of a surface-attached microbial consortium. Environ. Microbiol. 2, 59–68 (2000).

    Article  CAS  PubMed  Google Scholar 

  7. Christensen, B. B. et al. Molecular tools for study of biofilm physiology. Methods Enzymol. 310, 20–42 (1999).

    Article  CAS  PubMed  Google Scholar 

  8. Wolfaardt, G. M., Lawrence, J. R., Robarts, R. D., Caldwell, S. J. & Caldwell, D. E. Multicellular organization in a degradative biofilm community. Appl. Environ. Microbiol. 60, 434–446 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Weibel, D., Diluzio, W. & Whitesides, G. Microfabrication meets microbiology. Nature Rev. Microbiol. 5, 209–218 (2007). This review discusses the use of microfluidic technologies in microbiology.

    Article  CAS  Google Scholar 

  10. Park, S. et al. Influence of topology on bacterial social interaction. Proc. Natl Acad. Sci. USA 100, 13910–13915 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Park, S. et al. Motion to form a quorum. Science 301, 188 (2003).

    Article  CAS  PubMed  Google Scholar 

  12. Seymour, J. R., Ahmed, T., Marcos & Stocker, R. A microfluidic chemotaxis assay to study microbial behavior in diffusing nutrient patches. Limnol. Oceanogr. Methods 6, 477–488 (2008).

    Article  CAS  Google Scholar 

  13. Boedicker, J. Q., Vincent, M. E. & Ismagilov, R. F. Microfluidic confinement of single cells of bacteria in small volumes initiates high-density behavior of quorum sensing and growth and reveals its variability. Angew. Chem. Int. Ed. Engl. 48, 5908–5911 (2009). This study uses microfluidics to demonstrate that as few as one P. aeruginosa cell can initiate quorum sensing in a physically and chemically confined environment.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Cho, H. et al. Self-organization in high-density bacterial colonies: efficient crowd control. PLoS Biol. 5, e302 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. McDonald, J. C. et al. Fabrication of microfluidic systems in poly(dimethylsiloxane). Electrophoresis 21, 27–40 (2000). This article provides an overview of soft lithography techniques that are relevant to PDMS-based devices.

    Article  CAS  PubMed  Google Scholar 

  16. Mukhopadhyay, R. When PDMS isn't the best. What are its weaknesses, and which other polymers can researchers add to their toolboxes? Anal. Chem. 79, 3248–3253 (2007).

    Article  CAS  PubMed  Google Scholar 

  17. Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science 305, 1622–1625 (2004). This report describes the use of microfluidics to trap individual bacteria and study the response of bacterial persisters to antibiotic treatments.

    Article  CAS  PubMed  Google Scholar 

  18. Seymour, J. R., Ahmed, T., Durham, W. M. & Stocker, R. Chemotactic response of marine bacteria to the extracellular products of Synechococcus and Prochlorococcus. Aquat. Microb. Ecol. 59, 161–168 (2010).

    Article  Google Scholar 

  19. Ahmed, T., Shimizu, T. & Stocker, R. Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients. Nano Lett. 10, 3379–3385 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kim, H. J., Boedicker, J. Q., Choi, J. W. & Ismagilov, R. F. Defined spatial structure stabilizes a synthetic multispecies bacterial community. Proc. Natl Acad. Sci. USA 105, 18188–18193 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  21. Squires, T. M. & Quake, S. R. Microfluidics: fluid physics at the nanoliter scale. Rev. Mod. Phys. 77, 977–1026 (2005).

    Article  CAS  Google Scholar 

  22. Mao, H. B., Cremer, P. S. & Manson, M. D. A sensitive, versatile microfluidic assay for bacterial chemotaxis. Proc. Natl Acad. Sci. USA 100, 5449–5454 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kim, M., Kim, S. H., Lee, S. K. & Kim, T. Microfluidic device for analyzing preferential chemotaxis and chemoreceptor sensitivity of bacterial cells toward carbon sources. Analyst 136, 3238–3243 (2011).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  25. Stocker, R., Seymour, J., 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).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Seymour, J. R., Simo, R., Ahmed, T. & Stocker, R. Chemoattraction to dimethylsulfoniopropionate throughout the marine microbial food web. Science 329, 342–345 (2010).

    Article  CAS  PubMed  Google Scholar 

  27. Zhang, Z. et al. Microchemostat–microbial continuous culture in a polymer-based, instrumented microbioreactor. Lab Chip 6, 906–913 (2006).

