Engineered bacteria could boost corn yields

Bacteria isolated from the roots of a corn plant and endowed with an unwavering ability to break the bonds between two nitrogen atoms could help minimize the use of fertilizer in farming, according to a new study (ACS Synth. Biol. 2021, DOI: 10.1021/acssynbio.1c00049). The microbes, created and commercialized by the agricultural start-up Pivot Bio, fertilize soil more sustainably than synthetic fertilizer and are the first gene-edited bacteria developed for growing cereal crops such as corn.

Plants need nitrogen for efficient growth. Each year, farmers worldwide use more than 100 million metric tons of nitrogen fertilizer, which consists of ammonia, nitrates, or other nitrogen-containing compounds. However, at least half of nitrogen fertilizers that farmers put down gets washed away in rainstorms, which are becoming more severe as climate change accelerates. The runoff is a notorious source of water and air pollution.

Plants can also obtain nitrogen from naturally occurring soil bacteria that capture it from the atmosphere—a process called biological nitrogen fixation. Nitrogen in gaseous form (N₂) is abundant in air, but because the molecule is extremely stable, plants can’t use N₂ until it’s been broken down. With the help of an enzyme called nitrogenase, soil microbes split the triple bonds holding N₂ molecules together, helping transform them into compounds that plant roots can draw in. Bacteria that associate with legumes—such as lentils, soybeans, and peanuts—are reasonably efficient at fixing nitrogen, but those associated with cereals such as corn, rice, and wheat are less so.

In the new study, Pivot Bio explained the biology behind its corn-specific nitrogen-fixing bacteria, which launched commercially in 2019. “The goal here is to have a microbe that provides nitrogen with the same reliability and access that a synthetic fertilizer would provide,” says Keira Havens, Pivot Bio’s sustainability project manager and the study’s lead author.

Pivot Bio created their modified microbes by starting with an isolate of a soil bacterium called Klebsiella variicola that selectively colonizes the outer surface of corn plants’ roots and potently performs biological nitrogen fixation. Normally, the microbe suppresses its ability to perform this process when fixed nitrogen is already present. But the researchers deleted one of the two genes that controls this mechanism and moved a promoter within the genome so that nitrogen fixation capabilities stay on full-time. This allows growers to replace some of their fertilizer use with the altered microbe, which fixes 122 times more nitrogen than its naturally occurring counterpart.

“It’s a relatively simple technical change,” Havens says. The company distributed the microbes to growers, who used it in addition to the synthetic fertilizer they were already applying. Fields supplemented with Pivot Bio’s microbes showed a significantly greater yield than fields using synthetic fertilizer alone in trials on 48 large corn fields. Because the microbes don’t survive unless they are physically touching the corn’s roots, there’s little danger that they will wash away and pump out ammonia that persists in the environment, she explains.

“The microbes cannot replace all the synthetic fertilizer farmers use right now,” Havens says. But the idea was to demonstrate that supplementing with the microbes could reliably allow them to use less of it, she adds.

The gene-edited microbes are “an exciting and game-changing strategy” for farmers, said Shelley D. Minteer, a biological chemist at the University of Utah, in an email. “This paper clearly shows the commercial viability of this strategy.”