Chemistry in the Rhizosphere: Using Exometabolomics and Fabricated Ecosystems to Enable Engineering Microbiomes for Sustainable Agriculture and Soil Carbon Storage

Soil microbiomes are important drivers of plant health and soil carbon cycling. Plants release up to 20% of carbon they fix into the soil surrounding roots (the rhizosphere) to support soil microbes, many of which promote plant health. Overall, 95% of the carbon released by plant roots is returned to the atmosphere through microbial activities. Small-molecule metabolites mediate critical plant-microbe interactions and microbial respiration and can be directly probed using exometabolomics. However, the large variability and lack of control in natural environments makes it difficult to determine causal mechanisms. To address this need, we have developed methods for making and using fabricated plant ecosystems (EcoFABs) complete with synthetic rhizosphere microbial communities. Using these capabilities, we have found identified metabolites that are preferentially used by rhizosphere bacteria and those we predict will accumulate in soils. These findings and approaches help lay a foundation for matching plant hosts with beneficial microbes and harnessing plant and microbial systems for soil carbon storage.