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The Future of Food

Agriculture’s extremely tiny saviors

Custom-made microbes are coming to reduce farm pollution and make crops more productive.

Cotton plants designed to tolerate drought in a field in Arkansas.Indigo

To hear Geoffrey von Maltzahn talk, the future is in the dirt. But he means that in a good way. He is one of several entrepreneurs who are convinced that the toughest problems in agriculture can be solved in the ground by microbes — the teeming communities of microscopic life such as bacteria and fungi that shape the health and vitality of plants, people, and, basically, all life on this planet.

Von Maltzahn’s Boston-based company, Indigo Ag, intends to harness the marvelous abilities of microbes to nourish crops, protect plants from drought and heat, reduce agricultural pollution, use less fossil fuel for farming, and make corn, wheat, rice, soy, and cotton plants more vigorous and productive. It’s an attempt to capitalize on a phenomenon that scientists are still trying to fully understand: that the growth of food crops and other plants is heavily influenced not only by their own genetic codes, but by microbes that live in the plants’ stems and roots and in the soil around them.


“We think this is an area of science that’s going to be applicable to every one of the quadrillion seeds that gets planted” every year across the world, von Maltzahn says. Soil microbes even offer a solution to climate change, he says, because they could supercharge agricultural practices that suck carbon dioxide out of the air and bury it in farmland soil. These microorganisms might improve the health and vitality of cover crops, which are planted in cycles between cash crops like corn, or they might themselves increase the amount of carbon dioxide that gets deposited in the soil by plants.

Over eons, plants and microbes have evolved mutually beneficial partnerships that have become an appealing target for biotechnology researchers.

Starting in 2014, Indigo scientists and their collaborators began seeking out plants that were mysteriously thriving under conditions of drought, disease, or nutrient deficiency that killed neighboring plants. The team sampled the microbes living inside these super-survivor plants, coaxed those microbes to grow in a lab, and then tested what happened when they applied them to plants in greenhouses. Now the company sells seeds coated in these beneficial bacteria and fungi.


Cotton seeds coated in beneficial bacteria and fungi.Indigo
Cotton seeds coated in beneficial bacteria and fungi.

Indigo’s first product, released in 2016, was designed to help cotton tolerate drought. There are now more for other crops; Indigo says that as a group they boost yields by upwards of 5 percent. The company says its various microbial products have been used on 4 million acres of crops worldwide.

Investors are buying into this vision. Indigo Ag has raised roughly $850 million, making it the biggest and best-capitalized of dozens of startups developing microbes to address agricultural needs. (Indigo is also expanding beyond microbe mixes. The company provides a wide range of data analysis and technical consulting services to farmers.)

Several other ag-tech companies are hacking the best known natural relationship between plants and microbes. That’s the one in which bacteria provide essential nitrogen fuel for hungry plants. Inside the roots of legume plants like beans and peas, resident microbes suck nitrogen gas out of the air and convert it into a form plants can actually use. In return, plants feed those “nitrogen-fixing” bacteria with sugar.

Microbes that could do the same trick for corn, wheat, and rice could address a big problem in farming. Today, farmers feed these row crops with commercial fertilizer, which is synthesized from natural gas using massive amounts of energy.

Synthetic nitrogen fertilizer enables the eye-popping productivity of modern agriculture, where an acre of land now yields three times more corn than it did in the 1950s. It also uses about 1 percent of the entire world’s annual energy supply, and accounts for about 1 percent of all greenhouse gas emissions.

Farmers dump as much as 160 pounds of nitrogen per acre on their cornfields each year, because a lot washes away in rainstorms. That nitrogen runoff contaminates streams and rivers, causing nasty green slicks of algae that kill aquatic life. More nitrogen drifts off the fields as gas into the atmosphere, where it creates ozone pollution and accelerates global warming.

The idea of reducing the use of synthetic fertilizer by repurposing natural nitrogen-fixing bacteria is decades old. But the first wave of bacterial sprays that could be applied to fields — ”bugs in a jug” — weren’t too impressive, says farmer Jack Boyer, a retired engineer who grows corn, seed corn, soy, and cereal rye in Reinbeck, Iowa, and experiments with farming techniques. “The products that I have tried, I saw zero success,” he says. He’s had more success enriching his soil with cover crops planted in between cycles of cash crops.

But ag-tech companies are now using the tools of synthetic biology to create more effective organisms that can provide a consistent product. At the Berkeley, Calif.-based Pivot Bio, scientists began in 2011 by identifying microbes that have nitrogen-fixing genes that are currently inactive. By editing the DNA that regulates how these genes function, they figured out how to restart this dormant ability. The team then put those microbes into a product that is shelf-stable and cost-effective for farmers to spray on their fields during planting.

The resulting product, Proven, was launched for corn in 2019, promising to deliver 25 pounds of nitrogen per acre over the growing season and allowing farmers to reduce their applications of synthetic nitrogen. Nine field tests conducted last year by university partners showed an average increase of six bushels per acre when compared against fields without the boost.

This year, farmers are using Proven on hundreds of thousands of acres of corn, says Pivot Bio co-founder Karsten Temme. It sold out for the season. “We’re trying to make sure we can scale our supply chain to meet the demand, because it’s beyond our wildest expectations,” he says.

Joyn, a joint venture between Bayer and the Boston-based genetic engineering company Ginkgo Bioworks, is still in the early phases of its long-range plan: developing high-performance microbes that can be customized into a range of niche products by adding or modifying genes. Rather than genetically modifying the crops themselves, the idea is to engineer the bacteria that help them along. Joyn’s CEO, Michael Miille, envisions some that take nitrogen from the air, others that produce compounds that suppress weeds or pests, and still more that boost plant health in other ways.

Joyn is hoping to start field trials next spring, but likely won’t have a commercial product for at least four years. The dream of fully modular microbes may take a decade or more. “There’s no question that the need is there,” he says. “Ag needs innovation and new approaches.”

It’s still not clear, however, that microbes will deliver consistent cost-effective benefits on a commercial scale, and win over farmers who may be resistant to gambling on a new type of product. There’s little independent research to back up the claims made by Pivot and Indigo.

Boyer, the Iowa farmer, is open to giving it another try, as long as the price is right. “Farmers are interested in the environment too,” he says. “If you can do it — and make a living — they’re interested in doing it. "

Kat McGowan is a journalist in California who covers health, medicine, and science. Follow her on Twitter @mcgowankat.