Award details

Quantifying how host genotype and microbiome composition combine to influence susceptibility to plant disease.

Reference	BB/W020378/1
Principal Investigator / Supervisor	Dr Stephen Cavers
Co-Investigators / Co-Supervisors	Dr Annika Perry
Institution	UK Centre for Ecology and Hydrology
Department	Biodiversity (Penicuik)
Funding type	Research
Value (£)	37,025
Status	Current
Type	Research Grant
Start date	03/04/2023
End date	02/04/2026
Duration	36 months

Abstract

A key challenge in plant research is to understand how interactions between a plant host and its microbiome affect plant disease incidence and severity. These interactions are driven by genetic variation in the host, environmental conditions, and the dynamics of the microbial community, including the pathogens. Dissecting the relative importance of these components, ideally under controlled experimental conditions, can provide a major advance in understanding plant disease. We propose to use an integrative microbiome approach and focus on Dothistroma septosporum, the pathogen causing Dothistroma needle blight (DNB) in pine trees. However, the methods are applicable to diverse plant host-pathogen systems. DNB is a disease that detrimentally affects >100 economically and environmentally important pine species worldwide. By quantifying a host tree's genetic variation, disease incidence and their microbiome in concert, this project will enable a step change in our understanding of the host-microbiome-pathogen interaction. Our hypothesis is that, in a given environment, host genotype drives foliar microbiome composition and interactions to alter host susceptibility to DNB. To test this hypothesis we will 1) quantify the extent to which host genetic variation explains variation in microbial community composition and susceptibility to DNB, (2) evaluate temporal variation in microbiome composition and function during D. septosporum infection and (3) predict which microbiome community members interact with D. septosporum and which impact on host susceptibility to DNB. We will integrate existing host genotype data from our established common environment progeny-provenance trial for Scots pine with new amplicon and RNA sequencing data. We will apply association genetic analysis and Bayesian network modelling. Our project addresses key challenges within the BBSRC integrative microbiome research priority.

Summary

A key challenge in plant disease research is to understand how the interactions between the plant host and its associated microbiome (the bacteria, fungi and viruses that exist within/on the plant) affect plant disease incidence and severity. These interactions are affected by genetic variation in the host, environmental conditions, and the variety microbes in the host's microbiome. For this project we focus on the pine tree disease Dothistroma needle blight (DNB), that detrimentally affects the growth and life span of pine species worldwide. As trees will also play a critical role in combatting our current biodiversity and climate crises, an understanding of the factors governing the arrival and spread of tree diseases, and how they impact tree health, are important policy strategies. Innovative research on tree health, as proposed in our project, will deliver to these strategies. DNB is caused by Dothistroma septosporum, a UK listed quarantine fungus that is now found worldwide, where it affects more than 100 tree species including the commercial timber species Scots pine, Corsican pine and Lodgepole pine. DNB is a foliar disease affecting the pine needles that causes a variety of symptoms including premature needle loss. These symptoms result in reduced timber yields and can cause tree death. Currently the only treatment for DNB is tree stand management to reduce the favourable conditions for spread and the use of fungicides on nursery trees. In this project we will test our hypothesis that the genetics of the host tree drives microbiome composition and interactions of the pine needles to alter the trees susceptibility to DNB. To achieve this we will combine existing host genetic data from our established Scots pine tree trial with new nucleic acid sequencing information on the pine needle microbiome. We will use meta-genomic and meta-transcriptomic sequencing. Meta-genomic sequencing provides a microbe inventory ("what is there?") and meta-transcriptomic sequencing tell us which community members are active ("what are they doing?"). We have three specific objectives 1) quantify the extent to which host genetic variation explains variation in microbial community composition and susceptibility to DNB, (2) evaluate temporal variation in microbiome composition and function during D. septosporum infection and (3) predict which microbiome community members interact with D. septosporum and which impact on host susceptibility to DNB. Our proposal addresses key challenges within the BBSRC integrative microbiome research priority (1) relating host genotype to microbiome composition and health status, and (2) characterising functional properties of the microbiome and the genes driving the microbiome-host relationship. The benefits of this proposal are two-fold: (a) we will understand how host genetics and microbiome composition combine to influence susceptibility to DNB disease in pine trees and (b) we will develop publicly available methods to integrate multi-omics (metagenomics, meta-transcriptomics and genotyping) data which will be directly applicable to many different host-microbiome systems, from plants to humans. The project will benefit forest researchers with interests in tree disease management and agricultural researchers with interests in the effect of crop genetics on microbiomes and crop disease incidence and severity. The project will also benefit computational biologists and biologists integrating metagenomics, transcriptomics and genotyping datasets to answers diverse biological questions.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

Associated awards:

BB/W020394/1 Quantifying how host genotype and microbiome composition combine to influence susceptibility to Dothistroma needle blight disease in pine trees

BB/W020610/1 Quantifying how host genotype and microbiome composition combine to influence susceptibility to Dothistroma needle blight disease in pine trees.

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