    Article  CAS  PubMed  Google Scholar 

  28. Bigger, J. W. Treatment of staphylococcal infections with penicillin by intermittent sterilisation. Lancet 244, 497–500 (1944).

    Article  Google Scholar 

  29. Gefen, O. & Balaban, N. The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress. FEMS Microbiol. Rev. 33, 704–717 (2009).

    Article  CAS  PubMed  Google Scholar 

  30. Booth, I. R. Stress and the single cell: intrapopulation diversity is a mechanism to ensure survival upon exposure to stress. Int. J. Food Microbiol. 78, 19–30 (2002).

    Article  PubMed  Google Scholar 

  31. Lidstrom, M. E. & Konopka, M. C. The role of physiological heterogeneity in microbial population behavior. Nature Chem. Biol. 6, 705–712 (2010).

    Article  CAS  Google Scholar 

  32. Hitchens, A. P. & Leikind, M. C. The introduction of agar-agar into bacteriology. J. Bacteriol. 37, 485–493 (1939).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Koch, R. Die Aetiologie der Tuberculose. Berliner Klinische Wochenschrift 19, 221–236 (1882).

    Google Scholar 

  34. Koch, R. Classics in infectious diseases. The etiology of tuberculosis: Robert Koch. Berlin, Germany 1882. Rev. Infect. Dis. 4, 1270–1274 (1982).

    Article  CAS  PubMed  Google Scholar 

  35. Timp, W., Mirsaidov, U., Matsudaira, P. & Timp, G. Jamming prokaryotic cell-to-cell communications in a model biofilm. Lab Chip 9, 925–934 (2009).

    Article  CAS  PubMed  Google Scholar 

  36. Meyer, A. et al. Dynamics of AHL mediated quorum sensing under flow and non-flow conditions. Phys. Biol. 9, 026007 (2012).

    Article  CAS  PubMed  Google Scholar 

  37. Flickinger, S. T. et al. Quorum sensing between Pseudomonas aeruginosa biofilms accelerates cell growth. J. Am. Chem. Soc. 133, 5966–5975 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Dilanji, G. E., Langebrake, J. B., De Leenheer, P. & Hagen, S. J. Quorum activation at a distance: spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. J. Am. Chem. Soc. 134, 5618–5626 (2012).

    Article  CAS  PubMed  Google Scholar 

  39. Connell, J. L. et al. Probing prokaryotic social behaviors with bacterial “lobster traps”. mBio 1, e00202-10 (2010). This study uses MPL to confine cells in bacterial lobster traps and study their behaviour.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Kaehr, B. & Shear, J. B. Multiphoton fabrication of chemically responsive protein hydrogels for microactuation. Proc. Natl Acad. Sci. USA 105, 8850–8854 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Hill, R. T., Lyon, J. L., Allen, R., Stevenson, K. J. & Shear, J. B. Microfabrication of three-dimensional bioelectronic architectures. J. Am. Chem. Soc. 127, 10707–10711 (2005).

    Article  CAS  PubMed  Google Scholar 

  42. Kaehr, B., Allen, R., Javier, D. J., Currie, J. & Shear, J. B. Guiding neuronal development with in situ microfabrication. Proc. Natl Acad. Sci. USA 101, 16104–16108 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Yang, L. et al. In situ growth rates and biofilm development of Pseudomonas aeruginosa populations in chronic lung infections. J. Bacteriol. 190, 2767–2776 (2008).

    Article  CAS  PubMed  Google Scholar 

  44. Baca, H. K. et al. Cell-directed assembly of lipid-silica nanostructures providing extended cell viability. Science 313, 337–341 (2006).

    Article  CAS  PubMed  Google Scholar 

  45. Carnes, E. C. et al. Confinement-induced quorum sensing of individual Staphylococcus aureus bacteria. Nature Chem. Biol. 6, 41–45 (2010). This work demonstrates that a single S. aureus cell can initiate quorum sensing in a physically and chemically confined environment.

    Article  CAS  Google Scholar 

  46. Lu, Y. et al. Aerosol-assisted self-assembly of mesostructured spherical nanoparticles. Nature 398, 223–226 (1999).

    Article  CAS  Google Scholar 

  47. Harper, J. C. et al. Cell-directed integration into three-dimensional lipid–silica nanostructured matrices. ACS Nano 4, 5539–5550 (2010).

