E. coli to energy: UVA students head abroad with a clean-fuel idea

October 25, 2025
Katie Nichols in a laboratory at UVA loading samples into a centrifuge.

Biology major Katie Nichols is studying a novel idea for turning waste streams into hydrogen to provide a clean-energy fuel. She’s part of the team that is presenting its work in Paris this week. (Photo by Lathan Goumas, University Communications)

Katie Nichols envisions a future powered by clean energy. But she concedes there are challenges. Some areas of the Earth don’t get a lot of sun. Other areas don’t get a lot of wind.

“But waste,” she said, “is such a well-distributed resource.”

Populations all over the world both throw out food and go to the bathroom. So Nichols, a third-year biology student in the University of Virginia’s College of Arts & Sciences, and eight of her peers are working on an idea to turn organic waste – like food scraps and sewage – into clean energy by tinkering with bacterial DNA.

a team of UVA biomedical and bioengineering students conducting research.

The UVA student researchers wrap up work in their lab as they prepare to present their findings at the world’s largest synthetic biology exposition and competition. (Photo by Lathan Goumas, University Communications)

This week, the UVA team is in Paris at the iGEM Grand Jamboree – or International Genetically Engineered Machine contest – which bills itself as the world’s biggest synthetic biology competition, a place where biology and engineering combine.

They’ll face 400 international teams in a competition that is part science fair and part “Shark Tank.” The team’s months of research and work will come down to a five-minute presentation and a 25-minute grilling from the judges.

“That’s the biggest challenge that any team has, that any scientist has, and that is, ‘All right, I’ve done 10 months of work here. How do I get this into short and sweet so that a judge can understand?’” Sahvir Bhaskaruni, a third-year biomedical engineering student in the School of Engineering and Applied Science, said.

Here’s the idea they are presenting:

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Bacteria feast on organic waste. That’s well known. Lesser known is that these anaerobic bacteria belch tiny amounts of hydrogen. Lesser known still is that adding an amino acid called L-cysteine to that process triggers the bacteria to make even more hydrogen, enough to collect and use as a clean fuel.

It’s possible to just dump L-cysteine into a bacteria-and-waste soup, and plenty of commercial operations do that. But the UVA students arrived at a more natural solution. They’re taking another strain of bacteria, E. coli, and adding to its DNA. The extra DNA programs the E. coli to secrete the needed L-cysteine, which in turn makes the other bacteria spew more hydrogen.

So instead of just pouring L-cysteine into the mix, the UVA students have figured out how to engineer a safe strain of E. coli to do that work for them. The result, they believe, might one day turn waste into clean energy and help solve climate change.

Nichols and Zach Smith fill samples to place in a centrifuge.

Zach Smith, right, and Nichols find that adding new pieces of DNA to E. coli can both ramp up and shut down production of an amino acid that helps produce more hydrogen from the process of breaking down waste. (Photo by Lathan Goumas, University Communications)

The process to get that clean energy, Nichols explained, is called “dark fermentation.”

“So, officially, that is the light-independent process by which certain bacteria – these dark, fermentative bacteria – take a stream of organic waste and produce hydrogen from that waste,” she said.

“Specifically,” Bhaskaruni added, “it breaks down the sugars in these organic wastes and then converts them to hydrogen and some other byproducts.”

All of this takes place in a “bioreactor,” or a container the researchers control. By adding the modified E. coli, the reactor can produce a “commercially viable” amount of hydrogen.

But just as important, the students have also figured out how to add different DNA that broadcasts a “shut down” command – essentially a “kill switch” – when enough of the amino acid is produced, keeping everything in balance.

Sahvir Bhaskaruni and Michael Hunter reviewing their research on a laptop computer while preparing for a presentation.

Sahvir Bhaskaruni, team captain, and Michael Hunter will face a panel of judges in Paris to explain the science behind their work to turn waste into energy. The contest involves presentations that are part science fair and part “Shark Tank.” (Photo by Lathan Goumas, University Communications)

“The process of these two working together is really the novelty of what we have done here,” Bhaskaruni said.

The students have explained all of this in a video and website. Like the other teams, they have forwarded the materials to the judges so they won’t have to cover everything in their five minutes. And while it might seem a long way to go for such a short presentation, Nichols said the entire experience will be a learning process.

“It’s the largest synthetic biology exposition and competition in the world,” she said. “There are teams from all over the world, universities from hundreds of countries. And so it’s really getting to see what other undergraduates in all of these different places have been working on.”

“It’s just this great exchange of ideas,” Bhaskaruni added, “where you get really immersed in all parts of synthetic biology, not just the space that we’ve been working in, but the spaces other teams and schools and people from all around the world have been working in.”

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Mike Mather

Executive Editor University Communications

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