Researchers Use a New Two-Dimensional Analysis to Build a Map of Gene Expression in Plant-Fungi Interactions

The Science

In most plants, fungi are found in close association (symbiosis) with their roots. These fungi, called mycorrhizae, help plants obtain water and other nutrients. Meanwhile, plants provide the fungi with carbon nutrients generated through photosynthesis. This symbiosis occurs in microscopic structures called arbuscules that help transfer nutrients between the plants and the fungi. To better understand gene expression—how genes tell cells what to do—in plant/mycorrhizae symbioses, researchers analyzed roots of a model plant colonized by fungi. They used a combination of advanced techniques to measure gene activity in tens of thousands of individual cells and to visualize gene expression in two-dimensional sections of roots. The microscopic resolution of the analysis allowed the researchers to generate a spatial map of gene expression in both the root and the fungal cells.

The Impact

Symbioses between arbuscular mycorrhizae and plants occur in most ecosystems. These symbioses are important for agriculture, as the fungi provide critical nutrients to the plants. However, this interaction is restricted to a few root cells, making it difficult to study. This study’s spatial and single-cell examination of plant-fungal interactions sheds new light on this process. Understanding both sides of this symbiosis at the molecular level may enable researchers to make targeted improvements to the way plants and mycorrhizae interact. This could be applied to bioenergy crops to increase their productivity and their ability to store carbon.

Summary

The symbiotic interaction of plants with arbuscular mycorrhizal (AM) fungi is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant–fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions.

Researchers at the Joint Genome Institute (JGI), a Department of Energy (DOE) user facility, and the DOE Joint Bioenergy Institute used single-nucleus and spatial RNA sequencing to explore both Medicago truncatula and Rhizophagus irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated, spatially registered single-cell maps revealed infected and uninfected plant root cell types. The researchers observed that cortex cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi. This indicates dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. This study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.

Funding

This study was performed at the Department of Energy’s Joint BioEnergy Institute and Joint Genome Institute and was supported by the DOE Office of Science, Biological and Environmental Research Program. This study was also supported by a Laboratory Directed Research and Development award at Lawrence Berkeley National Laboratory and a DOE Early Career Research Program. Two of the researchers were funded by the Novo Nordisk Foundation.