Scientists and engineers at Rice University have engineered living bioelectronic sensors based on bacteria that can quickly sense and report on the presence of a variety of contaminants.

A team led by Rice synthetic biologists Caroline Ajo-Franklin and Jonathan (Joff) Silberg and lead authors Josh Atkinson and Lin Su, both Rice alumni, developed living bioelectronic sensors which can be programmed to identify chemical invaders and report within minutes by releasing a detectable electrical current. 

Their study in Nature shows that such “smart” devices could power themselves by scavenging energy in the environment as they monitor conditions in settings like rivers, farms, industry and wastewater treatment plants and to ensure water security, according to the researchers.

Buffalo Bayou Park

Source: Michael Carera

Buffalo Bayou Park

The environmental information communicated by these self-replicating bacteria can be customized by replacing a single protein in the eight-component, synthetic electron transport chain that gives rise to the sensor signal.

“I think it’s the most complex protein pathway for real-time signaling that has been built to date,” said Silberg, director of Rice’s Systems, Synthetic and Physical Biology PhD Program.

“To put it simply, imagine a wire that directs electrons to flow from a cellular chemical to an electrode, but we’ve broken the wire in the middle. When the target molecule hits, it reconnects and electrifies the full pathway.”

Ajo-Franklin said: “It’s literally a miniature electrical switch. You put the probes into the water and measure the current. It’s that simple. Our devices are different because the microbes are encapsulated. We’re not releasing them into the environment.” 

The methods used

The researchers’ proof-of-concept bacteria was Escherichia coli, and their first target was thiosulfate, a dichlorination agent used in water treatment that can cause algae blooms. They collected water from Galveston Beach and Houston’s Brays and Buffalo bayous.

At first, they attached their E coli to electrodes, but the microbes refused to stick in the presence of water

Enlisting co-author Xu Zhang, a postdoctoral researcher in Ajo-Franklin’s lab, they encapsulated sensors into agarose in the shape of a lollipop that allowed contaminants in but held the sensors in place, reducing the noise. 

With the physical constraints in place, the labs first encoded E coli to express a synthetic pathway that only generates current when it encounters thiosulfate. This living sensor was able to sense this chemical at levels less than 0.25 millimoles per liter, far lower than levels toxic to fish.

In another experiment, E. coli was recoded to sense an endocrine disruptor. This also worked well, and the signals were greatly enhanced when conductive nanoparticles custom-synthesized by Su were encapsulated with the cells in the agarose lollipop. The researchers reported these encapsulated sensors detect this contaminant up to 10 times faster than the previous state-of-the-art devices. 

Chance encounter

The study began by chance when Atkinson and Moshe Baruch of Ajo-Franklin’s group at Berkeley Lawrence National Laboratory set up next to each other at a 2015 synthetic biology conference in Chicago, with posters they quickly realized outlined different aspects of the same idea.

Within six months, the new collaborators won seed funding from the Office of Naval Research, followed by a grant, to develop the idea.

Silberg said the design’s complexity goes far beyond the signalling pathway.

“The chain has eight components that control electron flow, but there are other components that build the wires that go into the molecules,” he said. “There are a dozen-and-a-half components with almost 30 metal or organic cofactors. This thing’s massive compared to something like our mitochondrial respiratory chains.” 

Silberg said he sees engineered microbes performing many tasks in the future, from monitoring the gut microbiome to sensing contaminants like viruses, improving upon the successful strategy of testing wastewater plants for SARS-CoV-19 during the pandemic.

“Real-time monitoring becomes pretty important with those transient pulses,” he said. “And because we grow these sensors, they’re potentially pretty cheap to make.” 

To that end, the team is collaborating with Rafael Verduzco, a Rice professor of chemical and biomolecular engineering and of materials science and nanoengineering who leads a recent $2 million National Science Foundation grant with Ajo-Franklin, Silberg, bioscientist Kirstin Matthews and civil and environmental engineer Lauren Stadler to develop real-time wastewater monitoring.

Silberg said the Rice labs are working on design rules to develop a library of modular sensors. “I hope that when people read this, they recognize the opportunities,” he said.