Directed evolution of 3D printed microbial communities

This project investigates the role of the spatial arrangement of cells in denitrification, a central ecosystem process with important applications in biotechnology. Bacteria play a crucial role in both biotechnology and the functioning of ecosystems. These microbes are organized in specific spatial patterns and often interact with each other within communities.

It is known that spatial organization is central to how different species interact and to the resulting function of the community. However, a key challenge in microbial ecology is understanding how different aspects of the spatial network contribute to the overall function. The two main challenges in studying this problem are the vast number of possible spatial arrangements and the difficulty of manipulating microbes in space.

To overcome these challenges, this research uses evolutionary algorithms to efficiently explore different spatial arrangements, and a novel approach to print microbial communities in 3D which allows better system manipulation. These approaches are used to investigate how the spatial organization of different microbes affects the process of denitrification, an essential step in the nitrogen cycle, impacting the availability of nitrogen in ecosystems and farming soils.

This project advances the understanding of microbial communities and their function. It provides insight into the role of spatial structure on nitrogen cycling, informing soil research and applications for waste-water treatment. Moreover, the 3D printing approach developed in this research can be easily adapted to study other types of communities and their functions.

An indispensable component of this project is providing interdisciplinary mentorship to diverse groups of students and increasing access to science and technology through different science education programs and outreach to local communities.

Microbial communities perform important functions for our health and that of ecosystems. Many of these functions are performed in spatially structured microbial communities such as biofilms, microbial mats and soil aggregates. While it is well known that spatial structure can affect community functions and interactions, there is limited understanding of how the arrangement of different cells in space influences the function of the community.

Two important limitations in addressing this question are the large space of possible parameters and conformations for even the simplest community and a lack of technology to construct a pre-defined, stable spatial community. The research constructs pre-defined spatial communities of bacteria, both experimentally and computationally, and explores the effect of cells’ spatial arrangement on a community’s function, stability, and division of labor.

The model bacterial community is composed of a mix of culturable species of bacteria able to perform different steps of the denitrification pathway. While denitrification could be performed entirely by a single species, it is often performed by multiple bacterial species through division of labor, making it an ideal model system. This research project develops a spatially explicit computer simulation of denitrification, expands a novel polymer scaffold system to print entire denitrifying microbial communities with pre-specified spatial organization and uses evolutionary algorithms to select different spatial conformations of improved function in two and three dimensions.

Algorithms are evaluated by assessing these conformations through bio-printing with the scaffold system.

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.