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Appl. Environ. Microbiol. doi:10.1128/AEM.01163-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Spatiometabolic stratification of Shewanella oneidensis biofilms

Division of Biological Sciences and Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, 91125 and Howard Hughes Medical Institute

^* To whom correspondence should be addressed. Email: dkn{at}gps.caltech.edu.

	Abstract

Biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the environment. Although much is known about how biofilms form, develop and detach, very little is understood about how these events are related to metabolism and its dynamics. It is commonly thought that large sub-populations of cells within biofilms are not actively producing proteins or generating energy, and are therefore dead. We hypothesized that within the growth-inactive domains of biofilms, significant populations of living cells persist and retain the capacity to dynamically regulate their metabolism. To test this, we employed unstable fluorescent reporters to measure growth activity and protein synthesis in vivo over the course of biofilm development and created a quantitative routine to compare domains of activity among independently-grown biofilms. Here we report that S. oneidensis biofilm structures reproducibly stratify with respect to growth activity and metabolism as a function of their size. Within domains of growth-inactive cells, genes typically upregulated under anaerobic conditions are expressed well after growth has ceased. These findings reveal that, far from being dead, the majority of cells in mature S. oneidensis biofilms have actively turned on metabolic programs appropriate to their local microenvironment and developmental stage.

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