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Applied and Environmental Microbiology, February 2003, p. 769-778, Vol. 69, No. 2
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.2.769-778.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Monitoring Gene Expression in Mixed Microbial Communities by Using DNA Microarrays

Philip Dennis,1,{dagger} Elizabeth A. Edwards,1 Steven N. Liss,2 and Roberta Fulthorpe3*

Department of Chemical Engineering and Applied Chemistry, University of Toronto,1 Department of Chemistry, Biology, and Chemical Engineering, Ryerson University, Toronto,2 Division of Physical and Environmental Sciences, University of Toronto, Scarborough, Ontario, Canada3

Received 30 April 2002/ Accepted 7 November 2002

A DNA microarray to monitor the expression of bacterial metabolic genes within mixed microbial communities was designed and tested. Total RNA was extracted from pure and mixed cultures containing the 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Ralstonia eutropha JMP134, and the inducing agent 2,4-D. Induction of the 2,4-D catabolic genes present in this organism was readily detected 4, 7, and 24 h after the addition of 2,4-D. This strain was diluted into a constructed mixed microbial community derived from a laboratory scale sequencing batch reactor. Induction of two of five 2,4-D catabolic genes (tfdA and tfdC) from populations of JMP134 as low as 105 cells/ml was clearly detected against a background of 108 cells/ml. Induction of two others (tfdB and tfdE) was detected from populations of 106 cells/ml in the same background; however, the last gene, tfdF, showed no significant induction due to high variability. In another experiment, the induction of resin acid degradative genes was statistically detectable in sludge-fed pulp mill effluent exposed to dehydroabietic acid in batch experiments. We conclude that microarrays will be useful tools for the detection of bacterial gene expression in wastewaters and other complex systems.

* Corresponding author. Mailing address: University of Toronto at Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada. Phone: (416) 287-7221. Fax: (416) 287-7279. E-mail: fulthorpe{at}utsc.utoronto.ca.

{dagger} Present address: GeoSyntec Consultants, Guelph, Ontario N1G 5G3, Canada.

Applied and Environmental Microbiology, February 2003, p. 769-778, Vol. 69, No. 2
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.2.769-778.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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