The fate and transport of transition metals is of great interest because of metal toxicity and bioavailability. The growth of all organisms is dependent on the acquisition of essential metals. However, at higher concentrations heavy metals can inhibit the normal functioning of cells. Overall physiological effects of metals on biological systems are determined by metal speciation, not by their total concentration. Environmental fate and speciation of metals are influenced by interdependent biogeochemical variables such as pH, adsorption, complexation and biological interactions. Biofilms can generate three-dimensional physicochemical gradients that create microenvironments where local conditions are substantially different from those in the surrounding medium. The use of functional tomographic imaging microscopy of ratiometric core-shell silica nanoparticle sensors was shown to be an effective tool to study the spatial and temporal evolution of pH microenvironments in Escherichia coli PHL628 and mixed-culture wastewater biofilms. Curli are amyloid extracellular fibers expressed by E. coli and other bacterial species. The role of curli in the tolerance of E. coli PHL628 to Hg(II) was examined. Curli- producing strains proved to be more resistant than a curli-deficient mutant to Hg(II). Higher fluorescence was measured in a curli-deficient mutant than in the wild type following an addition of Hg(II) to cells harboring the merR-gfp reporter. Measurement of Hg(II) adsorption kinetics revealed that curli increases the rate and extent of Hg(II) adsorption. These findings indicate that curli sorb Hg(II) and reduce the amount of Hg(II) that reaches the cytoplasm. Microarray analysis of E. coli MG1655 cells grown in Hg(II) revealed upregulation of genes for arginine biosynthesis and transport. Increased resistance of E. coli to Hg(II) was not observed when the medium was supplemented with arginine. Induction of transcription of an arginine transport gene, artJ, by Hg(II) was confirmed with an artJlux reporter and exposure of this bioreporter to Zn(II) and Cd(II) revealed that these metals also induce the transcription of artJ. Furthermore, a merR-gfp bioreporter showed that arginine supplementation did not alter Hg uptake. These results indicate that group 12(IB) elements may act to induce the transport of arginine, but that arginine availability is not a strategy for alleviating their toxicity.