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Homeostasis of the phyllosphere microbiota as a mechanism to reduce agricultural losses due to disease

  • Full or part time
  • Application Deadline
    Tuesday, January 31, 2017
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Healthy plants, like all higher organisms, host an extensive commensal microbial community or microbiome. Non-pathogenic microbes are tolerated and in many cases benefit the host. This microbiome is even believed to have co-evolved with its host and, as a result, this collaboration between host and microbiome is often likened to a superorganism. In animals it plays an important role in disease prevention and so homeostasis of this microbiome is currently being considered as an important part of medicine. In plants, the root microbiome or rhizosphere has been extensively studied, particularly with a view to improving nutrient acquisition by the roots. However, the leaf microbiome, the phyllosphere, is less well studied. The phyllosphere community contains a wide range of bacterial and fungal species, including some that can become pathogenic but, as in animals, other microbes have been shown to play an important role in disease prevention. We have recently demonstrated that constitutive activation of plant immune responses mediated by the defence hormone, Salicylic Acid, causes a significant change in the balance of the phyllosphere microbiome which particularly targets the bacterial community. Using high-throughput, next generation sequencing technology, we demonstrated that these non-specific immune responses cause disruption of the microbial ecosystem, leading to a significant increase in bacterial diversity. Rather than allowing the establishment of a relatively small number of dominant bacterial species which fill the majority of the niche, a range of apparently opportunistic bacterial species compete equally. Furthermore, the majority of the dominant species established on normal plants were among those that have been found to be associated with the production of antimicrobials. This most likely enhances their success in the phyllosphere but will also be likely to benefit the host plant in actively preventing establishment of more-opportunistic pathogenic microbes at the same time. Protection from disease would, thus, become a system property of the microbiome. This experimental system, established in the model plant, Arabidopsis thaliana, therefore, forms the ideal model in which to test the importance of plant phyllosphere microbiome homeostasis for plant health. We will examine the effect of this disruption of the microbiome on the susceptibility of the plants to disease-causing microbes. This investigation will be of very real interest to farmers. A wide range of agricultural treatments such as pesticide, bactericide, fungicide, and even herbicide and fertiliser treatments will greatly alter the ecology of the plant phyllosphere and so will likely have a similarly-disruptive effect on the microbiome as a whole and on disease susceptibility of the host. We will examine the effects of these agricultural treatments on the phyllosphere microbial community and, furthermore, examine the effect of this disruption on susceptibility of the host plant to the establishment of pathogenic microbes. We will also examine the potential for probiotic treatment / microbiota transfer to help restore phyllosphere microbial homeostasis following the application of agricultural treatments. The project will be primarily based in the lab of Dr Paul Devlin at Royal Holloway University of London and is a collaboration with the lab of Prof. Pietro Spanu at Imperial College, London. It will involve high-throughput, next generation sequencing analysis of microbial communities as well as studies of plant-pathogen interaction.

Funding Notes

Applicants should already have or be expected to obtain a First or upper Second Class degree in a relevant discipline. This BBSRC DTP studentship is fully funded for four years. It includes a stipend at the standard Research Council rate (currently £16,296 per annum), covers research costs and tuition fees at the UK/EU rate, and is available for UK and EU students who meet the UK residency requirements View Website

A DTP Studentship is available on either a full-time or part-time basis. A student in part-time employment may be eligible for a part-time award. Students employed full-time are not eligible.


Vela-Corcia D, Bautista R, de Vicente A, Spanu PD, Pérez-García A. (2016) De novo Analysis of the Epiphytic Transcriptome of the Cucurbit Powdery Mildew Fungus Podosphaera xanthii and Identification of Candidate Secreted Effector Proteins, Plos One, Vol:11

How good is research at Royal Holloway, University of London in Biological Sciences?

FTE Category A staff submitted: 24.00

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