Ancient trait may hold key to agriculture’s future

By Jenna Gallegos

May 20, 2019

The ancient history of modern crops reveals a surprising story about their evolutionary relationship with fungi and bacteria. Unpacking that story could be the key to unlocking our dependence on synthetic fertilizers.

The development of nitrogen fertilizers in the early 20thcentury revolutionized agriculture, increasing yields of cereal crops like corn by roughly 200 percent and allowing us to feed a growing population of some 7.7 billion people.

But fertilizer use comes with significant environmental and economic costs. Much of the nitrogen applied to farms never makes it into crops, but instead leaches through the soil. Some of this excess nitrogen ends up in water ways, causing dead zones.

And high transportation costs make fertilizers prohibitively expensive, especially in many African nations. This has prevented farmers in remote regions of poorer countries from enjoying the same yield increases that transformed agriculture in the developed world.

In response, the Bill & Melinda Gates Foundation is funding a collaborative project — Engineering Nitrogen Symbiosis for Africa (ENSA) — with a simple vision: more food for smallholder farmers, without fertilizers.

So why do plants need fertilizer in the first place? Most of the nitrogen in the soil is not in a form that can be taken up by plants. But some plants have evolved their way around this problem. Legumes, like peas, beans and alfalfa, form nodules in their roots that house bacteria. These bacteria convert the nitrogen in the soil into a digestible form for the plant in exchange for other nutrients. This “symbiotic” relationship, called nitrogen fixation, is what ENSA hopes to recreate in all sorts of plants, especially cereal grains.

Rather than reinventing the nitrogen-fixing wheel, the ENSA team decided to do a deep dive into the genetics of plants that do and don’t form nodules to learn more about how the trait evolved.

They discovered that nitrogen symbiosis developed from an even more ancient plant partnership. Some 450 million years ago, before plants colonized land, they began sharing nutrients with fungi. Plants rely on this relationship, called mycorrhizal symbiosis, to extract phosphorous from their environment.

By looking at plant genes, the ENSA team determined that nitrogen symbiosis evolved from mycorrhizal symbiosis as early as 100 million years ago.

But many of the plants that don’t form nodules do have symbiotic relationships with their fungal friends. So why did these plants miss the evolutionary boat on nitrogen?

The ENSA team suggests they didn’t. Some more modern woody species, such as apples and walnuts, actually evolved from nitrogen-fixers but have since lost the ability to form nodules. To break up with their nitrogen-fixing bacterial partners, these pre-agricultural species really only had to lose three genes.

It’s not obvious why a plant would ever want to give up such a mutually beneficial relationship. There may not have been enough evolutionary pressure to keep nitrogen fixation. In many natural environments, water, phosphorous and other nutrients run out before nitrogen. And all a plant really wants to do is grow just enough to spread its seed.

But on farms, water and nutrients are controlled so that plants can reach their fullest potential. And crop plants are selectively bred in soil containing fertilizers. That means most plants shed their nodule-forming abilities and invested energy into other things, like producing big juicy fruits or growing tall enough to escape the shade.

Discovering that nodule-forming abilities were present in the ancient ancestors of most crops changes how we think about nitrogen fixation and the genes involved. Reintroducing the key nodule-forming genes lost to evolutionary history could be a strong first step towards engineering nitrogen fixation in grains and other crops.

It also means that many more of the genes necessary for N-fixation may already be present in cereals. With modern approaches such as genetic engineering and synthetic biology, re-awakening these ancient genes is a real possibility.

ENSA isn’t the only group working on these challenges. Researchers all over the world are pushing the bar on N-fixing cereals, from discovering wild species that have more of the genetic pathways intact to engineering soil bacteria to become better allies in N-fixing.

Nitrogen fertilizers revolutionized agriculture. Now it’s time to find new ways to break our dependency on them and unlock even greater yields. Genetic archeology from projects like ENSA bring us that much closer to determining whether the ancient ancestors of our domesticated crops hold the key.