Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

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 that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.

Editorial for Special Issue “Advances in Soil Microbiome”

“…A better understanding of how fertilization affects microbial communities or how air drying can change species presence and absence can both be explored through improved laboratory approaches. This can be helped though the use of synthetic soil testing systems, the development and analysis of which is explored in a paper by Dr. Smercina et al (“Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics”) [ 11 ]. These S ynthetic S oil A ggregate (SSA) devices are 3D printed and provide a chemically defined and translucent environment that mimics soil systems.…”