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Applied and Environmental Microbiology, May 2005, p. 2530-2538, Vol. 71, No. 5
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.5.2530-2538.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

DNA Microarray Analysis of Nitrogen Fixation and Fe(III) Reduction in Geobacter sulfurreducens{dagger}

Barbara A. Methé,1* Jennifer Webster,1 Kelly Nevin,2 Jessica Butler,2 and Derek R. Lovley2

The Institute for Genomic Research, Rockville, Maryland 20850,1 The University of Massachusetts, Amherst, Massachusetts 100032

Received 23 September 2004/ Accepted 2 December 2004

A DNA microarray representing the genome of Geobacter sulfurreducens was constructed for use in global gene expression profiling of cells under steady-state conditions with acetate as the electron donor and Fe(III) or fumarate as the electron acceptor. Reproducible differences in transcript levels were also observed in comparisons between cells grown with ammonia and those fixing atmospheric nitrogen. There was a high correlation between changes in transcript levels determined with microarray analyses and an evaluation of a subset of the genome with quantitative PCR. As expected, cells required to fix nitrogen had higher levels of transcripts of genes associated with nitrogen fixation, further demonstrating that the microarray approach could reliably detect important physiological changes. Cells grown with Fe(III) as the electron acceptor had higher levels of transcripts for omcB, a gene coding for an outer membrane c-type cytochrome that is essential for Fe(III) reduction. Several other c-type cytochrome genes also appeared to be up-regulated. An unexpected result was significantly higher levels of transcripts for genes which have a role in metal efflux, potentially suggesting the importance of maintaining metal homeostasis during release of soluble metals when reducing Fe(III). A substantial proportion (30%) of significantly expressed genes during Fe(III) reduction were genes of unknown function or hypothetical proteins, suggesting differences in Fe(III) reduction physiology among microorganisms which perform this metabolic process.

* Corresponding author. Mailing address: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850. Phone: (301) 795-7000. Fax: (301) 838-0208. E-mail: bmethe{at}tigr.org.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, May 2005, p. 2530-2538, Vol. 71, No. 5
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.5.2530-2538.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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