Industrial farming practices often deplete the soil of important nutrients and minerals, leaving farmers to rely on artificial fertilizers to support plant growth. In fact, fertilizer use has more than quadrupled since the 1960s, but this comes with serious consequences. Fertilizer production consumes massive amounts of energy, and its use pollutes the water, air, and land.
Plant biologists at the Salk Institute are proposing a new solution to help kick this unsustainable fertilizer habit.
In a new study, the researchers identified a key molecule produced by plant roots, a small peptide called CLE16, that encourages plants and beneficial soil fungi to interact with each other. They say boosting this symbiotic relationship, in which the fungi provide mineral nutrients to the plants through CLE16 supplementation, could be a more natural and sustainable way to encourage crop growth without the use of harmful artificial fertilizers.
The findings were published in The Proceedings of the National Academy of Sciences on April 18, 2025.
“Many plants evolved to engage in symbiotic relationships with other species, but industrial breeding techniques have dampened many symbiosis traits in our modern-day crops and cemented their dependence on chemical fertilizers,” says senior author Lena Mueller, an assistant professor at Salk. “By restoring the natural symbiosis between plant roots and fungi, we could help crops get the nutrients they need without the use of harmful fertilizers.”
In this mutually beneficial relationship, soil-borne arbuscular mycorrhizal fungi supply plants with water and phosphorus, which the plants accept in exchange for carbon molecules. These exchanges occur by specialized symbiotic fungal tendrils, called arbuscules, burying themselves into plant root cells. Around 80% of plants can trade resources with fungi in this way. However, the traits that support this symbiosis have been weakened over centuries of agricultural plant breeding that prioritized creating crops with the biggest yields.
Salk scientists say new crop varieties could be bred to strengthen these traits again — an opportunity they intend to explore through the Institute’s Harnessing Plants Initiative.
To begin discovering and strengthening these traits, Mueller’s lab started by growing a species of arbuscular mycorrhizal fungus together with Medicago truncatula, a small Mediterranean legume. Once the two had formed a symbiotic relationship, the researchers looked to see what genes were supporting this interaction.
The legumes had started to express large amounts of a small signaling molecule called CLE16 — a member of the CLE family of peptides. These small signaling molecules are present in many plant species yet have been relatively understudied. Until CLE16, the only plant CLE peptides scientists had studied were working against symbiosis.
“We found the first plant CLE peptide to actually favor and promote symbiosis,” says first author Sagar Bashyal, a graduate student in Mueller’s lab. “It’s really exciting from a scientific perspective to get such a surprising new insight into these peptides. It’s a huge step toward achieving sustainable plant-fungi relationships in the field.”
To confirm that CLE16 was promoting the symbiotic relationship, Bashyal added excess CLE16 to the soil to see what would happen. The extra dose of CLE16 caused the fungal arbuscules to become more robust and live longer, ultimately increasing the abundance of these nutrient-trading structures in the roots. The result was a self-amplifying pro-symbiosis signal: The more the beneficial fungus expanded inside the roots, the more CLE16 was produced by the plant, which then promoted even more fungal colonization.
The team then did a series of experiments to understand how CLE16 was encouraging this interaction between plants and beneficial fungi. Their findings revealed that CLE16 promotes the symbiosis via the signaling protein CORYNE (CRN), a component of the CLAVATA receptor complex known for its roles in plant responses to the environment.
As a plant becomes stressed, it enters a heightened immune state to protect itself from any further threats. However, this also inadvertently makes the plant less receptive to surrounding fungi. Mueller predicts that when CLE16 binds to the CRN-CLAVATA receptor complex, this reduces the plants’ stress levels and immune reactivity, allowing the beneficial fungus to enter the plant roots and begin the nutrient exchange.
Importantly, Mueller’s team showed that many arbuscular mycorrhizal fungi also produce their own CLE16-like peptides, which also promoted symbiosis when added to the soil. The researchers think that these fungal peptides imitate the plants’ own CLE16 peptides, thus enabling the beneficial fungus to amplify symbiosis by binding to the same plant CRN-CLAVATA receptor complexes.
With validation that both plant CLE16 and fungal CLE16-like peptide supplementation improved symbiosis, a similar supplementation on farmland may be the solution to kick-starting the growth of fungal networks that benefit crops year after year.
Future work will validate whether CLE16 peptides or fungal CLE16-like peptide mimics also promote symbiosis in important crops, like soy, corn, or wheat. If they do, harnessing these molecules to replace unsustainable, polluting chemical fertilizers with beneficial fungi will begin.
“Beyond acting as a biological fertilizer, arbuscular mycorrhizal fungi also add a layer of natural protection to plants that could help us reduce pesticide use, too,” says Mueller. “If we can leverage beneficial fungi and other microbes to help plants establish these symbiotic relationships, we can make our crops, fields, and soils more sustainable and healthier in the long run.”
The work was supported by start-up funds from the University of Miami and the Hess Foundation, as well as the United States Department of Agriculture’s National Institute of Food and Agriculture (2022-67013-42820).
