Microbes are ubiquitous in nature. Existing in every imaginable habitat, they form complex communities that carry out diverse functions enabling them to modulate systems that impact a wide swath of biological domains ranging from human health to environmental and biotechnological applications. Members of microbial communities communicate and interact by producing and responding to signaling molecules, exchanging genetic materials, and competing or collaborating to gain resources or cope with stress. These myriad of interactions raise several fundamental questions regarding the evolutionary and ecological forces that shape the function and stability of microbial communities. Leveraging the observation that a microbial community is often partitioned into sub-communities that differ with respect to composition and local interactions, investigators use a combination of mathematical modeling and experimental analysis of engineered microbial consortia to explore the fundamental mechanisms underlying spatial partitioning and maintenance of biodiversity and function. Molecular to community scale mathematical models developed as a result of the project will be used to discover generalizable rules relating spatial partitioning and interactions of microbes to microecological scale phenotypes and dynamics. Such insights can form the foundation of design principles that govern the development and use of synthetic microbial consortia. The project will also provide opportunities for undergraduates and graduate students to participate in interdisciplinary research through the "The Blue Devil Resistome Project", a hands on one-year project that involves students in the collection, survey, and analysis of environmental bacteria across the Duke University campus.

Extensive progress has been made in elucidating the function and dynamics of microbial communities, primarily relying on survey-oriented approaches (e.g., sequencing analysis of natural communities). While these studies have generated insight regarding the composition of microbial communities and how composition correlates with environmental conditions, they offer limited mechanistic insights into the maintenance and function of microbial communities. To date, efforts to address this question have focused on how microbes interact and how such interactions shape the dynamics and function of the overall community. This project explores a global, yet underappreciated, factor in microbiome organization and function, the partitioning of a microbial community into isolated or semi-isolated local communities. Partitioning often arises from spatial segregation in a given environment, such as spatial partitioning of the gut or microecological niches in the soil microbiome resulting from different soil particle sizes. Investigators use synthetic biology and microfluidic methods to engineer cooperative or competitive communities of varying spatial partitions, and employ systems and ecologically driven mathematical modeling to explore how spatial partitioning differentially impacts engineered synthetic consortia composed of competitive, cooperative, or complex mixtures of cooperative and competitive species. As the field of microbial ecology shifts from characterizing the structure of natural microbial communities to determination of community function and maintenance, results from this project will contribute to the discovery of fundamental principles that govern biodiversity, the emergences of microecological niches in various biological environments, and inform the development of design rules and constraints for the development of synthetic microbial consortia. This award was co-funded by Systems and Synthetic Biology in the Division of Molecular and Cellular Biosciences and the Mathematical Biology Program of the Division of Mathematical 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.

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Duke University
United States
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