How do plants produce their own nitrogen fertilizer?

A recent study has shed light on how certain plants evolved the ability to produce their own nitrogen through symbiotic relationships with bacteria. This discovery is crucial for efforts to develop crops that can fix nitrogen, reducing reliance on fertilizers. 

Multiple genetic pathways 

According to lead author Heather Rose Kates, who conducted the research while at the Florida Museum of Natural History, this understanding could enhance crop improvement by considering multiple genetic pathways rather than focusing on a single model species.

“Breeding and crop improvement efforts often focus on a single model species, which can overlook the evolutionary context of traits,” she said. Instead of focusing solely on one method, this study indicates multiple genetic approaches could be effective. 

“Only looking at what you could think of as one version of the trait could limit the effectiveness of engineering that trait in other plants.”

Nitrogen-fixing microbes

Nitrogen, essential for all life on Earth, is challenging to obtain due to stiff competition in natural environments despite its abundance in the atmosphere. 

Up to 78% of the air we breathe consists of nitrogen, but in a molecular form that most living organisms cannot use directly. Diazotrophs are the only microbes capable of fixing atmospheric nitrogen.

About 17,000 plant species form mutualistic relationships with diazotrophs. These microbes infect plant roots, prompting the formation of knob-like structures called nodules. Within these nodules, bacteria receive sugar from the plant and, in return, provide usable nitrogen.

This mutualistic relationship is primarily found in a group of closely related plants called the nitrogen-fixing clade, though even within this group, the trait is inconsistently present. 

Forming root nodules 

Most nitrogen-fixing plants are legumes, such as soybeans, peanuts, and clover. Non-legume nitrogen-fixers include species from the birch family, rose family, and some gourd relatives.

Creating nodules is genetically complex, leading researchers to theorize it evolved once in this plant group. This suggests a single genetic switch might enable nodulation in species that currently lack this trait, including many agricultural crops. 

“When a trait involves a lot of genes and also has a high cost to the plant in terms of energy, which we know forming root nodules does, we expect there to be a strong selective pressure against evolving that trait. So, in that context, a single origin hypothesis makes sense,” Kates explained.

Nodulating plants and their relatives

The scientists tested this hypothesis by reconstructing the evolutionary history of nodulating plants and their relatives using genetic data from nearly 15,000 species. They created the largest tree of life for this group. The sheer volume of data required them to develop new organizational methods. 

“We had basically two years to assemble 15,000 tissue samples from the nitrogen-fixing clade, sequence them and build a tree,” said co-author Robert Guralnick, curator of biodiversity informatics at the Florida Museum.

Many specimens were old and had degraded DNA, but the team’s extraction and sequencing methods addressed these issues. “We were quite surprised about the generally high quality and quantity of recovery and usable genetic data from our samples,” noted Guralnick.

Evolution of nitrogen fixation

The results suggest nodulation evolved in two steps. First, the ancestor of the group developed a basic genetic toolkit for producing nodules, passing it on to descendants. 

However, additional genetic instructions were needed to activate nodulation, which evolved independently at least 16 times. Some species also lost the ability to nodulate on 10 separate occasions.

The findings indicate nodulation isn’t controlled by a single genetic switch but by a complex circuit breaker requiring multiple switches. The researchers identified and sequenced many genes involved in nodulation, and future research will focus on their functions and traits.

Genetics of nitrogen fixation

“The overall goal is to use what we learned from these evolutionary studies to help us understand the underlying genetics and processes involved in nitrogen fixing symbiosis, and then use that information for engineering,” said co-author Pam Soltis, a curator at the Florida Museum.

Most commercial crops, like wheat and rice, cannot form nodules and rely on nitrogen fertilizers. Many bioengineering studies focus on legumes, but co-author Doug Soltis suggests this might not be the best approach. 

“Our phylogenetic tree suggests you might want to look at other models. Nitrogen fixation might have evolved differently in legumes than it did in the rose family or birch family, so there may be different roadmaps,” he concluded.

The study was published in the journal Nature Communications.

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