Engineered bacteria are weaning farms away from synthetic fertilizers

The world’s farms depend on synthetic nitrogen fertilizers to increase crop yields, but the production and use of these chemicals generates billions of tonnes of greenhouse-gas emissions every year. Now, scientists are making progress on a greener alternative: bioengineered bacteria.

This approach takes a cue from natural bacteria that ‘fix’ nitrogen into a useful form and provide it to certain plants. Scientists are engineering genetic features into bacteria with the aim of enabling them to fix nitrogen for important food crops, such as maize (corn) and wheat, that don’t have such natural microbial partners.

In a comment published on 10 November in Nature Biotechnology¹, researchers suggest that bioengineered bacteria could eventually replace up to half of synthetic fertilizers. The bacteria deliver nitrogen more efficiently to roots than synthetic fertilizers do, which could reduce greenhouse-gas emissions and nitrogen pollution of waterways. But this would require a slew of advances, from getting different microbial species to work together to more-rigorous field trials.

Some of these ‘biofertilizers’ have been augmented with genes and genetic snippets from viruses or distantly related bacteria. This means that the engineered microbes are classified as transgenic — altered to include DNA from other species. The bacteria are now being trialled on small plots of maize on farms in the Midwestern United States. The bacteria, developed by Switch Bioworks in San Carlos, California, are the first example of a transgenic biofertilizer approved for testing on fields in the country.

In September, Switch Bioworks received approval from the Brazilian regulatory agency, the National Technical Commission on Biosafety (CNTBio), to test its strains there. This is the first time that a transgenic bacterium of any kind has been approved for field tests in Brazil, says molecular biologist Mario Murakami, who is the president of CTNBio in Campinas.

Companies that have focused on editing bacterial genes rather than producing transgenic microbes are further along. Pivot Bio in Minneapolis, Minnesota, has applied its gene-edited biofertilizers to tens of millions of hectares of US farmland over the past decade, says the company’s chief technology officer Travis Frey. Some of Pivot Bio’s products have also been tested in Canada, Argentina, Kenya and Brazil.

Greedy microbes

Most plants can’t use the form of nitrogen that is present in the air. Some crops, including soya beans and peanuts, host colonies of bacteria that can convert atmospheric nitrogen into a usable form. The plant takes up that nitrogen and, in return, provides carbon that fuels bacterial growth. But most staple crops lack these microbial partners, leading farmers to rely on synthetic nitrogen fertilizers. These chemical fertilizers account for 5% of global greenhouse-gas emissions, and drive damaging nutrient pollution in waterways.

For decades, researchers have tried to get bacteria to fix nitrogen for staple crops. Until recently, the approach was to collect wild strains of nitrogen-fixing bacteria from soil and apply them to seeds or spray them onto plants. “It doesn’t work,” says Jean-Michel Ané, a bioengineer at the University of Wisconsin–Madison, who is working on microbial fertilizers. The wild microbes fail to thrive when applied to crops that don’t provide them with carbon.

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