Living systems persist by balancing the expediency of function with the capacity for adaptation through regulatory and evolutionary means. Synthetic biology efforts disrupt this balance, most often by crudely enhancing function at the expense of stability. Whether in the bioreactor, the human gut, or the rhizosphere, engineered microbial systems are not intended to operate over evolutionary time scales, suggesting genome design rules that prioritize cellular resources for function over adaptation could define a new balance that does not compromise stability. We are exploring genetic circuit design and genome engineering approaches that exploit stochastic and dispensable gene expression to create microbial strains and communities with defined persistence phenotypes. We characterize the parameter space of our designs using high-throughout gene assembly and genome integration approaches applied both to E. coli and to non-model soil and rhizosphere isolates. Our efforts include the design and implementation of a genetic toggle switch to engineer self-destructive altruism in bacteria, increasing cellular capacity for production of antimicrobial compounds through genome reduction, and the metabolic addiction of bacteria to exuded plant root metabolites. Ultimately, we aim to establish genome design rules to create dynamical, field-deployed microbial systems contained by defined spatial and temporal ecological that promote plant health and can be extended to other complex environments.