Synthetic metal oxide nanomaterials exert toxicity via two general mechanisms: Release of free ions at concentrations which exert toxic effects upon the target cell, or specific surface-mediated physicochemical processes leading to the formation of hydroxyl free radicals and other reactive oxygen species which act to disrupt cell membranes and organelles. From a regulatory standpoint this presents a potential problem since it is not trivial to detect free metal ions in the presence of nanoparticles in biological or natural media. This makes efforts to identify the route of uptake difficult. Although in vitro studies of zinc oxide nanoparticles suggest that toxicity to the soil bacterium Cupriavidus necator is exerted in a similar manner to zinc acetate, we found no free Zn ion is associated with nanoparticle suspensions. The proteome of cells subjected to equal concentrations of either the nanoparticle or zinc acetate suggest that the mode of toxicity is quite different for the two forms of Zn, with a number of membrane-associated proteins up-expressed in response to nanoparticle exposure. Our data suggests that nanoparticles act to interrupt cell membranes thereby causing cell death rather than exerting a strictly toxic effect. We also identify potentially useful genes to serve as biomarkers of membrane disruption in toxicogenomic studies with nanoparticles or to engineer biosensor organisms.