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Investigating fungal spore dispersal in UK arable crop systems under current and future environmental conditions.

   Biointeractions and Crop Protection

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  Dr Kevin King, Prof J West, Dr Y Huang  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

A four-year PhD project hosted between Rothamsted Research (supervisors: Dr Kevin King & Prof Jon West) and The University of Hertfordshire (supervisor: Dr Yongju Huang) is offered subject to funding with a start date of 1st October 2023.

  • Plant pathogens cause substantial losses to agricultural crops and threaten UK national and international food security.
  • Understanding spore dispersal of fungal plant pathogens across multiple spatial scales is essential to underpin knowledge on disease epidemiology.
  • (1) Metagenomics-based molecular studies are required to profile and compare fungal communities in soil, plant surfaces and air to understand what fungi are released into the air, and how this might change between arable crop rotations.
  • (2) Work is needed to determine the role of airborne spores in driving UK arable crop disease epidemics, and how such spore release patterns might be changing.
  • (3) Studies are further required to investigate how extreme weather events. such as drought and flooding that are expected to increase under future climate change, will impact on the development of fungal fruiting bodies that release spores driving crop disease outbreaks. 

The PhD Project

This project seeks to improve understanding of fungal pathogen spore dispersal in UK arable crop systems and how this might be changing, with the overall aim of improved disease management. The project has three inter-related work streams:

1.  Understanding spore dispersal via fungal metagenomic analysis.

Three types of sample (plants, soil, and air) will be sampled at multiple time points throughout the growing season (September, November, April, June). Soil and plant samples will be taken from wheat and oilseed rape plots at Rothamsted Farm. Air samples will be taken by positioning spore samplers above the same wheat/WOSR plots from which the soil samples were taken and also from roof-based traps at Rothamsted. Sampling will be done over three field seasons. Environmental DNA (eDNA) will be extracted from the plants, soil, and air samples, and fungal DNA sequenced via metagenomics (via minION third generation sequencing). The fungal communities present in the different sample types will be profiled bioinformatically and compared statistically (using GAIA software) and used to investigate fungal spore dispersal and explore how fungal communities might change between crop rotations.

2.  Understanding regional spore dispersal in air.

We will focus on a disease of wheat WW (Fusarium (Fusarium graminearum)) and three diseases of OSR (Phoma (Plenodomus spp.), Sclerotinia (Sclerotinia sclerotiorum) and light leaf spot (Pyrenopeziza brassicae)). Air will be sampled daily using a 7-day Burkard roof-based spore trap at Rothamsted Research (i.e., to sample at a regional scale). DNA will be extracted from air samples, and quantitative PCR (qPCR) used to explore the timing and release of airborne spores of these fungal pathogens. The patterns of airborne spore release will be monitored and compared over multiple growing seasons and combined with archived data available at Rothamsted to explore how they might be changing over time.

3.  Understanding spore dispersal under changing environmental conditions.

We will investigate how extreme weather events, including drought and flooding, will impact on fungal fruiting bodies that release spores driving arable crop disease outbreaks. Soil containers containing OSR debris with Phoma/light leaf spot symptoms, sclerotia of the Sclerotinia fungus and Fusarium infected wheat grain will be incubated outdoor at Rothamsted between June to April. Three containers will be exposed to natural weather conditions (controls); three to natural conditions plus simulated flood events (one week of complete water immersion in October, January, and April); and three to natural conditions plus simulated drought events (each covered for four weeks with an elevated plastic sheet) in August and April. The development and maturation of fruiting bodies of the fungal pathogens will be monitored visually and by microscopy to determine the potential impacts of flooding and drought stress on spore release.

Student Training and Stipend

The PhD offers training in a range of techniques including microbiology and plant pathology, molecular biology and diagnostics, genomic analysis and bioinformatics. Postgraduate training courses will be offered both at Rothamsted Research and the University of Hertfordshire covering applications such as statistics, research writing, bioinformatics, business and biotechnology, and presentation skills.

The four-year PhD will have a start date of 1 October 2023 and is offered subject to award of funding. The PhD will be based primarily at Rothamsted research but with opportunities for study periods at the nearby University of Hertfordshire.

Applications and Further Information

There is an application deadline of 30 September 2022. Candidates should hold, or be forecast to graduate with, a minimum 2:1 degree in a relevant biological science subject. Please send both a CV with academic details and a cover letter explaining interest in the PhD by e-mail to Dr Kevin King at [Email Address Removed], or Prof Jon West ([Email Address Removed]).

Funding Notes

The PhD follows standard UK Research Council conditions including full support for tuition fees and a tax-free annual stipend (currently £16,062 per year for 2022 entry). Non UK-resident students are not eligible for funding.
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