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Understanding how glycan patterning in the rhizosphere drives microbial niche differentiation

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  • Full or part time
    Prof W Willats
    Dr W Dawson
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Crop production faces significant challenges in relation to sustainability, resilience and profitability. Increased output is required to meet the needs of a growing population, but this must be achieved in the face of increasing herbicide and pesticide resistance, a stricter regulatory environment and a diminishing repertoire of agrichemicals, climate change and increasingly globalised production. Meeting these challenges requires us to develop an in-depth knowledge of the molecular mechanisms underpinning crop performance and soil health. Armed with this knowledge, we are in a better position to develop sustainable strategies to boost crop productivity. The aim of this PhD project is to obtain detailed insight into how polysaccharides deposited by plant roots into the rhizosphere help develop and sustain highly diverse populations of microbes. This is important because the rhizosphere microbial diversity is an important factor in determining soil and plant health. During the project you will acquire training in a variety of state-of-the-art bio-imaging and molecular techniques, and experience different working environments at Newcastle and Durham Universities and the James Hutton Institute in Dundee. One of the challenges traditionally associated with studying roots and soils is that biological activity is hidden underground. In this project, you will work with a novel imaging system in which roots are grown in artificial transparent soils that have physical and chemical properties that closely match those found in natural soils. This system allows us to observe and track interactions between microbes, polysaccharides, soil particles and live roots simultaneously, and in real time. In addition, you will be trained in a range of biochemical techniques to study polysaccharide structures and learn how to assess microbial communities in real soils using state of the art genetic sequencing techniques. Being competent in these techniques will allow you to manipulate soils, roots and polysaccharides in controlled ways and assess the impact on microbial diversity. This knowledge will make a significant contribution to future efforts to enhance soil health and crop performance.


Applications should be made by emailing [Email Address Removed] with a CV (including contact details of at least two academic (or other relevant) referees), and a covering letter – clearly stating your first choice project, and optionally 2nd and 3rd ranked projects, as well as including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project(s) and at the selected University. Applications not meeting these criteria will be rejected.
In addition to the CV and covering letter, please email a completed copy of the Additional Details Form (Word document) to [Email Address Removed]. A blank copy of this form can be found at:
Informal enquiries may be made to [Email Address Removed].

Funding Notes

This is a 4 year BBSRC studentship under the Newcastle-Liverpool-Durham DTP. The successful applicant will receive research costs, tuition fees and stipend (£15,009 for 2019-20). The PhD will start in October 2020. Applicants should have, or be expecting to receive, a 2.1 Hons degree (or equivalent) in a relevant subject. EU candidates must have been resident in the UK for 3 years in order to receive full support. Please note, there are 2 stages to the application process.


Pea Border Cell Maturation and Release Involve Complex Cell Wall Structural Dynamics Plant Physiology, 174 (2) 1051-1066; DOI: 10.1104/pp.16.00097, 2017

Mechanisms of early microbial establishment on growing root surfaces. Vadose Zone Journal, 15(2), 2016

Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo. Plant Signalling and Behavior, 9, Article No. E29878, 2014

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis. Plant, Cell and Environment, 38, 1213-1232, 2015

A new versatile microarray-based method for high throughput screening of carbohydrate-active enzymes. The Journal of Biological Chemistry, 290(14), 9020-9036, 2015

A small number of low-abundance bacteria dominate plant species-specific responses during rhizosphere colonization. Frontiers in Microbiology, 8: 975, 2017

Versatile High Resolution Oligosaccharide Microarrays for Plant Glycobiology and Cell Wall Research. The Journal of Biological Chemistry, 287(47), 39429-39438, 2012

Identifying the role of soil microbes in plant invasions. Journal of Ecology 104: 1211-1218, 2016

New live screening of plant-nematode interactions in the rhizosphere. Scientific Reports, 8, Article No. 1440, 2018

Root development impacts on the distribution of phosphatase activity: Improvements in quantification using soil zymography. Soil Biology and Biochemistry, 116, 158-166, 2018

Related Subjects

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