Describing the Persistence Landscape for Introducing Microbes into Complex Communities

The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the community, its persistence in the microbiome to serve a specified purpose, and constraint of the organism and its activity to the intended environment. A theoretical framework is needed to represent the complex interactions that drive these dynamics. Building on the concept of the community functional landscape, we define the persistence landscape as the metabolic, genetic, and broader functional composition and ecological context of the target microbiome that can be used to predict the environmental fitness of an introduced organism. Here, we discuss critical aspects of persistence landscapes that impact interactions between an introduced organism and the target microbiome, including the communitys genetic and metabolic complementation potential, cellular defense strategies, spatial and temporal dynamics, and the introduced organisms ability to compete for resources to survive. Finally, we highlight important knowledge gaps in the fields of microbial ecology and microbiome engineering that limit characterization and engineering of persistence landscapes. As a model for understanding microbiome structure and interaction in the context of microbiome engineering, the persistence landscape model should enable development of novel containment approaches while improving controlled colonization of a complex microbiome community to address pressing challenges in human health, agronomy, and biomanufacturing.