Breakthrough imaging and genomic mapping in rice roots show that the vital structures of nutrient exchange in plant-fungi interactions are far more dynamic and diverse than previously believed – challenging 50 years of agricultural assumptions.
Researchers at the Crop Science Centre (CSC), part of the Department of Plant Sciences at the University of Cambridge, have unveiled a new level of complexity in one of nature’s most important relationships: the symbiosis between plants and arbuscular mycorrhizal (AM) fungi.
By observing rice roots at sub-cellular resolution, they found that arbuscules – the microscopic fungal structures responsible for nutrient transfer in this partnership – are not identical units, but vary wildly in their lifespan, gene expression, and capacity to deliver nutrients.
Using pioneering imaging and spatial transcriptomics technologies, the team captured the growth and collapse of arbuscules over their entire lifespans for the first time and have provided the highest-resolution view yet of plant and fungal gene expression during symbiosis.
This work redefines our understanding of AM symbiosis and will help guide strategies to improve nutrient-use efficiency in crops like rice and reduce fertiliser use.
Professor Uta Paszkowski, CSC Director and Head of the Cereal Symbiosis group said: “These are exciting times where we can finally follow the dynamics of arbuscule development from birth to death and also capture the transcriptional activities of both plant and fungal partners at tissue level - it is as if a dream has come true.”
The findings are published in two studies from CSC’s Cereal symbiosis group in the journals Nature Communications and The Plant Cell.
Unmasking arbuscule individuality
At the heart of AM symbiosis – the mutually beneficial partnership between AM fungi and most land plants – are the arbuscules. These tree-like structures which form inside plant root cells are where the fungi deliver nutrients such as phosphate foraged from the soil to the plant, in exchange for sugars and lipids.
Until now understanding arbuscule activity over time – the development, collapse and all-important nutrient exchange – was elusive. Because arbuscules develop inside plant roots hidden in the soil, studying them generally meant uprooting and killing the fungi and plant to provide a snapshot in time of the number of arbuscules present.
Central to this latest research is the innovation of a new non-invasive imaging tool called AMSlide, which allowed the team to track individual arbuscules in rice roots in unprecedented resolution from ‘birth to death’. This showed that while most arbuscules last only a few days, their developmental trajectories and lifespans are highly variable ranging from less than 24 hours to more than 3 days.
Dr Jen McGaley, Postdoctoral Research Associate at the University of Cambridge and lead-author of the Nature Communications study, said: “The most significant finding is that the arbuscules are not identical ‘units’ of nutrient exchange. They are highly dynamic and environmentally responsive. Just because an arbuscule is present, you cannot tell how long it will be there or what it is doing in terms of nutrient delivery.”
Mapping gene expression uncovers hidden functional diversity
A parallel study from the Paszkowski lab published in The Plant Cell supports these findings. The team created a high-resolution map showing plant and fungal gene activity across space and time during the symbiotic relationship between rice roots and beneficial fungi.
By combining spatial transcriptomics to track individual transcripts of both species with a method called TRAP-seq to track plant transcripts being actively translated, they saw significant changes in how genes are expressed and used to build proteins across various cell types and fungal structures. These results reveal surprising variations even between similar arbuscules, uncovering a much more precise level of biological control than previously thought.
One striking discovery was that arbuscules can look similar under a microscope yet differ significantly in how they exchange nutrients. This suggests a hidden layer of control underpinning functional diversity at the level of individual cells. They also observed broad shifts in the markers that define a cell’s identity during colonization, illustrating how profoundly this symbiosis reshapes the root's cellular state.
Dr Gabriel Ferreras-Garrucho, co-lead author of The Plant Cell paper said: “We are motivated by the idea that one of the most important plant-microbe interactions is controlled by extremely local, fast-changing decisions inside single root cells. These new tools let us uncover hidden layers of regulation that were previously inaccessible.”
Fine-tuning nutrient exchange
Together these studies reveal a multi-tiered system governing how plants and fungi trade nutrients. This layered regulation ensures the process is both precisely timed and highly responsive to the environment.
By studying a specific phosphate-transporting protein in rice called PT11, the researchers discovered that the presence of an arbuscule does not guarantee its function. Advanced imaging shows that even when arbuscules look identical in shape, their ability to transport nutrients varies significantly.
Crucially, this variation depends on how much phosphate the plant needs:
- In nutrient-poor soil, arbuscules are dominated by the PT11 protein, indicating a high capacity for nutrient uptake.
- In nutrient-rich conditions, such as when high levels of fertilizer are used, the abundance of PT11 is suppressed, reducing the capacity for nutrient exchange.
This fine-tuning mechanism means the plant can turn the activity of its nutrient-exchange structures up or down as needed, rather than them simply being ‘on’ or ‘off’.
These findings also offer some explanation for the commonly observed phenomenon in which the amount of AM colonisation in a root does not correlate with the nutritional benefits gained by the plant.
Significance for sustainable agriculture
The discovery that arbuscule presence does not guarantee nutrient transfer has profound implications for how we assess the success of AM symbioses in both the lab and the field. Traditionally, the amount of colonisation in a root was used as a direct metric for the benefit a plant received. This research suggests that such simple quantification is insufficient; it indicates that the functional state of the arbuscules is likely to be what truly determines the outcome for the plant.
By understanding the abiotic and biotic factors – such as fertiliser regimes or microbial communities – that control arbuscule plasticity, scientists can develop more targeted strategies to improve nutrient-use efficiency in crops like rice. This knowledge is critical for reducing dependence on chemical fertilisers while maintaining high yields in a sustainable manner.
A new benchmark in symbiosis research
Together, these studies set a new benchmark for dissecting complex plant-microbe interactions. They reveal a symbiosis that is extremely local, fast-changing, and nuanced, governed by decisions made inside single root cells. The revelation of arbuscule individuality and functional plasticity changes the fundamental narrative of AM fungi from a uniform supply line to a highly regulated, tuneable dialogue between two decentralised organisms.
Ultimately, this research moves us closer to decoding the molecular language that has allowed this partnership to shape life on land for over 400 million years.
A beautiful microbial world beneath our feet
Dr McGaley said: “Aside from the scientific interest, the arbuscules are strikingly beautiful, so to finally capture and share their intricate development is a privilege.”
“Beyond the field, I hope that revealing the behaviours and beauty of AM fungi will engage more people with the organisms beneath their feet. Many people only have their eyes opened to the amazing lives of plants when seeing their growth sped up to human-perceptible timeframes – it is my hope that this research will do the same for fungi. The images and videos produced will be incorporated into my outreach work to help spread awareness and consideration of fungi in people's everyday lives.”
References:
- Chancellor T., Ferreras -Garrucho G., et al. ‘Spatiotemporal regulation of arbuscular mycorrhizal symbiosis at cellular resolution.’ The Plant Cell (2026), DOI: 10.1101/2025.10.31.685811
- McGaley, J., Orvošová, M., Schneider, B. et al. 'Symbiotic phosphate transporter dynamics in rice expose functional plasticity of the arbuscules.' Nature Communications (2026). DOI: 10.1038/s41467-026-71496-8
Image: Confocal fluorescence microscope image of arbuscular mycorrhizal fungi inside rice roots. The image is coloured by depth in the root to reveal the 3D structure. Credit: Jen McGaley.