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Background   Geobacter  species are δ- Proteobacteria  and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth of  Geobacter  in changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established for  Escherichia coli  chemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand how  Geobacter  thrives in natural environments and better their use in microbial fuel cells.    Results  The genomes of  G. sulfurreducens, G. metallireducens , and  G. uraniireducens  contain multiple (~70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). Unlike the single gene cluster of  E. coli , the  Geobacter  clusters are not all located near the flagellar genes. The probable functions of some  Geobacter  clusters are assignable by homology to known pathways; others appear to be unique to the  Geobacter  sp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP) homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression in  Geobacter  differs from  E. coli . The sequences of predicted promoter elements suggest that the alternative sigma factors σ 28  and σ 54  play a role in regulating the  Geobacter  chemotaxis gene expression.    Conclusion  The numerous chemoreceptors and chemotaxis-like gene clusters of  Geobacter  appear to be responsible for a diverse set of signaling functions in addition to chemotaxis, including gene regulation and biofilm formation, through functionally and spatially distinct signaling pathways.

Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function