Bean plants have an ancient trick that could transform farming

For thousands of years, farmers have used beans not just for food but also for what they leave behind. The ancient Greeks noticed something strange about bean plants – the soil seemed richer after the beans were pulled from it. They didn’t know exactly why, but now we do.

Beans, along with some other plants, have a built-in trick. Their roots host bacteria that can take nitrogen from the air and turn it into a form plants can actually use.

Most plants can’t do this. They rely on whatever nitrogen is already in the soil, which often isn’t enough. But beans have bacteria that do the heavy lifting. And here’s the big idea: What if all crops could do what beans do?

Nitrogen fuels all life

Every living thing needs nitrogen. It’s in our DNA, proteins, and pretty much every cell in our body. Plants need it to grow. But the type of nitrogen that fills the air – dinitrogen – is basically locked up. It’s got one of the strongest chemical bonds in nature, and almost nothing can break it.

Early life on Earth struggled because of this. Billions of years ago, the only natural ways to break dinitrogen were lightning strikes or meteor impacts. That wasn’t enough. But eventually, some microbes figured it out.

They built an enzyme called nitrogenase, made of iron and molybdenum, that could break dinitrogen into ammonia – a usable form of nitrogen.

This breakthrough changed everything. Life spread and evolved. But plants, animals, and fungi never figured out how to make nitrogenase themselves. Instead, many plants – especially beans and their relatives – formed partnerships with the bacteria that could.

Roots strike bacterial deals

When these plants grow, they don’t start off with nitrogen-fixing bacteria in their roots. They have to find them. The roots send out chemical signals, kind of like a “help wanted” ad. Certain bacteria, like Rhizobium and Frankia, respond by sending back a chemical password.

If the password matches, the plant lets them in. A root hair curls around the bacteria, and they sneak inside.

This sets off a chain reaction inside the root, leading to the formation of little nodules. Inside these nodules, bacteria go to work turning dinitrogen into ammonia, feeding the plant in return for shelter and sugar. It’s a win-win – but it doesn’t happen in all plants.

The puzzle of bean nodules

For years, scientists have gone back and forth on a major question: Did the ability to form nitrogen-fixing nodules evolve once, or did it pop up multiple times in different plant groups?

It’s a tricky problem. Only about 8,000 out of 30,000 species in the nitrogen-fixing group actually make nodules. So did the others lose the ability over time? Or did nodules appear separately, through different genetic paths?

Until recently, no one knew for sure. Now, researchers from multiple institutions, including the Florida Museum of Natural History, have found something important.

They studied the genes that allow plants to recognize nitrogen-fixing bacteria and found these genes had evolved at least three separate times.

“That was probably followed by a series of separate origins, as well as recurring loss events throughout this group,” said study co-author Douglas Soltis, a distinguished professor at the Florida Museum. “This study shows, for the first time, that there are other roads to Rome. There are multiple ways to get to nitrogen-fixing symbiosis.”

Bean plants inspire greener farming

Humans already figured out how to break dinitrogen in the 20th century. That’s what fertilizer is. But industrial nitrogen fixation is expensive and pollutes the environment. We’ve dumped tons of it into the soil to grow more crops for a growing population.

If we could engineer corn, wheat, or rice to form nodules like beans do, farmers could use way less fertilizer. It would save money and reduce damage to the environment.

To do that, scientists need to know how nodules work, where the genes came from, and whether there’s one universal method or several – knowledge that could reshape farming.

Password sensors from ancient genes

In this new study, led by Christina Finegan during her doctoral work at the University of Florida, the team looked at the genes plants use to recognize bacterial partners – basically, the “password sensors.”

These genes didn’t appear out of nowhere. They evolved from genes that used to recognize fungi called mycorrhizae, which help most plants absorb nutrients. At some point, ancient plants duplicated these genes, and some of the copies mutated and took on new roles.

“The machinery was kind of just sitting there, and that made a lot of room for evolution to play with and repurpose it,” said Finegan.

Different plants, different genes

Using a massive plant family tree built from DNA of over 12,000 species, the team examined the gene duplications in 28 species – some with nodules, some without. They found the relevant genes had been duplicated nine times. In three of those cases, the duplicates had clearly been repurposed for nodulation.

In the bean plant family, for example, species without these duplications didn’t make nodules. That supports the idea that nodules evolved more than once.

But there was a twist. Two nodulating species – the common alder and the swamp she-oak – didn’t show any gene duplications. These trees form partnerships with Frankia bacteria and likely use a totally different genetic system.

“It’s hard to get down to the right part of the root to study the nodule,” said Pamela Soltis, contributing author of the study.

Most research has focused on small plants that grow easily in labs. The diversity in how different plants form nodules suggests there’s more than one genetic route to the same result.

“By taking this broad evolutionary perspective, we were able to take the power of biodiversity and find evidence of processes that you can’t find if you’re just sticking with model organisms,” said Soltis.

From bean plants to biotech

For crop engineering, the results offer both hope and a challenge. If nodules evolved only once, researchers might only need to tweak a single genetic pathway. If they evolved multiple times, the task might be harder – but it also means there’s more than one way to make it happen.

“One good thing about convergent evolution is you can narrow down on what’s truly needed because you’ve arrived at the same thing through independent pathways,” Finegan said.

The beans may have known the secret all along. Now it’s up to science to figure out how to use it to help farming.

The full study was published in the journal Proceedings of the National Academy of Sciences.

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