Programmable Bacteria to Decontaminate Drinking Water

With a $1.4 million NSF grant, BU and UMass Amherst researchers are teaming up to create microscopic, programmable “living devices” that can detect and neutralize toxic contaminants found in drinking water. Professor Douglas Densmore (ECE) and Research Assistant Professor Samuel Oliveira (ECE) believe that this research could help provide the foundation for far-reaching future applications of synthetic biology to some of the most urgent challenges facing our society and planet.

Life at the microscopic level is far more cosmopolitan and conversational than we might imagine. Colonies of bacteria live together in interspecies communities, communicating with their fellows via species-specific biochemical signaling mechanisms. Now, suppose researchers can find a way to manipulate these signals and convince different species of cohabiting bacteria to “talk” to one another. In that case, they should be able to “program” them to enact specific processes collectively.

Researchers could then engineer synthetic bacterial communities customized for such tasks, so-called “living devices,” or “interspecies genetic circuits,” which could achieve all kinds of desirable outcomes, from analyzing and cleaning drinking water to creating environmentally term, Densmore envisions members of the research community at large downloading the DAMP Lab’s software as well as the list of hardware used and assembly directions, so that other companies and universities can build their own bioreactors on the same model.

“That’s how we democratize biology with computing,” Densmore says. Instead of hoarding its “secret sauce” and running a unique “Michelin five-star restaurant,” as Densmore puts it, BU in a sense will franchise the DAMP Lab, standardizing equipment, software and processes all over the country. But, because BU’s eVOLVER-based, DAMP Lab–scaled bioreactor is infinitely adaptable, those replica labs won’t be producing identical studies and products. Other researchers will apply their creativity and generate their own solutions.

To use one more food analogy, Densmore points out that most people don’t bake their own bread, because it’s simply not an efficient use of their time. But, in biology, too much time is sunk into tasks that would be better automated and standardized, freeing researchers to use their minds.

“Pragmatically, that’s the only way to advance science and society,” Densmore says. “Right now, biology is baking a lot of bread.” By making BU’s packaged sliced bread available everywhere, “I’m saying, ‘Let’s get to making some cool sandwiches.’” friendly biofuels or novel therapeutic strategies for human health.

Densmore’s co-PI at UMass Amherst, Assistant Professor of Chemical Engineering Lauren Andrews, will lead the investigation into interspecies intercellular communication, while Densmore and Oliveira will leverage the infrastructure of the DAMP (Design, Automation, Manufacturing & Processes) Lab to develop a microfluidic platform for studying and maintaining bacterial communities. This platform can then be used to develop a database of models to predict the signaling dynamics of the bacterial communities.

Eventually, Densmore and Oliveira envision a proliferation of automation, shared resources, open-source databases and libraries of biological components that will allow for the scaled-up production of synthetic biological systems like the “living devices” they are working toward with Andrews. As such, the effort to understand, replicate and synthetically reengineer microbial processes in this study represents a step towards bioengineering a better future, starting with cleaner drinking water.

allison kleber