Making agriculture greener, from self-fertilizing crops to more resilient seeds

Agriculture is both a victim and a culprit of climate change. Growing and producing food, fiber, and biofuels generates about one-quarter of all human-caused greenhouse-gas emissions. At the same time, yields of the world’s major food crops are projected to decline in the coming decades as the climate warms, causing droughts, heat waves, or heavier-­than-normal rains. In some areas it is already happening.

A group of MIT researchers hopes to tackle both sides of the problem.

Christopher Voigt, the Daniel I.C. Wang Professor in the Department of Biological Engineering and co-director of MIT’s Synthetic Biology Center, is leading a Climate Grand Challenges flagship project that aims to reduce emissions from agriculture, largely from fertilizer, and boost yields of major food crops.

“Our focus is on decarbonizing agriculture,” Voigt revealed. “And underlying that is biotechnology. How do we use plant and microbial engineering, and biotechnology, to chip away at carbon emissions from agriculture? That’s one piece. The other [focus of our project] is developing crops that are more resilient.”

Through six related sub-projects, the Voigt-led interdisciplinary team of MIT researchers will tackle one of the greatest challenges the world faces as the global population heads toward 10 billion. That is expected to happen by 2050, and demand for food is expected to double over the next century.

“MIT is not historically known as a leader in the agricultural research space,” team member Mary Gehring, a plant biologist at the Whitehead Institute for Biomedical Research and an associate professor of biology at MIT, said in a public presentation of the group’s project in April. “But we are a leader in many other disciplines that are crucial for facing the climate crisis, from synthetic biology to economics.”

Roughly one-third of all agriculture-­derived GHGs come from the production of nitrogen-based fertilizer, so figuring out a way to reduce those emissions became an obvious target.  

Ammonia, the main ingredient of synthetic fertilizer, is made through the Haber-Bosch process, which takes nitrogen from the air and mixes it with hydrogen at high temperatures. “The addition of nitrogen fertilizer to soils has been absolutely critical for huge gains in crop productivity,” Gehring said. “But it has come at a cost.”

“Haber-Bosch requires high temperatures and big infrastructure to do in cost-effective ways,” Voigt noted. “Synthetic nitrogen has to be made in large factories, and it doesn’t scale down.”

What’s more, a primary source of the required hydrogen is natural gas, and the fertilizer production process itself is energy intensive: it consumes as much as 2% of the world’s energy and 5% of its natural gas.

So the team plans to reduce the carbon footprint of fertilizer by genetically engineering plants and soil microbes to, in effect, make their own.

The symbiotic relationship between rhizobia, a type of soil bacteria, and some legumes may offer a blueprint for developing these “self-fertilizing” plants. Rhizobia infect legumes, which provide them a home in the form of nodules in their roots. The rhizobia return the favor by converting nitrogen in the atmosphere into ammonia that is used by the plant. As a result, the plants require far less applied nitrogen fertilizer than other staple crops.

Voigt says one of his team’s goals is to genetically engineer non-legume cereal crops and soil microbes so the crops, some of which require massive amounts of synthetic fertilizer, can also self-fertilize.

“The tools for manipulating plants have been pretty ineffective to date. But now you can introduce many genes into plants—and not just the plants, but the soil microbes associated with plants,” Voigt explains. “One teaspoon of soil can have more genes than 1,000 human genomes. The capacity for getting function into that space through genetic engineering has become extraordinary.”

The other major goal of the project – creating more resilient crops – will also rely on genetic engineering. Through one of the six sub-projects, Gehring aims to develop more vigorous crops whose offspring share their hardier traits.  

The cereal crops widely grown today aren’t able to pass on what’s known as 'hybrid vigor' – their best traits from both parents – to the next generation. But if scientists can get these crops to replicate asexually, they will be able to create copies of themselves that retain these traits in each generation of seed.

Gehring’s lab researches epigenetics – biological information that influences heritable traits but is not encoded in the DNA sequence. In her research, she is focusing on a certain gene in a plant called Arabidopsis thaliana that is linked to asexual development of the endosperm, the “food storage” part of a seed that provides starch to the embryo. If relevant interacting genes can be epigenetically tweaked, Gehring says, that work can be combined with research on asexual embryo production to achieve their goal of preserving hybrid vigor.

But some of the team’s efforts are much less complex. In her presentation, Gehring showed two photographs of bean plants. The seed that produced one plant had been coated with bacteria encased in a silk-based biopolymer to help it withstand the arid conditions where it was planted; the other seed had not. Only the seed with the coating produced a plant that yielded beans.

“Even relatively simple solutions can have a big impact,” Gehring said.

As with the other Climate Grand Challenges flagship projects, a key aim of this one is to ensure that its end products end up in the hands of people who need them most but can afford them least.

Much of the world’s depleted agricultural land is in developing countries, where lack of access to fertilizer and crop technology has led to declining crop yields and increasing food insecurity.

“They haven’t had access to synthetic fertilizers,” Voigt explains. “The yield growth in some areas hasn’t changed in the past 50 years.”