Engineered microbes could cut crop dependence on chemical fertilisers

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Fertilizer is crucial for the global food supply, but making it uses a lot of energy and produces a lot of emissions. Some companies hope microbes can help.

A growing body of research shows that seeding the soil around a crop’s roots with beneficial microbes can help feed the plant, providing crucial nitrogen to help it grow. This could help reduce the need for chemical fertilizer, production of which accounts for roughly 2% of global greenhouse-gas emissions. It could also cut costs for farmers, a big boon—especially as the Iran war has sent energy and fertilizer prices skyrocketing in recent months.

Humans have used biological fertilizers like manure for thousands of years, and companies have long been developing microbial fertilizers, including some that rely on genetic engineering. But it’s difficult to engineer microbes that can reliably provide nitrogen for crops while also thriving themselves.

A startup called Switch Bioworks is taking a new approach that essentially allows microbes to establish themselves and grow into healthy colonies before shifting into nitrogen-producing mode. “We have to reinvent fertilizer,” says Tim Schnabel, the company’s founder and CEO.

The air is nearly 80% nitrogen, but plants can’t use that “free” nitrogen directly because it doesn’t react readily with other elements. Instead, they rely on so-called fixed nitrogen, which has been converted into more reactive compounds such as ammonia. In nature, microbes can perform this nitrogen fixation. Some plants, like legumes, even have symbiotic relationships with nitrogen-fixing bacteria, housing them in nodules in their roots. Synthetic fertilizer is essentially industrial nitrogen fixation via the Haber-Bosch process , which uses natural gas to make ammonia that’s applied to fields.

Biological fertilizers aim to replace some of the synthetic fertilizer with microbes that can help fix nitrogen for plants. But one challenge microbial fertilizer companies have run into is that it’s energetically expensive for microbes to make and release ammonia. Putting all their energy into nitrogen fixation can hamper their growth.

There’s a certain level of colonization you want to see around the roots, Schnabel explains. It’s too expensive and logistically challenging to put all those microbes on the plant, so you have to rely on a smaller number of microbes to grow and divide, establishing the population.

Tim Schnabel walks in a corn field where Switch is engaged in early trials. COURTESY OF SWITCH BIOWORKS

Switch Bioworks is betting that a genetic switch is the answer. A genetic switch is a section or sections of DNA that controls how genes are turned on and off. In this case it works by activating genes that help trigger ammonia production in and release from the cell. The company is working on several options for setting off this change in its microbes. The leading one is to have the microbes react to the nitrogen level in the soil: Once it drops to a certain level, they begin producing ammonia.

“You have this inherent biological reality, where it’s really expensive for microbes to fix nitrogen,” says Dan Blaustein-Rejto, director of food and agriculture at the Breakthrough Institute. It takes a lot of energy, and if they do fix the nitrogen, they want to use it for themselves, to build proteins and survive, he says. Adding genetic switches could help microbes grow and thrive and then help fertilize crops.

Switch is currently trialing its product in six US states, though it’s two to three years from a commercial product, Schnabel says. It’s initially focused on corn, the most-planted crop in the US, with over 90 million acres in 2026.

“It’s too early to tell exactly how well this works in the field,” Schnabel says. The company plans to harvest the plants in late October or early November, though as of August, some corn plants treated with Switch microbes already looked visibly healthier than those that hadn’t. And it’s still developing the products that will eventually make it to the market, he says.

Switch’s products could significantly help to clean up agriculture. “There’s a lot of potential for these companies and products to help farmers reduce emissions,” Blaustein-Rejto says. “This could be a really important solution for a quite hard-to-abate sector.”

While lab results have been promising, field trials are a crucial step in proving a product, Blaustein-Rejto says: “This is one of the final steps before they can go to market and make strong claims to farmers.” Independent trials are important as well, he adds, since there can be a large gap between a company’s reported data and what independent researchers find.

Pivot Bio is another company working to bring microbes to fields. Since it was founded in 2011, its products have been used on millions of acres of crops. The company now produces a range of products: Some versions can be added when seeds are planted, while others are applied to seeds before they’re even on a farm. The company also recently expanded beyond corn to make microbial fertilizers for cotton, wheat, and small grains including sorghum and barley.

Pivot’s initial challenge was trying to get microbes to produce nitrogen, whether they sensed it in the soil or not. Now the company is working to figure out how to make fitter, more robust colonies no matter the environment, says Travis Frey, the company’s chief technology officer.

“Growers right now are experiencing a double whammy from the farm economics point of view,” he says. Fertilizer costs are going up, and the price of commodity crops like corn has dropped. That’s a big opportunity for Pivot and others in the industry, Frey says: “This next decade is when biologicals on the farm are going to go mainstream.”

Fertilizer and seeds are two of the biggest costs for many growers, so reducing dependence on synthetic fertilizers could be a major help for agriculture, says John Havlin, a professor in the department of crop and soil sciences at North Carolina State University.

“I’m very excited about the future of the use of these products,” Havlin says. “They’ll eventually have a role to play to reduce the load of nitrogen that’s being applied.”

However, there’s a ceiling to the amount of fertilizer we can expect microbes to replace. Switch’s modeling suggests that around 50% is likely the maximum, though the initial product will likely be able to replace about 25% of a farm’s synthetic fertilizer, according to the company. Pivot has said its products can replace about one-quarter of the fertilizer used currently.

That means synthetic fertilizer will be around for a long time. “There is no clear and plausible vision for replacing it entirely in the foreseeable future,” Blaustein-Rejto says. “So other ways to reduce emissions and reduce other types of nitrogen pollution from farms remain really critical.”