PNNL

Abstract

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate, and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates – parameters which are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within the SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution DNA extraction, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a two-member synthetic microbial community and find that it is significantly different from the spatial organization of the same strains in liquid culture, indicating a potential for the SSAs to reproduce naturally occurring emergent community phenotypes.