    Article  CAS  PubMed  Google Scholar 

  48. Voskerician, G. et al. Biocompatibility and biofouling of MEMS drug delivery devices. Biomaterials 24, 1959–1967 (2003).

    Article  CAS  PubMed  Google Scholar 

  49. Song, H. & Ismagilov, R. F. Millisecond kinetics on a microfluidic chip using nanoliters of reagents. J. Am. Chem. Soc. 125, 14613–14619 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Thorsen, T., Roberts, R. W., Arnold, F. H. & Quake, S. R. Dynamic pattern formation in a vesicle-generating microfluidic device. Phys. Rev. Lett. 86, 4163–4166 (2001).

    Article  CAS  PubMed  Google Scholar 

  51. Song, H., Tice, J. D. & Ismagilov, R. F. A microfluidic system for controlling reaction networks in time. Angew. Chem. Int. Ed. Engl. 42, 768–772 (2003).

    Article  CAS  PubMed  Google Scholar 

  52. Link, D. R., Anna, S. L., Weitz, D. A. & Stone, H. A. Geometrically mediated breakup of drops in microfluidic devices. Phys. Rev. Lett. 92, 054503 (2004).

    Article  CAS  PubMed  Google Scholar 

  53. Churski, K., Michalski, J. & Garstecki, P. Droplet on demand system utilizing a computer controlled microvalve integrated into a stiff polymeric microfluidic device. Lab Chip 10, 512–518 (2010).

    Article  CAS  PubMed  Google Scholar 

  54. Anna, S. L., Bontoux, N. & Stone, H. A. Formation of dispersions using “flow focusing” in microchannels. Appl. Phys. Lett. 82, 364–366 (2003).

    Article  CAS  Google Scholar 

  55. Baret, J. C. et al. Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity. Lab Chip 9, 1850–1858 (2009).

    Article  CAS  PubMed  Google Scholar 

  56. Eun, Y. J., Utada, A. S., Copeland, M. F., Takeuchi, S. & Weibel, D. B. Encapsulating bacteria in agarose microparticles using microfluidics for high-throughput cell analysis and isolation. ACS Chem. Biol. 6, 260–266 (2011).

    CAS  Google Scholar 

  57. Ahn, K. et al. Dielectrophoretic manipulation of drops for high-speed microfluidic sorting devices. Appl. Phys. Lett. 88, 024104 (2006).

    Article  CAS  Google Scholar 

  58. Churski, K. et al. Rapid screening of antibiotic toxicity in an automated microdroplet system. Lab Chip 12, 1629–1637 (2012).

    Article  CAS  PubMed  Google Scholar 

  59. Leung, K. et al. A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc. Natl Acad. Sci. USA 109, 7665–7670 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Bard, A. J. & Mirkin, M. V. Scanning Electrochemical Microscopy (Marcel Dekker, 2001).

    Book  Google Scholar 

  61. Liu, X. et al. Real-time mapping of a hydrogen peroxide concentration profile across a polymicrobial bacterial biofilm using scanning electrochemical microscopy. Proc. Natl Acad. Sci. USA 108, 2668–2673 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  62. Koley, D., Ramsey, M. M., Bard, A. J. & Whiteley, M. Discovery of a biofilm electrocline using real-time 3D metabolite analysis. Proc. Natl Acad. Sci. USA 108, 19996–20001 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Watrous, J. D. & Dorrestein, P. C. Imaging mass spectrometry in microbiology. Nature Rev. Microbiol. 9, 683–694 (2011). This article provides a comprehensive summary of the ionization sources and mass analysers used in IMS, as well as a review of their applications in microbiology.

    Article  CAS  Google Scholar 

  64. Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D. & DeLong, E. F. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293, 484–487 (2001).

    Article  CAS  PubMed  Google Scholar 

  65. Treude, T. et al. Consumption of methane and CO2 by methanotrophic microbial mats from gas seeps of the anoxic Black Sea. Appl. Environ. Microbiol. 73, 2271–2283 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Musat, N., Foster, R., Vagner, T., Adam, B. & Kuypers, M. M. Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol. Rev. 36, 486–511 (2012).

