Cobalt and nickel ion synergy promotes gene duplication amplification and enables stable metal resistance in Shewanella oneidensis

Microbial species are integral in environmental homeostasis and have thus developed diverse strategies to adapt, survive, and proliferate under exogenous stress. The growing demand for nanoscale battery materials has led to increasing environmental concentrations of nanomaterials and their constituent metal ions. Previous work has shown that the gram-negative bacterium Shewanella oneidensis is able to rapidly evolve resistance to one such nanomaterial, lithiated nickel manganese cobalt oxide (NMC). Yet, the specific stimuli that trigger resistance evolution and the ensuing genomic changes were previously unknown. Here, we demonstrate that the combination of cobalt and nickel ions released from NMC trigger a gene duplication amplification (GDA) event that enables stable nanomaterial and metal resistance. Amplification copy number is highly dynamic over the period of study, yet amplification events persist over prolonged recovery in the absence of metal stress. Growth rate comparisons reveal no physiological cost associated with high copy GDA. The stability of this genomic mutation combined with the lack of observable fitness cost distinguishes this genomic perturbation from previously reported GDA events. Lastly, the observed GDA event was unique to the combination of cobalt and nickel, which implies that the intracellular targets of these metal ions have a specific interaction that yield resistance. Ultimately, we report a dynamic and specific GDA event that allows S. oneidensis to survive metal stress. This work not only illuminates the broader ecological consequences associated with introducing nanomaterials and metals into the environment but also provides insight into the larger scope of bacterial resistance mechanisms. ImportanceStudying mechanisms of microbial adaptation and resistance evolution is critical for understanding the role of bacteria in the environment and developing new strategies to combat antimicrobial resistance to modern therapeutics. Technological innovation has often led to the introduction of novel environmental stressors that impart pressure on microbes to evolve resistance. This may ultimately lead to novel resistance genes or gene cassettes in the environmental gene pool, which could further promote antimicrobial resistance in pathogenic organisms. In this study, we highlight the importance of identifying GDA events as a mechanism of bacterial resistance to environmental toxins. We demonstrate that amplification events can exist within a population in the absence of selection pressure and without a clear fitness cost. Identifying specific stimuli that trigger these events will help understand factors that accelerate bacterial resistance evolution and have the potential to disrupt the balance of the ecosystem.