The U.S. Department of Energy had a vision: Slash in half the amount of a potent greenhouse gas that enters the atmosphere when growing corn and sorghum for biofuel.

That gas — nitrous oxide — mostly comes from spraying chemical fertilizer onto fields. So in practice, achieving the agency’s goal meant figuring out how to grow those crops with dramatically less nitrogen fertilizer, but without cutting into harvests.

If that sounds ambitious, it’s because the idea came from a branch of the energy department that officials like to call the Moonshot Factory.

Scientists in Kansas, Colorado, Missouri, Texas, Illinois and other states believed they knew how to make the change happen. They were ready to launch the work this year, with benefits not just for fighting climate change but also reducing pollution in rivers, lakes and the Gulf of Mexico.

But 10 days after taking office, the Trump administration decided to hold off on this $38 million investment that the energy department had previously boasted could save farmers $6 billion in fertilizer spending.

Months later, the funding freeze hasn’t thawed and the energy department isn’t saying whether it ever will.

“ We were hoping that because of the obvious benefits of this type of research, that we might be allowed to go ahead,” said Maggie Wagner, an expert in plant genetics at the University of Kansas. “Who can argue with something that would save farmers billions of dollars?”

The energy agency didn’t respond to a media inquiry about the paused funding.

The agency’s moonshot branch — formally the Advanced Research Projects Agency-Energy — had at least three reasons to train its sights on growing corn and sorghum with less fertilizer.

These grains are key sources for making the ethanol that goes into cars and other biofuel that goes into airplanes.

But nearly a quarter of what farmers shell out to grow their crops goes toward buying fertilizer. The agency aimed to cut that expense to keep farmers cost-competitive.

The agency also wanted to make U.S. biofuel less dependent on imported fertilizer to bring crops to harvest.

And it wanted to cut the emissions footprint of biofuels.

Chemical fertilizer pumps gases into the atmosphere that are warming the planet and destabilizing precipitation patterns.

Manufacturing it produces carbon dioxide. Then, after the product is sprayed onto farm fields, only part of it actually helps plants grow.

Some ends up feeding soil bacteria that release a portion of what they gobbled up back into the atmosphere as nitrous oxide — a greenhouse gas far more potent than carbon dioxide.

This gas is about 265 times more effective at trapping heat over a 100-year period. It also eats into the ozone layer that shields life on the Earth from harmful radiation.

Since the Industrial Revolution, humans have increased the amount of nitrous oxide in the atmosphere by 20%, according to the Intergovernmental Panel on Climate Change.

Unlike the increase in carbon dioxide that mostly comes from burning fossil fuels, the extra nitrous oxide in the atmosphere mostly comes from industrialized farming — and nitrogen fertilizer is the top source.

“By reducing the need for those fertilizers,” the energy department said shortly before the Trump administration took office, the U.S. “could prevent up to 78 million metric tons of new emissions generated during nitrogen fertilizer production.”

The advanced project branch at the energy department is effectively an incubator.

It seeks out and funds early-stage ideas that have the potential to reshape entire markets in ways that would strengthen U.S. energy independence and reliability. And for many of them, it aims to see these through until the work is far enough along to attract private sector investors and take flight.

It’s part of a vision to ensure the U.S. leads the world on clean energy technology.

The nine projects that were chosen to cut fertilizer use and emissions from biofuel crops would take varied approaches.

Colorado State University scientists are poised to launch an extensive search for corn varieties that thrive with less fertilizer — and to identify the genes and traits that make this possible.

Corteva, one of the world’s biggest players on the multibillion-dollar crop seed market, is on board. This gives the academic scientists access to a treasure trove of material.

“Not only does Corteva have all this diversity of really high-performing corn (genetics),” said John McKay, a professor of soil and crop sciences at Colorado State, “but they’re the best at actually trialing corn for their breeding program.”

McKay, an expert in evolutionary genetics, is the lead scientist on the project.

Seed companies test their varieties the way they know U.S. farmers will grow them, and this means applying generous amounts of synthetic fertilizer. So it’s unclear how the vast majority of existing varieties might do without that boost.

But McKay has conducted other research with Corteva — also with funding from the energy department’s advanced projects arm — that found some varieties of corn perform just as well with far less.

“Farmers are already growing things that … they could be getting almost the same yield with half the nitrogen,” he said. “Other farmers are growing things that would have a huge yield reduction.”