    Article  CAS  PubMed  Google Scholar 

  67. Watrous, J. D., Alexandrov, T. & Dorrestein, P. C. The evolving field of imaging mass spectrometry and its impact on future biological research. J. Mass Spectrom. 46, 209–222 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Orphan, V. J., House, C. H., Hinrichs, K.-U., McKeegan, K. D. & DeLong, E. F. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc. Natl Acad. Sci. USA 99, 7663–7668 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Dekas, A. E., Poretsky, R. S. & Orphan, V. J. Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science 326, 422–426 (2009).

    Article  CAS  PubMed  Google Scholar 

  70. Lechene, C., Luyten, Y., McMahon, G. & Distel, D. Quantitative imaging of nitrogen fixation by individual bacteria within animal cells. Science 317, 1563–1566 (2007).

    Article  CAS  PubMed  Google Scholar 

  71. Lechene, C. et al. High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry. J. Biol. 5, 20 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  72. Foster, R. A. et al. Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses. ISME J. 5, 1484–1493 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Watrous, J., Hendricks, N., Meehan, M. & Dorrestein, P. C. Capturing bacterial metabolic exchange using thin film desorption electrospray ionization-imaging mass spectrometry. Anal. Chem. 82, 1598–1600 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Nagahara, L. A., Thundat, T. & Lindsay, S. M. Preparation and characterization of STM tips for electrochemical studies. Rev. Sci. Instrum. 60, 3128–3130 (1989).

    Article  CAS  Google Scholar 

  75. Sun, P., Zhang, Z. Q., Guo, J. D. & Shao, Y. H. Fabrication of nanometer-sized electrodes and tips for scanning electrochemical microscopy. Anal. Chem. 73, 5346–5351 (2001).

    Article  CAS  PubMed  Google Scholar 

  76. Slevin, C. J., Gray, N. J., Macpherson, J. V., Webb, M. A. & Unwin, P. R. Fabrication and characterisation of nanometre-sized platinum electrodes for voltammetric analysis and imaging. Electrochem. Commun. 1, 282–288 (1999).

    Article  CAS  Google Scholar 

  77. Sun, P. & Mirkin, M. V. Kinetics of electron-transfer reactions at nanoelectrodes. Anal. Chem. 78, 6526–6534 (2006).

    Article  CAS  PubMed  Google Scholar 

  78. Amemiya, S., Bard, A. J., Fan, F. R., Mirkin, M. V. & Unwin, P. R. Scanning electrochemical microscopy. Annu. Rev. Anal. Chem. (Palo Alto Calif) 1, 95–131 (2008).

    Article  CAS  Google Scholar 

  79. Garstecki, P., Fuerstman, M. J., Stone, H. A. & Whitesides, G. M. Formation of droplets and bubbles in a microfluidic T-junction-scaling and mechanism of break-up. Lab Chip 6, 437–446 (2006).

    Article  CAS  PubMed  Google Scholar 

  80. Tuson, H. H., Renner, L. D. & Weibel, D. B. Polyacrylamide hydrogels as substrates for studying bacteria. Chem. Commun. (Camb.) 48, 1595–1597 (2012).

    Article  CAS  Google Scholar 

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Acknowledgements

The authors acknowledge members of the Whiteley laboratory and the Parsek laboratory for their thoughtful discussions and careful editing of the manuscript.

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Author notes

  1. Aimee K. Wessel and Laura Hmelo: These authors contributed equally to this work.

Authors and Affiliations

  1. Section of Molecular Genetics and Microbiology, Institute of Cell and Molecular Biology, The University of Texas at Austin, Austin, 78712, 1 University Station, A5000, Texas, USA

    Aimee K. Wessel & Marvin Whiteley

  2. Department of Microbiology, University of Washington, Seattle, 98195, Washington, USA

    Laura Hmelo & Matthew R. Parsek

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Glossary

Microcolonies

Small aggregates of bacteria. The number of cells within an aggregate is not officially defined, but in this Review this term refers to aggregates of less than 100 cells.

Microfluidic devices

Devices that rely on micrometre-scale features to move, mix and trap fluids.

Microenvironments

Small, defined regions of the environment. In microbial communities, a microenvironment refers to the area immediately surrounding a single cell or small group of cells and is generally distinct from its environs on the basis of characteristics such as nutrient availability and mass transfer.

Flow cells

50–250 μl channels bored out of polycarbonate, mounted on a glass coverslip and used for cultivating large numbers of cells (106–108) under continuous-flow conditions. In combination with microscopy techniques, flow cells allow for non-invasive, real-time observations of biofilms in three dimensions. Some flow cells can establish reproducible two-dimensional environmental gradients.

