DECODING THE INTERNAL AND EXTERNAL DRIVERS OF PLANT DEFENCE MEMORY

Details

BACKGROUND

Plants can increase their defensive capacity after recovering from disease. This stress memory can be achieved through both internal and external strategies (1). Internal stress memory is encoded by epigenetic modifications within the plant genome, which keep defence genes in a “primed” state after the initial stress has passed (2). Plants can also develop external stress memory by altering their root exudation chemistry, which selects for a disease-suppressive soil microbiome (3).

Although both strategies contribute to long-term disease suppression, their relative importance and reciprocal interactions remain largely unknown (4). This PhD position is funded by the ERC-Advanced Grant ‘PlantMemo’ (PI: Prof Jurriaan Ton; 5) and will be part of an interdisciplinary team investigating plant defence memory across molecular, microbial, and ecological scales. By addressing the objectives below, the PhD student will investigate how internal and external defence memory interact and contribute to long-lasting disease suppression in the short-lived annual Arabidopsis and the longer-living perennial tomato:

OBJECTIVE-1: CONTRIBUTIONS OF INTERNAL AND EXTERNAL DEFENCE

MEMORY

To determine the contributions of internal and external defence memory to long- lasting disease suppression, you will employ soil sterilisation techniques (e.g. γ-irradiation), which remove the microbial (external) component and allow you to attribute the remaining disease suppression to the epigenetic (internal) component.

Subsequent ‘dilution-to-stimulation’ experiments with microbial extracts from conditioned (disease-suppressive) soils, combined with metataxonomic and metagenomic profiling, will enable you to characterise the microbial drivers of external defence memory.

OBJECTIVE-2: IMPACTS OF GENETIC AND EPIGENETIC VARIATION ON

EXTERNAL STRESS MEMORY

You will investigate how plant genotype and epigenotype influence the capacity of the plant microbiome to store defence memory. By taking advantage of existing GWAS populations and epigenetic recombinant inbred lines (epiRILs) of Arabidopsis and tomato, you will identify (epi)genetic loci that shape disease-suppressive soil communities driving external defence memory.

OBJECTIVE-3: EPIGENETIC REGULATION OF ROOT EXUDATION CHEMISTRY

Using a customised hydroponic growth system and epigenomic datasets generated by the PlantMemo project, you will work alongside other team members to examine how stress-inducible epigenetic changes at biosynthetic genes alter root exudation chemistry. By linking stress-induced changes in DNA methylation and chromatin accessibility to shifts in the root transcriptome, exudome, and microbial communities, you will determine how internal epigenetic memory interacts with external microbial memory.

TRAINING AND SKILLS

This PhD offers advanced training in plant–microbe interaction assays, microbiome analysis, and metabolite profiling. You will gain experience in plant disease phenotyping, soil microbiome profiling (amplicon/metagenomic sequencing), and high-resolution mass spectrometry analysis of root exudates. The project also provides opportunities to develop computational data analysis skills.

CANDIDATE PROFILE

We seek a highly motivated student with a degree in plant biology or microbiology and a keen interest in chemical soil ecology. Experience with bioinformatics or programming (e.g. R/Python) is desirable. We welcome applicants from diverse backgrounds who enjoy combining ‘wet-lab’ experiments with computational approaches to uncover how plants integrate epigenetic stress responses with microbial mechanisms to adapt to disease stress.

Please apply for this project using this link: https://www.sheffield.ac.uk/postgraduate/phd/apply/applying