Summary: The combined impact of changing climate, population growth, environmental contamination, and soil degradation represent one of the greatest challenges facing humanity. Harnessing microbes will be a cornerstone of future sustainable agricultural and land management practices. Our laboratory uses mass spectrometry and fabricated ecosystem approaches to study the dynamic and reciprocal processes by which microbes interact to transform the organic molecules within their environment. Through the use of exometabolite profiling, we predict microbial metabolic webs in soils, sediment, and the rhizosphere for testing in fabricated ecosystems (EcoFABs) through the use of synthetic communities. Together these studies are providing insights into how microbes can be used to restore soil carbon, promote plant growth, and remove environmental contaminants.