How Engineered Microbes Could Help Feed the World’s Crops

Microbes Take Aim at Fertilizer’s Dirty Secret

Fertilizer is the lifeblood of the global food supply. But making it is an energy-hungry, emissions-heavy process that accounts for roughly 2% of global greenhouse-gas emissions, and that's a heavy toll for something so vital. Engineered microbes crops could soon share the load with synthetic fertilizer, and a handful of startups are betting that the future of farming depends on tiny organisms doing the heavy lifting. So a growing body of research suggests that adding beneficial microbes to the soil around a crop's roots can supply nitrogen to help plants grow, which could cut both emissions and costs for farmers. It's a big bet.

That second part matters more than ever. Energy and fertilizer prices have skyrocketed in recent months, squeezing growers who are already dealing with thin margins. Reducing dependence on synthetic fertilizer could be a major financial relief, not just an environmental one.

The Nitrogen Problem, Explained

The air around us is nearly 80% nitrogen, but plants can’t use it directly. That “free” nitrogen doesn’t react readily with other elements, so crops depend on fixed nitrogen, which has been converted into reactive compounds like ammonia. In nature, microbes perform this nitrogen fixation. Some plants, like legumes, have even evolved 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. It’s a heavy, energy-hungry system. But biological fertilizers aim to replace some of that synthetic input with microbes that can fix nitrogen for plants, and those microbes work with the crop’s own roots, turning atmospheric nitrogen into a usable form without the fossil fuel demand. So it’s a quieter shift. They don’t eliminate the need for synthetic options overnight.

For thousands of years, humans have used biological fertilizers like manure, and that's a practice as old as farming itself, yet companies have also long been developing microbial fertilizers, including some that rely on genetic engineering. But there's a stubborn problem with this approach. It takes a lot of energy for microbes to produce and release ammonia.

The Energy Cost That Holds Back Microbes

A microbe pouring everything into nitrogen fixation can hamper its own growth. That's a dealbreaker in the field. You need a healthy, thriving population of microbes clustered around the roots to actually do the work, and if they're struggling just to survive, they can't fix enough nitrogen to help the crop. So it's a tough trade-off.

There’s a certain level of colonization you want to see around the roots," says Tim Schnabel, founder and CEO of a startup called Switch Bioworks. 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. That's the trick. But the cost and logistics force a leaner approach, one where a few must multiply into many, and the whole system hinges on their quiet, relentless expansion. They can't all be applied directly. They have to earn their place.

That’s the core tension. The microbes need to grow first, but the act of fixing nitrogen drains the energy they need for growth.

## A Genetic Switch Flips the Script

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. The company 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. It's a simple concept, but the execution is anything but. In this case, it works by activating genes that help trigger ammonia production in and release from the cell. But that's just one piece of the puzzle. The company is working on several options for setting off this change in its microbes, and they're exploring different triggers to find the most effective and reliable way to flip that switch. So don't expect a single answer. They've got a few tricks up their sleeves.

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.

Here's the clever part. The microbes get to grow and thrive first, building up their population. Then, when the soil signals that nitrogen is running low, they switch into fertilizer mode, a two-phase strategy that sidesteps the energy trade-off that has tripped up other approaches. It's simple. And it works.

It's really expensive for microbes to fix nitrogen. That's the inherent biological reality, says Dan Blaustein-Rejto, director of food and agriculture at the Breakthrough Institute, and it takes a lot of energy to pull off. And if they do fix the nitrogen, they want to use it for themselves, to build proteins and survive, he says. So genetic switches could change that. Adding those switches could help microbes grow and thrive, and then they could help fertilize crops.

Schnabel puts it more bluntly: “We have to reinvent fertilizer.”

Field Trials Are the Moment of Truth

Switch is trialing its product in six US states right now. But Schnabel says it's still two to three years away from a commercial product, and that's a critical window for a company that's betting big on the future of agriculture. Corn is the initial focus, and it's the most-planted crop in the US, with over 90 million acres planted in 2026. That's a massive market.

Harvest comes in late October or early November. That's the plan. As of August, some corn plants treated with Switch microbes already looked visibly healthier than those that hadn't been treated, which offers a glimmer of hope, though Schnabel remains wary. But it's too early to tell exactly how well this works in the field, he cautions.

That caution is warranted. While lab results have been promising, field trials are a key next step in proving a product works, says Blaustein-Rejto.

“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’s Decade of Microbe Development

Switch Bioworks isn’t alone in this space. Pivot Bio has been at it for over a decade. 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.

Pivot has expanded well beyond corn. They're now making microbial fertilizers for cotton, wheat, and small grains including sorghum and barley. That initial hurdle was simple to name but brutal to solve: getting microbes to produce nitrogen whether they sensed it in the soil or not. But the company's chief technology officer, Travis Frey, says they're now focused on building stronger, more adaptable colonies that thrive regardless of the environment. It's a tough shift. So they're pushing forward.

