Collaborative Research: Model-guided design of bacterial interspecies interactions and trans-organismic communication in living intercellular circuits

Bacteria in the environment live in multispecies communities with dynamic interactions that can bring about complex collective behaviors. Bacteria use biochemical cell-to-cell communication via diffusible molecules and gene regulatory elements to bring about large-scale responses. The ability to predictably design multicellular responses in diverse bacterial communities would have a wide range of applications including efficient biomanufacturing, bioenergy conversion, novel therapeutic strategies, sustainable agriculture, and bioremediation.

To date, numerous naturally occurring interactions and modes of communication within bacterial communities have been identified, yet there is not the ability to engineer synthetic bacterial communities that have these complex interactions and dynamic responses among diverse bacteria. This collaborative project aims to improve understanding of interspecies biochemical cell-cell communication that can occur in natural microbial communities and allow us to leverage the highly complex functions afforded by these systems within synthetic diverse bacterial communities as programmable living devices.

This project will create synthetic bacterial consortia for biosensing and bioremediation of many hazardous water contaminants, including some of the most dangerous drinking water and aquatic ecosystem contaminants. This project will provide education and research training for numerous K-12, undergraduate, and graduate students. Hands-on workshops will be run at UMass Amherst and Boston University each year for high school students to learn about studying and engineering bacterial communities.

Many undergraduate opportunities for synthetic biology research training will be created. These educational activities will increase K-12 STEM education, help address the underrepresentation of women and minorities in synthetic biology, and train the next generation of scientists and engineers.

The goal of this project is to establish a generalizable framework for the design of multicellular transcriptional regulatory networks distributed within bacterial communities containing gram-negative and gram-positive bacteria. The universality of recent discoveries of homoserine lactone-mediated quorum sensing in gram-positive bacteria will be determined using libraries of LuxRI-type quorum sensing systems and model gram-positive bacteria.

This work will generate a set of standardized quorum sensors for gram-positive bacteria that allow for controlling interspecies communication between diverse bacteria. The sequence-function relationship for these quorum sensing systems will be determined using statistical design and systematic mutagenesis. Using these quorum sensors, the team will test fundamental questions about the evolution of quorum sensing in bacteria.

A high-throughput multilayer microfluidics platform for studying and maintaining bacterial communities will be developed to analyze temporal signaling at single-cell resolution. This platform will be used to develop a database of parameters and models to predict the signaling dynamics of these distributed transcriptional regulatory networks. This work aims to enable researchers to create diverse bacterial communities that have complex interactions, designable interspecies communication, and prescribed dynamic responses.

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.