2024-B36 Not so sweet; Investigating the adaptive potential of the generalist pathogen Honey fungus under future climates

Project highlights

The disease caused by Armillaria mellea, commonly known as the Honey fungus, is a generalist pathogen of hundreds of plants species. This pathogen causes a terminal disease that poses a huge threat to natural ecosystems, especially forests.
This project will investigate the population structure and adaptive potential of this pathogen under elevated CO2 and temperature to investigate whether under a warming climate this pathogen will increase or decrease in pathogenicity.
The project is jointly supervised by the Royal Horticultural Society (RHS) and will utilise and existing collection of Armillaria isolates (+100). The RHS has extensive outreach and public engagement opportunities through both its 100K+ membership and garden events, which the student will have the opportunity to engage with the broader public about their work and findings.
Our state-of-the art Wolfson Advanced Glasshouses at the University of Birmingham enable experiments under elevated CO2; a unique opportunity to test how a pathogen will behave in our future climate.

Overview

Armillaria root rot is a lethal fungal infection of plant roots. The range of plants affected spans woody, rhizomatous and herbaceous plants, with over 400 known host genera. An extensive survey conducted by the RHS over four years identified 468 unique site and host records where Armillaria spp. were isolated. Approximately 80% of these samples were identified as A. mellea, which confirmed that this species is the dominant pathogen the UK. However, the “weakly pathogenic” A. gallica was also isolated from ~15% of these samples, indicating that this species also contributes significantly to plant decline or death.

Currently there is a dearth of genomic resources available for these two species, which prohibits studies that can leverage this amazing collection of isolates. We also know little about the spread of this pathogen in the UK and its potential for wider disease epidemics under a warming climate.

This project seeks to plug this knowledge gap by developing long-read reference assemblies for both A. mellea and A. gallica. These assemblies will be used for foundational population genetic studies with the remaining isolates to investigate:

How do Armillaria spp. spread over different special scales in the UK?
What are the genes associated with virulence/pathogenicity?
Which genetic loci underpin temperature adaptation in Armillaria sp?
Will this pathogen increase or decrease in pathogenicity due to climate change?

We hypothesise that warmer temperatures and drought-driven stress will make this pathogen more virulent. We aim to test this hypothesis by performing in planta infection assays with A. mellea and A. gallica in our Wolfson advanced glasshouses under both ambient and elevated CO2. Together this experimental and genomic information will be used to assess the threat that this pathogen poses to our natural ecosystems under a warming climate.

Figure 1: From left to right, Brown Armillaria mellea rhizomorphs growing in agar towards another fungal saprophyte (white hyphal growth). An infected strawberry crown with A. mellea myclelal fans visible (white growths on outer edge of the root. Infected strawberry plants showing severe leaf wilting and stunted growth due to A. mellea.

Host

University of Birmingham

Theme

Climate and Environmental Sustainability
Organisms and Ecosystems

Supervisors

Project investigator

Megan McDonald, University of Birmingham, [email protected]

Co-investigators

Jassy Drakulic (Royal Horticultural Society), [email protected]

How to apply

Each host has a slightly different application process.
Find out how to apply for this studentship.
All applications must include the CENTA application form.
Choose your application route

Methodology

This project will utilise a broad spectrum of DNA sequencing techniques to build a high-quality reference genome for both A. mellea and A. gallica, the two dominant pathogenic species in the UK. To do this, high-molecular weight DNA extractions will be sequenced with the Oxford Nanopre Promethion. RNA-sequencing of fungal strains grown in a mixture of both in planta and in vitro conditions will be used to generate a high-quality reference genome for both species. These genomes will be used as the foundation for a population genomics study. A collection of 100+ isolates will be re-sequenced using Illumina-next-gen sequencing and single nucleotide polymorphisms will be used to investigate the population structure of these species across the UK.

In parallel glasshouse experiments using multiple plant hosts will be conducted with Armillaria isolates selected based on their genetic differentiation. We will measure the effect of elevated CO2, elevated temperature, alone and combined, on disease progression and severity.

Training and skills

Students will be awarded CENTA2 Training Credits (CTCs) for participation in CENTA2-provided and ‘free choice’ external training. One CTC equates to 1⁄2 day session and students must accrue 100 CTCs across the three years of their PhD.

The lab provides training in reproducible workflow tools such as Jupyter Notebooks, NextFlow and Snakemake. It is expected that upon graduation the PhD candidate will be proficient in many coding environments, including but not limited to R, Python and bash. The theoretical skills gained during this PhD will center on phylogenomics/population genetics as well as genome-wide association methods (GWAS).

In addition to the computational skills listed above the student will gain experience in the growth and maintenance of both plant and fungi in a controlled environment (glasshouse assays) and in sterile techniques required to isolate and handle microorganisms.

Partners and collaboration

The Royal Horticultural Society is contributing multiple well-characterised isolates of A. mellea and A. gallica for sequencing and population genomics studies. The RHS press office and editorial teams from The Garden magazine, podcast and website will be available to promote the project and its results to reach a multi-sector audience. The RHS also will provide expertise in the growth and maintenance of Armillaria spp. as well as advice on DNA extraction from this fungal tissue.

This project will be integrated into the Birmingham Institute of Forest Research, which will provide the student with a network of labs and individuals all working together to investigate tree diseases. This provides the student with opportunities to investigate other areas of research including soil diversity and chemistry, as well as biosystems modelling.

Further details

Further details on how to contact the supervisor for this project and how to apply for this project can be found here:

For any enquiries related to this project please contact Megan McDonald, University of Birmingham, [email protected].

To apply to this project:

You must include a CENTA studentship application form, downloadable from: CENTA Studentship Application Form 2024.
You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.
Please submit your application and complete the host institution application process via: https://sits.bham.ac.uk/lpages/LES068.htm. Please select the PhD Bioscience (CENTA) 2024/25 Apply Now button. The CENTA application form 2024 and CV can be uploaded to the Application Information section of the online form. Please quote CENTA 2024-B36  when completing the application form.

Applications must be submitted by 23:59 GMT on Wednesday 10th January 2024.

Royal Horticultural Society Disease Showcase: https://www.rhs.org.uk/disease/honey-fungus

Royal Horticultural Society Projects: https://www.rhs.org.uk/science/plant-health-in-gardens/pathology/projects/Improving-honey-fungus-advice

Wolfson Advance Glasshouses: https://www.birmingham.ac.uk/research/facilities/glasshouses/index.aspx

BIFoR: https://www.birmingham.ac.uk/research/bifor/research/index.aspx

Possible timeline

Year 1

Literature review
High-Molecular Weight DNA extraction, Nanopore-sequencing. These data will be used to assemble a high-quality phased reference genome for A. mellea isolate CG440 and A. gallica isolate CG510.
RNA-sequencing of both in vitro and in planta material infected with A. mellea isolate CG440 and A. gallica isolate CG510 will be used to generate reads used for genome annotation.
Trial glasshouse assay with a subset of plant species and fungal individuals.

Year 2

Illumina sequencing of Armillaria spp. populations and population genomics studies.
Large glasshouse assay under eCO2 and temperature.
In vitro assays with Armillaria populations to look for growth defects under elevated temperature.

Year 3

Population genetic analyses and GWAS analyses
Statistical analysis and assessment of Glasshouse assay
Thesis write-up and publications

Year 4: Thesis write-up and publications.