Polydimethylsiloxane

(PDMS). An optically clear silicone-based organic polymer with elastic properties. PDMS can be topographically patterned to isolate individual cells, or can be sealed against flat surfaces to create microfluidic systems with diverse applications. PDMS is a particularly popular material in microbiological devices because it is biocompatible, non-reactive, transparent, gas permeable and inexpensive.

Soft lithography

A set of techniques used to pattern soft materials, such as polydimethylsiloxane, with topographical features on the order of micrometres to nanometres.

Video microscopy

A technique that relies on a charge-coupled device (CCD) camera paired with a light microscope. The CCD camera records a series of high-speed images (10–30 frames per second) that can be played back in the form of a movie.

Confocal laser scanning microscopy

A technique that enables the detection of emitted light at specific x, y and z coordinates. Emitted light is detected by a photomultiplier tube or other detector. Using this technique, a three-dimensional image can be acquired either through an attached camera or through a computer that detects electrical signals generated by photomultiplier tubes.

Nutrient patches

Microscale ephemeral nutrient point sources that can contain biologically labile organic compounds at concentrations two to three orders of magnitude higher than in the surrounding bulk environment.

Nutrient plumes

Microscale regions of elevated nutrient levels. These plumes often form in the wake of a sinking point source of nutrients (for example, sinking detritus or faecal pellets) in an aqueous environment.

Cloud condensation nuclei

Submicrometre-scale particles (aerosols) around which cloud droplets condense from water vapour in the atmosphere.

Chemostats

Bioreactors that are used for continuous culture of microorganisms. Fresh medium is continuously added to the bioreactor as equal volumes of culture liquid are removed to maintain a constant culture volume. By changing the rate with which medium is added to the bioreactor, microbial growth rate is easily controlled.

Bacterial persistence

A phenomenon in which a small number of phenotypic variants within an isogenic population display tolerance to antibiotic treatment but produce antibiotic-sensitive progeny.

Hydrogels

Hydrophilic networks of biocompatible crosslinked polymers that can be used to create environments with defined mass transfer properties.

Optical trapping

A technique that uses a tightly focused laser beam to manipulate the physical location of individual cells. Cells (and other nanometre- to micrometre-sized dielectric particles) are attracted along an electric field gradient towards the location of the strongest electric field, which is at the centre of the narrowest point of the focused beam.

Quorum sensing

An intercellular communication system that coordinates microbial group behaviour via the production and sensing of small signalling molecules.

Multiphoton lithography

(MPL). A technique in which a highly focused laser beam initiates a nearly simultaneous absorption of multiple photons at a single focal point (<1 μm voxel), forming crosslinks between the photo-oxidizable side chain residues of protein molecules. The laser beam is raster scanned and sequentially focused deeper into a protein solution, enabling the fabrication of three-dimensional structures with submicrometre-sized features. The photo-crosslinked protein structure can have a mechanical stiffness similar to polydimethylsiloxane.

Ultramicroelectrode

An extremely small electrode that can be used to quantify changes in current. The tip of such an electrode has a radius of ∼10 nm to 25 μm, depending on the tip material.

Feedback approach curve

A method used in scanning electrochemical microscopy to determine the location of an animate or inanimate surface. The curve is a plot of current detected by the ultramicroelectrode as a function of distance above a given substrate. Plotting these variables enables investigators to calculate both the positional location and concentration of a given redox-active small molecule.

Electrocline

A gradient of redox potential.

Desorption electrospray ionization

An ionization technique that uses a stream of high-pressure charged solvent to desorb molecules from a solid sample.

Syntrophic metabolism

The cooperation of multiple species to catabolize a substrate that, on their own, the individual species could not catabolize.

Matrix-assisted laser desorption–ionization

A soft ionization technique that is appropriate for the ionization of fragile biomolecules and large organic molecules before their introduction into a mass spectrometer. This technique produces molecular ions (providing data about the molecular weight of the ion precursor) of 300–5,000 Da, although it can be used to analyse mass fragments of molecules with a molecular mass of up to 50,000 Da.

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Wessel, A., Hmelo, L., Parsek, M. et al. Going local: technologies for exploring bacterial microenvironments. Nat Rev Microbiol 11, 337–348 (2013). https://doi.org/10.1038/nrmicro3010

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