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Study uncovers mechanism that helps fungi to colonize plant roots
Plants are constantly on guard. Their roots are equipped with molecular alarm systems that detect invading microbes and trigger immune responses. Yet beneficial soil fungi routinely enter living root cells and establish close partnerships essential for plant nutrition. Scientists have now discovered that these fungi send small RNAs into the plant that may quietly switch off selected defence systems from within.
Researchers from the Max Planck Institute of Molecular Plant Physiology and LMU Munich report in Nature Plants that symbiotic fungi deliver tiny RNA molecules into plant root cells. These molecules act like precise molecular lock-picks, guiding the plant’s own gene-silencing machinery to temporarily deactivate specific genes—including those involved in immunity. The process, known as cross-kingdom RNA interference, enables fungi to colonize roots without triggering defensive immune responses.
An ancient underground alliance
Arbuscular mycorrhiza symbiosis is a partnership between approximately 80% of land plant species—including crops like wheat and corn as well as garden vegetables and trees— and fungi belonging to a clade called Glomeromycotina. Based on fossil evidence the symbiosis emerged about 400-450 million years ago. These fungi enter plant roots and form intricate, tree-like structures called arbuscules inside root cells. Through these structures, fungi deliver mineral nutrients such as phosphorus, while plants provide carbon compounds.
While scientists have long understood this nutrient exchange, one major mystery remained: how can fungi enter living plant cells without triggering the plant’s immune system?
Engaging with the plant’s own machinery
To investigate this mystery, the research team studied the model fungus Rhizophagus irregularis colonizing roots of the legume Lotus japonicus. They focused on ARGONAUTE1 (AGO1), a plant protein that functions like molecular scissors. It binds small RNAs and is guided by them to messenger RNAs. AGO1 then destroys the messenger RNAs leading to gene silencing.
When the scientists isolated this protein from colonized roots of Lotus japonicus and analysed its cargo via small RNA sequencing, they found not only plant small RNA molecules attached to it, but fungal small RNAs as well. This suggested that fungal RNAs had crossed into plant cells and were actively directing the plant’s own gene-silencing system.
Bioinformatic analyses predicted that these fungal RNAs target plant genes involved in immune signaling and cell wall remodeling. Both normally help plants resist microbial entry. Several genes were experimentally validated to be targets and in vitro cleavage assays confirmed that fungal RNAs can guide plant AGO1 to slice corresponding plant messenger RNAs.
Direct evidence inside living roots
To confirm that cross-kingdom RNA interference occured inside the living roots, the team used a specialized reporter system developed by Arne Weiberg’s laboratory at the LMU Munich (now at University of Hamburg). The reporter was activated specifically in root cells containing fungal structures, which presented clear, real-time evidence that fungal RNAs entered plant cells and switched off genes.
To test whether these RNAs were functionally important, the researchers used a short-tandem-target-mimic (STTM) strategy. These RNA sequences act like molecular sponges that capture specific small RNAs. When four key fungal small RNAs were blocked in this way, root colonization by the fungus was significantly reduced. This demonstrated that the transferred RNAs are not accidental passengers. They actively enable the symbiosis.
Importantly, the effect was highly localized. Only cells in contact with the fungus showed the positive reporter signal. Thus, immune activity was potentially reduced in a very localised manner, allowing the plant to maintain defenses in surrounding tissues.
“It’s as if the fungus uses the plant’s own security controls to temporarily lower defenses in the exact cells it wants to enter,” explains co-first author Manisha Haag. Co-first author Dr. An‑Po Cheng adds: “What intrigues us is that fungal RNAs selectively target a small set of plant genes that potentially regulate immunity, allowing the fungus to establish symbiosis while the plant likely keeps its overall defense system intact.”
“We will now study in which way the predicted plant target genes counteract symbiosis” says director Prof. Caroline Gutjahr, one of the senior authors of the study.
Implications for sustainable agriculture
The discovery reveals a previously hidden layer of communication between plants and beneficial fungi and suggests that such molecular exchanges evolved early in the history of life on earth.
Understanding how fungi fine-tune plant immunity could help scientists develop tools to make crops cooperate more efficiently with beneficial soil organisms. This may improve nutrient uptake and reduce dependence on synthetic fertilizers.
Prof. Dr. Caroline Gutjahr
Director
Max Planck Institute of Molecular Plant Physiology
Mail: gutjahr@mpimp-golm.mpg.de
Usländer, A., Haag, M.V., Cheng, AP. et al. Cross-kingdom RNA interference promotes arbuscular mycorrhiza development. Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02247-2
https://www.mpimp-golm.mpg.de/2890487/news_publication_26244963_transferred
Co-first authors Dr. An-Po Cheng and Manisha Haag studied the legume Lotus japonicus and its relatio ...
Quelle: MPI-MP/sevens+maltry
Copyright: MPI-MP/sevens+maltry
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Co-first authors Dr. An-Po Cheng and Manisha Haag studied the legume Lotus japonicus and its relatio ...
Quelle: MPI-MP/sevens+maltry
Copyright: MPI-MP/sevens+maltry
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