Resolving temporal immune responses of Arabidopsis roots to infection by Fusarium oxysporum at the single-cell level

Pathogen-caused diseases represent one of the biggest problems in agriculture.

A detailed mechanistic understanding of plant defenses against pathogenic invasion and disease progression is therefore a vital research topic, forming the foundation for the creation of more resistant crop varieties.

However, at present, most studies aimed at this utilize ‘omics’ approaches or mutant analyses, which lack resolution and only allow limited understanding of plant-pathogen interactions at the single-cell level. Thus, our current models of plant-pathogen interaction do not include strictly local or temporal responses.

The aim of this proposal is to address this with a pathosystem consisting of the model plant Arabidopsis thaliana and strains of Fusarium oxysporum, a destructive fungal pathogen of several food crops.

A unique near-native imaging setup, enabling the simultaneous study of growth and infection of plant and fungus with single-cell resolution, will be used.

The work in this proposal will probe the responses of individual plant cells to both pathogenic and beneficial F. oxysporum strains, in a native tissue context from the onset of invasion to full disease development.

This will generate novel insights into cellular mechanisms employed by plants to fight off pathogenic invaders, while accommodating beneficial endophytes.

By using a novel in vivo cell-labeling technique, exploiting the fungal avirulence effector secretion system, a single-cell transcriptome atlas exclusively of cells undergoing acute colonization will be generated.

Moreover, as root barriers represent a physical hindrance for pathogen invasion, mutants affected in physical defenses will be tested.

Combined, this proposal will expand our current models of immune responses to include specific cells, regions or tissues, and temporal aspects with high resolution.

Such knowledge is important to develop next-generation agricultural tools and will be applicable to combat current and arising diseases.