Exploring Diverse Approaches to Iterative Microbiome Passaging in Soil and Plant Systems

Abstract

Efficient use of managed land depends on our ability to optimize relevant processes (e.g., crop growth) in that space. Microbial activities are critical to this goal, given their enormous contributions to biogeochemical flux and organismal health. Unfortunately, we still cannot predictably harness their potential in the same way that we can introduce nutrients or manipulate plant composition, for example. In recent years, iterative microbiome passaging has been investigated as an approach for capturing and optimizing groups of microorganisms that contribute additively to functions of interest, such as plant growth promotion or litter decomposition. Early trials show that this approach can alter microbiome function, but functional gains can seem almost stochastic, unlike archetypes of breeding within individual lineages. In this Perspective, we highlight the importance of continuing to explore diverse approaches to iterative microbiome passaging in soil and plant systems, given our limited knowledge about how this process works. There is no single “best” approach, but experimental design choices can have large impacts on outcomes. Ultimately, we believe that a better understanding of different forms of iterative microbiome passaging will allow us to (i) leverage the power of uncultivated microbes, additive/synergistic microbial contributions, and intermicrobial interactions and (ii) understand how land use choices will shape the functional trajectories of microbiomes through time