Ecosystem fabrication: New strategies for assessing microbial interactions in plant and soil microbiomes

The ability to engineer microbiomes is desirable both to understand how microbial communities function and increasingly as a strategy to alter in situ environments. Analogous to how probiotics are being used to improve human health, microbial amendments are sought after to improve plant and soil health. However, the variability and complexity of these ecosystems coupled with our lack of understanding of microbial interactions limit scientific examination and engineering approaches.

Most of what we know about microorganisms, including their gene functions and growth dynamics have been derived from single-organism studies in benchtop experiments or from correlations based on observations made in complex systems. To bridge the gap between fully-constrained single organism laboratory experiments and high-dimensional ecosystem analyses, we have been developing EcoFABs (Ecosystem Fabrication; www.eco-fab.org; https://doi.org/10.3791/57170) which are small chambers constructed using common microfluidic procedures that can be used to study and engineer microbiomes living on and around the root surface. The devices are designed to be amenable to a number of analyses including microscopy of the root zones and soils, metabolomics analyses, and spatial sampling of the microbial communities. Over a dozen different plant varieties have been grown in EcoFABs, and a number of growth conditions are supported including hydroponics, solid substrate and live soils.

This focus on rhizosphere microbiomes is both based on their importance in agriculture and the fact that the root surface provides a reproducible and relevant habitat for laboratory experimentation. Recently, a multi-laboratory EcoFAB study growing the model plant Brachypodium distachyon demonstrated reproducible plant phenotypes and metabolomics including significant differences between treatments that were retained across laboratories (https://doi.org/10.1111/nph.15662). Current efforts are focused on the development of fully defined fabricated ecosystems that can be disseminated between laboratories. These include the EcoFAB devices, standardized microbiomes, protocols, equipment and software.