Gene-edited wheat turns soil microbes into fertilizer

Scientists have engineered wheat to nudge soil bacteria into producing plant-ready nitrogen, a shift that could cut fertilizer use, curb pollution, and lower farm costs without sacrificing yields.

The plants overproduce a natural compound, leak the excess into the soil, and in doing so jumpstart nearby microbes that “fix” nitrogen from the air into forms crops can use.

In this work, a team at the University of California, Davis, led by Eduardo Blumwald, used CRISPR to dial up a wheat metabolite and tested the effect under low-nitrogen conditions.

The study extends earlier proof-of-concept in rice, with efforts underway to translate the approach to other staple cereals.

Synthetic nitrogen fuels global harvests

Worldwide, synthetic nitrogen fuels modern harvests but at a steep environmental and economic price. Wheat alone accounts for about 18 percent of global nitrogen fertilizer use. Of the hundreds of millions of tons produced each year, plants capture only 30 to 50 percent.

The remainder washes into rivers and coasts, feeding oxygen-starved dead zones, or escapes as nitrous oxide, a potent greenhouse gas. For smallholder farmers, especially in low-income regions, cost and access make fertilizer a gamble.

“In Africa, people don’t use fertilizers because they don’t have money, and farms are small, not larger than six to eight acres,” Blumwald said. “Imagine, you are planting crops that stimulate bacteria in the soil to create the fertilizer that the crops need, naturally. Wow! That’s a big difference!”

Wheat learns microbes’ nitrogen trick

Nitrogen fixation is carried out by specialized bacteria using an enzyme called nitrogenase, which only functions in low-oxygen conditions. Legumes such as beans and peas solve this by hosting the microbes in root nodules, which are tiny oxygen-poor chambers.

Cereals like wheat lack nodules, which is why they rely on bagged nitrogen. Rather than trying to give cereals nodules or force microbes to colonize roots – a strategy that has long struggled to stick – the team flipped the problem.

The researchers screened roughly 2,800 plant-made chemicals and found a small set, including flavones, that prompt soil bacteria to form protective biofilms. Those sticky microbial coats reduce oxygen exposure enough for nitrogenase to work.

“For decades, scientists have been trying to develop cereal crops that produce active root nodules, or trying to colonize cereals with nitrogen-fixing bacteria, without much success. We used a different approach,” Blumwald said.

“We said the location of the nitrogen-fixing bacteria is not important, so long as the fixed nitrogen can reach the plant, and the plant can use it.”

Gene edit flips fertilizer switch

Using CRISPR, the researchers boosted wheat’s production of apigenin, a common flavone. Plants kept what they needed and exuded the surplus through their roots.

In soil tests, the extra apigenin encouraged local bacteria to spin up biofilms, protecting nitrogenase, fixing nitrogen, and making ammonium available for the crop. In low-fertility conditions, edited wheat assimilated the microbially supplied nitrogen and outyielded control plants.

The amazing thing lies in what the plant does automatically. It manufactures the signal, leaks it when nitrogen is scarce, and benefits from the neighborhood effect. No external inoculants are required, and the microbes remain free-living in the soil rather than locked inside a root.

Pollution down, resilience up

If scaled, the approach could trim the fertilizer footprint that drives water pollution and climate forcing in wheat and other crops. Less soluble nitrogen applied to fields means less runoff during storms, smaller algal blooms, and fewer oxygen crashes in lakes and coastal zones.

Cutting back on industrial nitrogen also reduces upstream emissions from natural-gas-intensive fertilizer production.

Because the mechanism amplifies microbial activity already present in many soils, it may also help stabilize yields under input constraints. In places where fertilizer is scarce or prohibitively expensive, the crop’s own chemistry becomes a lever to unlock atmospheric nitrogen.

Billions saved with less fertilizer

The United States alone saw nearly $36 billion in fertilizer spending in 2023. Cereals cover close to 500 million acres nationally. Even modest reductions in inputs translate into real money while lowering risk in volatile markets.

“Imagine, if you could save 10 percent of the amount of fertilizer being used on that land,” Blumwald said. “I’m calculating conservatively: That should be a savings of more than a billion dollars every year.”

Those savings would not come solely from buying less nitrogen. Fewer passes to apply fertilizer mean lower fuel use and less soil compaction. Reduced losses to waterways could also ease regulatory pressure and improve community relations in vulnerable watersheds.

Proving stability across soil types

The road from greenhouse pots to farm fields is long, but the milestones are clear. Researchers will need to confirm that the nitrogen boost holds under diverse soils, climates, and microbiomes, and that it plays nicely with existing rotations and management.

They will need to show stable performance across seasons and varieties, measure effects on soil ecology, and ensure that yields and grain quality are maintained.

Because the edit increases a native metabolite rather than introducing a foreign gene, regulatory pathways may be more straightforward in some jurisdictions. Still, farmers and policymakers will want transparent data on environmental outcomes, fertilizer savings, and return on investment.

If the results scale, gene-edited cereals like wheat that recruit their own microbial fertilizer factories could become a practical tool in the nitrogen toolbox – cutting costs where budgets are tight, trimming pollution where waters run foul, and building resilience in the breadbaskets of a warming world.

The study is published in the Plant Biotechnology Journal.

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