This new project would carry the research much farther.

“We could exhaustively search for more of those genotypes” that don’t need as much nitrogen fertilizer, he said. “Once you understand the traits that are involved, then you can actually on purpose try to breed for that.”

The scientists also intend to look at specific crop genetics that can influence bacteria in the soil.

This could unlock two benefits. It could help farmers plant corn that supports more soil bacteria that pull nitrogen out of the atmosphere and naturally fertilize their plants.

It could also help them plant corn that ultimately reduces the problematic bacterial interactions that convert fertilizer into nitrous oxide that escapes into the air.

Colorado State’s research should have started this month.

Using less fertilizer would have other benefits

Though the energy department was focused on strengthening the biofuel market’s resilience and cutting its emissions, the scientists slated to do the work knew that doing so would reap rewards well beyond that.

Perhaps the most notable: helping to turn a page on one of the country’s most stubborn water pollution problems.

Fertilizer washes off of farm fields into waterways. It fuels toxic algae blooms in lakes across Kansas and other states. It is one of the top reasons for a giant dead zone in the Gulf of Mexico that becomes almost entirely devoid of life each summer.

Nitrate from fertilizers also percolates into aquifers, infiltrating the drinking supplies of the many cities and towns that depend on underground water.

In recent decades, more and more of those communities have started pouring millions or tens of millions of dollars into building treatment facilities to process water that has become unsafe to drink because it now contains so much nitrate.

“ The reduction in groundwater pollution that would result from this” research program that is now on pause, said Wagner, “would be such a big deal for for people – especially people living in agricultural communities, but also way downstream in the Gulf.”

Wagner will work on the Colorado State project if it moves forward. She is an associate professor in KU’s Department of Ecology and Evolutionary Biology. She’s also an associate scientist at the Kansas Biological Survey and Center for Ecological Research.

Closer to home, south-central Kansas is among the regions where underground water has been hardest hit by fertilizer pollution. That’s in part because nitrate easily percolates through its sandy soils.

Kansas State University geologists have found increases in nitrate in south-central Kansas wells over the past four decades that count among the biggest nationally. The city of Pratt has had to shut down two of its wells — which provided one-quarter of its water supply — because of the pollution.

Not only is treating water for nitrate expensive, but it makes water conservation more difficult. For example, one common method of treatment can result in 20% of the water being discarded as a waste stream. For communities in regions with dwindling aquifers, that’s a steep price to pay.

In 2024, the energy department put out its call for projects to slash the fertilizer needed for corn and sorghum.

On Jan. 10 this year, the agency announced the nine projects it picked. On Jan. 20, the Trump administration took office.

On Jan. 30, the Department of Energy sent a short email to scientists on the projects – two sentences thanking them, but saying the funding process was paused.

To McKay, what worries him even more than the fate of his project is seeing U.S. scientific research as a whole grind to a halt.

The Trump administration has frozen funding on a massive scale — at the National Science Foundation, the Department of Energy and other agencies.

“Basically all the scientific ideas, hypotheses and well-designed experiments that have already been approved,” he said, “the money is appropriated and it’s just sitting there.”

Here is a snapshot of the projects related to biofuel crop emissions that were announced in January. More institutions are involved than the leads listed here.

• Texas A&M AgriLife Research ($3.8 million) would work on new sorghum traits and hybrids.
• The Danforth Plant Science Center in St. Louis ($5.6 million) would work on corn with better root systems for taking up nitrogen from soil fungi.
• Colorado State University ($5.4 million) would work with industry giant Corteva on corn varieties that do better with less fertilizer application
• The University of Illinois, Urbana-Champaign, ($5 million) would work on a new variety of corn called NSave and integrate traits from a wild relative of corn.
• The University of Wisconsin-Madison ($5.5 million) would work on improving the ability of certain bacteria to deliver nitrogen to crops – and on introducing nitrogen-fixing traits into corn and sorghum.
• Switch Bioworks in California ($2 million) would work on alternatives to synthetic fertilizers.
• The Lawrence Berkeley National Lab in California ($3 million) would work on microbes that can help sorghum grow better with less nitrogen fertilizer.
• New York University ($5.6 million) would work on using artificial intelligence to tackle genetic questions related to nitrogen efficiency in corn.
• The University of Tennessee ($2.5 million) would work on cutting how much nitrous oxide escapes from the soil and developing cultivars that take in nitrogen better.