Ionomic responses to increasing environmental copper: results from experimental evolution of the bacterium Serratia marcescens

Divalent cations such as copper (Cu) occur in trace amounts yet play critical roles in bacterial physiology. Despite its essentiality, Cu is toxic at elevated concentrations and is widely applied as a bactericide, requiring cells to balance uptake, sequestration and efflux. Although molecular responses to Cu stress are well characterized, less is known about how prolonged Cu exposure reshapes cellular elemental composition as an integrated multi-element system (i.e. ionome). Here, we experimentally evolved Serratia marcescens under a gradient of increasing Cu concentrations and quantified growth rate, biomass yield and intracellular quotas of Cu alongside 13 additional elements. We tested whether adaptation to Cu alters growth across environments and induces coordinated, system-wide shifts in the ionome rather than changes limited to Cu alone. Evolutionary history and assay environment strongly interacted to shape growth and yield: Cu exposure reduced both traits in the ancestor, whereas evolved lineages exhibited context-dependent trade-offs between growth rate and biomass production. Cellular Cu quotas reflected environmental supply; however, within each Cu level, lineages evolved without accumulating more Cu than Cu-adapted lineages, consistent with altered metal homeostasis rather than increased accumulation. Compositional data analysis revealed ionomic restructuring across multiple elements, demonstrating that long-term Cu stress drives ionome-wide reorganization.