Researchers have used CRISPR to engineer rice that encourages soil bacteria to fix nitrogen, which is required for their growth. The findings may reduce the amount of nitrogen fertilizers needed to grow cereal crops, save farmers in the United States billions of dollars annually, and benefit the environment by reducing nitrogen pollution.

“Plants are incredible chemical factories,” said Eduardo Blumwald, PhD, a distinguished professor of plant sciences from the University of California, Davis, who led the research. His team used CRISPR to enhance apigenin breakdown in rice. They found that apigenin and other compounds induced nitrogen fixation in bacteria.

Their work was published in Plant Biotechnology (Genetic modification of flavone biosynthesis in rice enhances biofilm formation of soil diazotrophic bacteria and biological nitrogen fixation).

Nitrogen is essential for plant growth, but plants cannot directly convert nitrogen gas from the air into a form that they can utilize. Instead, plants rely on the uptake of inorganic forms of nitrogen, such as ammonia, produced by bacteria in the soil. Agricultural operations depend on nitrogen-containing chemical fertilizers to increase plant productivity.

“If a plant can produce chemicals that make soil bacteria fix atmospheric nitrogen gas, we could modify the plants to produce more of these chemicals,” he said. “These chemicals will induce soil bacterial nitrogen fixation and the plants will use the ammonium formed, reducing the amount of fertilizer used.”

Blumwald’s team used chemical screening and genomics to identify compounds in rice plants—apigenin and other flavones—that enhanced the nitrogen-fixing activity of the bacteria.

Then they identified the pathways generating the chemicals and used CRISPR gene editing technology to increase the production of compounds that stimulated the formation of biofilms. Those biofilms contain bacteria that enhanced nitrogen conversion. As a result, nitrogen-fixing activity of the bacteria increased, as did the amount of ammonium available for the plants.

“When grown at limiting soil nitrogen conditions, modified rice plants displayed increased grain yield,” the researchers wrote in their paper. “Our results support the manipulation of the flavone biosynthetic pathway as a feasible strategy for the induction of biological nitrogen fixation in cereals and a reduction in the use of inorganic nitrogen fertilizers.”

The pathway could also be used by other plants. A patent application on the technique has been filed by the University of California and is pending. The research was funded by the Will W. Lester Endowment. In addition, Bayer Crop Science is supporting further research on the topic.

“Nitrogen fertilizers are very, very expensive,” Blumwald said. “Anything you can do to eliminate that cost is important. The problem is money on one side, but there are also the harmful effects of nitrogen on the environment.”

Much of the fertilizer that is applied is lost, leaching into soils and groundwater. Blumwald’s discovery could help the environment by reducing nitrogen pollution. “What this could do is provide a sustainable alternative agricultural practice that reduces the use of excessive nitrogen fertilizers,” he said.

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