Frey sees a market ripe for disruption. Growers are getting crushed right now, he says, from a farm economics standpoint that's delivering a brutal, double-barreled blow to their bottom line. Fertilizer costs are climbing. And the price of commodity crops like corn has dropped, which is a stark reversal that squeezes margins from two opposite directions at once. That's a big opportunity for Pivot and others in the industry. It's a moment they can't waste.

“This next decade is when biologicals on the farm are going to go mainstream,” Frey says.

How Much Can Microbes Actually Replace?

There’s a ceiling to the amount of fertilizer we can expect microbes to replace, and it’s worth being honest about that. 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. So don’t expect microbes to do all the work. Pivot has said its products can replace about one-quarter of the fertilizer used currently. That’s a real chunk, but we’ve got to keep our expectations grounded in the data, not in wishful thinking about some perfect biological fix that never quite arrives.

Synthetic fertilizer isn't going anywhere soon. Blaustein-Rejto doesn't mince words about it: there's no clear and plausible vision for replacing it entirely in the foreseeable future, so cutting emissions and other nitrogen pollution from farms still demands serious attention. But that's the real battle. And it's one we can't afford to lose.

John Havlin, a professor in the department of crop and soil sciences at North Carolina State University, is optimistic but realistic. He knows the stakes. 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, and that's a shift that won't come easy, but it's worth chasing. So he keeps his hope grounded in the dirt.

Havlin’s excited about what’s coming. “I’m very excited about the future of the use of these products,” he says, and that enthusiasm stems from a simple, practical truth: these tools will eventually carve out a real role in cutting the nitrogen load that farmers currently apply. They’ll help. But it won’t happen overnight, and we’ve got to be patient with the science. So the promise is clear.

The Bottom Line for Farmers

Switch's products could significantly help clean up agriculture. There's a lot of potential for these companies and products to help farmers reduce emissions, Blaustein-Rejto says, and that's a big deal because agriculture is one of the toughest sectors to make greener. So this could be a really important solution for a quite hard-to-abate sector. But it's not a silver bullet.

But the proof is in the dirt, not in the lab. Field trials across six states will tell the real story. The company plans to harvest in late October or early November, and the early signs are encouraging, with treated corn plants looking visibly healthier as of August.

There is one detail worth pausing on. The economics of this shift aren’t just about emissions. They’re about survival for many growers. With fertilizer costs climbing and crop prices dropping, anything that cuts input costs without sacrificing yield is going to find a receptive audience.

Still, the transition won’t be instant. Even if Switch’s product works perfectly in trials, it’s two to three years from a commercial product. Pivot has a head start, with products already on millions of acres, but the category as a whole is still young.

The era of cheap, abundant synthetic fertilizer is clearly giving way to something more nuanced. Not a wholesale replacement, but a partnership. Microbes that grow first, then switch on their nitrogen-producing machinery when the soil needs it. It's a biological solution to an industrial problem, and it might just work. But that solution relies on timing, on soil conditions, on a delicate balance between microbial growth and the plant's demand for nutrients, which is why this isn't a simple swap but a careful choreography. So don't count out chemistry just yet.

For now, the harvest clock is ticking. The plants are in the ground, the microbes are doing their work, and the results will speak for themselves come late October.

Frequently Asked Questions

What is the main environmental problem with synthetic fertilizer mentioned in the article?

The article states that making synthetic fertilizer is an energy-hungry, emissions-heavy process that accounts for roughly 2% of global greenhouse-gas emissions. This is described as a heavy toll for something so vital to the food supply.

Why is nitrogen fixation by microbes an energy-intensive process that hinders their growth?

The article explains that it takes a lot of energy for microbes to produce and release ammonia, and if they pour everything into nitrogen fixation, it can hamper their own growth. This is a problem because a healthy, thriving population of microbes is needed around roots to fix enough nitrogen to help crops.

How does Switch Bioworks' genetic switch approach work to overcome the energy trade-off?

Switch Bioworks uses a genetic switch that allows microbes to grow and establish healthy colonies first before shifting into nitrogen-producing mode. The leading trigger is having microbes react to soil nitrogen levels; once nitrogen drops to a certain level, they begin producing ammonia, sidestepping the energy trade-off.

What does the article say about Pivot Bio's history and the range of products they offer?

Pivot Bio has been developing microbial fertilizers for over a decade, since its founding in 2011. Their products have been used on millions of acres and now cover corn, cotton, wheat, and small grains including sorghum and barley, with versions for seed treatment or application at planting.

According to the article, what is the realistic potential for microbes to replace synthetic fertilizer?

Switch's modeling suggests that around 50% is likely the maximum replacement, with their initial product able to replace about 25% of a farm's synthetic fertilizer. Pivot has said its products can replace about one-quarter of current fertilizer use, and synthetic fertilizer isn't going away soon.