Collaborative Research: Elucidating and Manipulating Carbon Metabolic Niches in Soil Microbiomes using Synthetic Communities for Sustainable Agriculture

Healthy soil microbiome is essential for productive agriculture, influencing plant nutrition, growth, and resilience. This project seeks to understand the molecular and ecological principles that govern soil microbiome composition and function, with the goal of developing strategies to reintroduce and maintain beneficial microbes in agricultural systems. The insights gained from this study will enable precision engineering of native and synthetic microbial communities that improve nutrient uptake and drought tolerance in crops and promote sustainable agriculture. Educational activities will bring microbiome science to the broader community through workshops, public events, and student-led programming, helping train the next generation of scientists while addressing the US national priorities in food security. This research combines microbial ecology, synthetic biology, and plant-microbe interaction studies to investigate how carbon metabolism shapes microbial community structure and function in soil. Despite the importance of soil microbial communities, the mechanisms governing their assembly, stability, and persistence remain poorly understood. Using a well-defined synthetic microbial community, the project will identify carbon substrate preferences among plant-beneficial bacteria, engineer bacterial strains to enhance nutrient solubilization and plant drought resilience, and develop novel biocontainment strategies using selective carbon auxotrophy. By integrating high-throughput phenotyping, metagenomics, and microbial engineering, this work will generate new tools and knowledge for precision microbiome engineering in agriculture, with broad relevance to other ecosystems and biotechnological applications. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.