BIO-AI: Designing plant rhizobacteria communities for sustainable agriculture

Microbial communities living on and around plants influence plant growth and health in positive or negative ways, but the factors that determine these outcomes are not well understood. Gaining insight into how these microbial communities function is essential for improving crop performance, reducing losses to disease, and supporting food security. This project will investigate how the composition and characteristics of root-associated microbial communities shape plant development and health. By combining biology, engineering, and machine learning, the team will identify bacterial strains that, when assembled into communities, promote plant growth and help protect against disease. These findings will support the development of beneficial microbial products that enhance crop performance and reduce agricultural inputs. The project will also train undergraduate and graduate students, provide summer research opportunities for high school students, and support K–12 science education through a training workshop for local teachers on plant microbiomes and related science and engineering topics. Although plant microbiomes play a major role in influencing plant outcomes, we have a poor understanding of the causal links between the functional properties of microbiomes and plant host phenotypes. This project will use a well-characterized collection of plant-associated bacterial strains to construct a variety of synthetic communities and study how specific combinations affect plant growth and pathogen resistance. DNA barcoding will enable precise tracking of microbial colonization, and high-throughput imaging will capture plant phenotypes over time. The project will support the development of machine learning models to analyze these data and identify community features that optimize plant performance by balancing growth and health outcomes. It will also investigate the genetic basis of beneficial microbial effects using mutagenesis and functional screening. Together, these efforts will uncover how microbial communities and their functions influence plant outcomes, while generating new experimental and computational tools for plant biology and microbiome engineering. The findings will guide the development of beneficial microbial communities for crops and support continued innovation in agriculture. This project is supported by the Systems and Synthetic Biology Cluster of the Division of Molecular and Cellular Biosciences, the Plant Biotic Interactions program of the Division of Integrative Organismal Systems, and the Emerging Frontiers Division in the Directorate for Biological Sciences. 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.