Microfluidic and Nanofabrication Tools to Study Bacteria Felix J

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Microfluidic and Nanofabrication Tools to Study Bacteria Felix J Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria Felix J. H. Hol and Cees Dekker Science 346, (2014); DOI: 10.1126/science.1251821 This copy is for your personal, non-commercial use only. If you wish to distribute this article to others, you can order high-quality copies for your colleagues, clients, or customers by clicking here. Permission to republish or repurpose articles or portions of articles can be obtained by following the guidelines here. The following resources related to this article are available online at www.sciencemag.org (this information is current as of October 23, 2014 ): Updated information and services, including high-resolution figures, can be found in the online version of this article at: http://www.sciencemag.org/content/346/6208/1251821.full.html This article cites 112 articles, 48 of which can be accessed free: http://www.sciencemag.org/content/346/6208/1251821.full.html#ref-list-1 This article appears in the following subject collections: on October 23, 2014 Techniques http://www.sciencemag.org/cgi/collection/techniques www.sciencemag.org Downloaded from Science (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by the American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. Copyright 2014 by the American Association for the Advancement of Science; all rights reserved. The title Science is a registered trademark of AAAS. RESEARCH ecosystems in which the spatial eco-evo- REVIEW SUMMARY lutionary dynamics of bacterial communi- ties can be explored. Various approaches MICROBE ANALYSIS to mimic the intricate spatial structure of natural bacterial habitats now contribute to our understanding of competition and co- Zooming in to see the bigger picture: operation within bacterial populations. Mi- crofluidic platforms have boosted research Microfluidic and nanofabrication on unculturable environmental species by eliminating the need for pre-analysis cul- turing. On-chip whole-genome amplifica- tools to study bacteria tion of environmental isolates has recently Felix J. H. Hol and Cees Dekker* provided a first genotypic glimpse on this “dark matter of biology.” BACKGROUND: Nanotechnology and bac- dynamic and well-defined environments teriology at first sight may seem like two and has been used to address long-standing OUTLOOK: Looking ahead, it is clear that disparate worlds, but a rapidly moving questions concerning bacterial aging and the doors that nanofabrication and micro- field of research has formed at the inter- antibiotic persistence. Biological insights fluidics have opened will continue to make face of these disciplines in the past decade. have been gained by exploring bacterial important contributions to basic bacteri- Bacteria experience spatial structure at growth and movement in nanofabricated ology research. A comprehensive inves- many scales: Individual bacteria interact constrictions and revealed that bacteria can tigation of the uncultured majority with with nanoscale surface features, whereas penetrate constrictions as narrow as only microfluidic technologies, for instance, bacterial communities are shaped by land- half their width. Fur- may uncover the vast potential of currently scape structure down to the microscale. ON OUR WEB SITE thermore, nanofabrica- unknown species. Practical applications Nanofabrication and microfluidics are tion has been used to such as microbial fuel cells or antibacterial Read the full article ideally suited to define and control the en- at http://dx.doi discriminate between surfaces will benefit from the understand- vironment at those scales, allowing us to .org/10.1126/ competing hypotheses ing of bacterial behavior at the nanoscale. zoom in on the peculiarities of individual science.1251821 regarding the mecha- Microfluidic devices are now beginning to cells and to broaden our understanding nisms that underlie be commonly used in microbiology labs of the processes that shape multi-species intercellular electron transport. Confine- because of a demand for precise measure- communities. Recently developed nanoto- ment of single bacteria in tiny volumes has ments in complex environments that can be ols provide unprecedented control over provided an individualistic perspective on controlled at the microscale. This trend will the bacterial microenvironment and have collective phenotypes and demonstrated undoubtedly continue as scientists delve been key to the discovery of new phenom- that density-dependent behaviors can even deeper into the complex lives of bacteria. ■ ena in bacteriology. be exhibited by individuals. Bacteria grow- ing in nanofabricated chambers adopt pre- ADVANCES: Nanofabrication and