Open Access Highly Accessed Research article

Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis

James P Folsom1, Lee Richards12, Betsey Pitts1, Frank Roe13, Garth D Ehrlich4, Albert Parker1, Aurélien Mazurie5 and Philip S Stewart1*

Author Affiliations

1 Center for Biofilm Engineering and Department of Chemical and Biological Engineering, P. O. Box 173980 Montana State University - Bozeman Bozeman, Montana 59717-3980, USA

2 Halliburton, P.O. Box 439, Pinedale, WY 82941, USA

3 1658 Eligio Lane, Davis, CA 95618, USA

4 Center for Genomic Sciences Allegheny Singer Research Institute 320 E. North Ave. Pittsburgh, PA 15212, USA

5 Bioinformatics Core, Montana State University, Bozeman, Montana, USA

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BMC Microbiology 2010, 10:294  doi:10.1186/1471-2180-10-294

Published: 17 November 2010



Transcriptome analysis was applied to characterize the physiological activities of Pseudomonas aeruginosa grown for three days in drip-flow biofilm reactors. Conventional applications of transcriptional profiling often compare two paired data sets that differ in a single experimentally controlled variable. In contrast this study obtained the transcriptome of a single biofilm state, ranked transcript signals to make the priorities of the population manifest, and compared ranki ngs for a priori identified physiological marker genes between the biofilm and published data sets.


Biofilms tolerated exposure to antibiotics, harbored steep oxygen concentration gradients, and exhibited stratified and heterogeneous spatial patterns of protein synthetic activity. Transcriptional profiling was performed and the signal intensity of each transcript was ranked to gain insight into the physiological state of the biofilm population. Similar rankings were obtained from data sets published in the GEO database webcite. By comparing the rank of genes selected as markers for particular physiological activities between the biofilm and comparator data sets, it was possible to infer qualitative features of the physiological state of the biofilm bacteria. These biofilms appeared, from their transcriptome, to be glucose nourished, iron replete, oxygen limited, and growing slowly or exhibiting stationary phase character. Genes associated with elaboration of type IV pili were strongly expressed in the biofilm. The biofilm population did not indicate oxidative stress, homoserine lactone mediated quorum sensing, or activation of efflux pumps. Using correlations with transcript ranks, the average specific growth rate of biofilm cells was estimated to be 0.08 h-1.


Collectively these data underscore the oxygen-limited, slow-growing nature of the biofilm population and are consistent with antimicrobial tolerance due to low metabolic activity.