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Use of complex metal oxide nanoparticles has drastically risen in recent years, especially due to their utility in electric vehicle batteries. However, use of these materials has outpaced our understanding of how they might affect environmental organisms, which they could encounter through release during manufacture, use, and disposal. In particular, little is known about the effects of chronic exposure to complex metal oxide nanoparticles. Here, we have focused on an environmentally-relevant bacterial species, Shewanella oneidensis, which is ubiquitous in nature and responsible for bioremediation of heavy metals, and assessed the toxic effects of nanoscale lithiated nickel manganese cobalt oxide (NMC), which is an emerging battery cathode material for electronic devices. We previously reported that chronic exposure of S. oneidensis to NMC results in the emergence of an adaptive phenotype where the bacteria are able to tolerate otherwise lethal concentrations of NMC. In the present study, we aim to investigate the role of reactive oxygen species (ROS) and changes in phenotype of the NMC-adapted bacterial population. We found that NMC-exposed bacteria possess ROS-containing membrane vesicles, as well as an increased propensity to generate random DNA mutations and harbor other DNA damage. Thus, our data indicate substantial genetic-level variation in bacteria that results from chronic exposure to toxic complex metal oxide nanomaterials.