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Scientists discover genetic off-switch in legume plants that limits ability to source nutrients


A genetic “off switch” that shuts down the process in which legume plants convert atmospheric nitrogen into nutrients has been identified for the first time. It could be key to understanding how to increase the crop’s capacity to convert nitrogen from the air and improve soil quality. The results are published in Nature.

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Legumes like beans, peas and lentils are unique among crops for their ability to interact with soil bacteria to convert or “fix” nitrogen into a usable form of nutrients. However, this energy-intensive biological process is reduced when nitrogen is already abundant in the soil either through natural processes or through the application of synthetic fertiliser.

Increasing the biological ability of legumes to fix nitrogen could help increase crop growth and yield while also reducing the need for synthetic fertilisers, which contribute to agriculture’s environmental footprint.

Now a team from La Trobe University (Australia), Aarhus University (Denmark), the Universidad Politécnica de Madrid (Spain) and the ESRF, as part of the international Enabling Nutrient Symbioses in Agriculture (ENSA) project, has discovered the genetic regulator that turns off nitrogen fixation when soil nitrate levels are high. This allowed scientists to remove the gene in model legumes, ensuring they continued to fix nitrogen regardless of the soil environment.

“From an agricultural perspective, continued nitrogen fixation could be a beneficial trait that increases nitrogen availability, both for the legume and for future crops that rely on the nitrogen left behind in the soil after legumes are grown,” says Dugald Reid, lead author and researcher with ENSA.

“This helps lay the foundations for future research that provides new ways for us to manage our farming systems to reduce nitrogen fertiliser use, increase farm incomes and reduce the impact of nitrogen fertiliser use on the environment.”

Fixation Under Nitrate

The team discovered the regulator known as “Fixation Under Nitrate” (FUN) after screening 150,000 individual legume plants in which genes had been knocked out to identify how plants control the switch from nitrogen fixation to soil nitrogen uptake.

FUN, which is a type of gene known as a transcription factor and controls the levels of other genes, was found to be present in legumes regardless of whether it was active or inactive, and irrespective of nitrogen levels.

Zinc is key

The team then used a combination of techniques, including X-ray fluorescence on ID21 at the ESRF, where they tracked the distribution of zinc in the root nodules of Lotus plants in low-nitrate soils and in nitrate-rich soils.

This led to the secondary discovery that zinc levels play a role in triggering FUN to become active and shut down nitrogen fixation.

“We found that changing soil nitrogen alters the levels of zinc in the plant. Zinc had not previously been linked to the regulation of nitrogen fixation, but our study found that a change in zinc levels in turn activates FUN, which then controls a large number of genes that shut down nitrogen fixation,” said Kasper Andersen, co-author and ENSA researcher.

“Removing FUN therefore creates a condition in which nitrogen fixation is no longer shut down by the plant.”

The researchers are now investigating how common legume crops such as soybean and cowpea perform when they lose FUN activity.

The ENSA project is currently funded by Bill & Melinda Gates Agricultural Innovations (Gates Ag One), a non-profit organisation that invests in breakthrough agricultural research to meet the urgent and neglected needs of smallholder farmers in sub-Saharan Africa and South Asia.


Lin, J. et al, Nature, 26 June 2024. DOI: 10.1038/s41586-024-07607-6

Top image: X-ray fluorescence map of Zinc in the Lotus root nodule.