microflu- defined shapes and have been used to study Department of Bionanoscience, Kavli Institute of Nanoscience, idics have expanded our view on a myriad the geometry dependence of intracellular Delft University of Technology, Delft, Netherlands. *Corresponding author. E-mail: [email protected] of bacterial phenomena. Microfluidics pro- processes. Microfluidics and nanofabrica- Cite this article as: F. J. H. Hol, C. Dekker, Science 346, vides ways to study individual bacteria in tion have been combined to create synthetic 1251821 (2014). DOI: 10.1126/science.1251821 Studying bacteria using A B nanofabrication and micro- uidics. (A) Escherichia coli bacteria use their agella to ex- ploit submicrometer crevices for surface attachment [Re- printed with permission from (5) (reference list of full paper online)]. (B) Bio lm stream- ers form in a meandering ow channel ( Pseudomonas aeruginosa, red; extracellular polymeric substances, green) [Reprinted with permission C from (93)]. (C) E. coli un- dergo a shape transition when squeezing into a nanofabri- cated channel as shallow as half their width [Reprinted with permission from (26)]. Scale bars, (A) 2 µm; (B) 200 µm; and (C) 5 µm. 438 24 OCTOBER 2014 • VOL 346 ISSUE 6208 sciencemag.org SCIENCE Published by AAAS RESEARCH ◥ brief outlook on new opportunities at the inter- REVIEW face of bacteriology and nanotechnology. Bacterial growth and shape MICROBE ANALYSIS Microfluidics and nanofabrication provide pow- erful tools to control, shape, and manipulate the environment of individual bacteria. In this sec- Zooming in to see the bigger picture: tion, we describe microfluidic approaches that address long-standing questions concerning bacte- rial growth, and we discuss how nanofabrication Microfluidic and nanofabrication opens doors to studying bacterial growth and tools to study bacteria shape. Mysteries of bacterial growth Felix J. H. Hol and Cees Dekker* solved with microfluidics Monitoring an individual cell for extended pe- The spatial structure of natural habitats strongly affects bacterial life, ranging from riods in a well-defined environment is crucial to nanoscale structural features that individual cells exploit for surface attachment, to answer fundamental growth and aging-related micro- and millimeter-scale chemical gradients that drive population-level processes. questions. However, long-term imaging of a sin- Nanofabrication and microfluidics are ideally suited to manipulate the environment at gle cell in a constant environment is challenging; those scales and have emerged as powerful tools with which to study bacteria. Here, because of exponential growth rates and resource we review the new scientific insights gained by using a diverse set of nanofabrication consumption, a bacterial colony creates internal and microfluidic techniques to study individual bacteria and multispecies communities. chemical gradients and reaches an unmanageable This toolbox is beginning to elucidate disparate bacterial phenomena—including aging, size within a few generations, precluding the electron transport, and quorum sensing—and enables the dissection of environmental tracking of a single cell for long periods. One communities through single-cell genomics. A more intimate integration of microfluidics, model species for bacterial aging, Caulobacter nanofabrication, and microbiology will enable further exploration of bacterial life at the crescentus,helpstosolvethisproblembyonly smallest scales. dividing as long as it is attached to a surface. While the dividing mother cell is stuck to the tfirstglance,nanotechnologyandbacteri- bacteria—test tubes and petri dishes—are not bottom of a channel, the planktonic progeny can ology may seem like two disparate worlds. compatible with long-term monitoring of an get flushed out (12). In many other species, how- However, in the past decade a dynamic individual cell or the precise manipulation of ever, growth and dispersal are not mutually ex- and rapidly expanding field of research has its microenvironment. As a result, seemingly clusive, hence their aging process remained a formed at the interface of these two dis- simple questions such as “How long can a bacte- mystery until recent microfluidic innovations Aciplines. Many “nanotools” have been developed rium live?” or “What is the smallest constriction allowed the long-term (in principle, indefinite) to study individual bacteria as well as multi- abacteriumcanpassthrough?” remained un- monitoring of an individual bacterium in a con- species communities in complex yet well-defined answered until recently. Answers to such long- stant environment. To accomplish this, Wang et al. environments. In addition to a host of exciting standing questions are now emerging at the immobilized bacteria
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