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Understanding how glycan patterning in the rhizosphere drives microbial niche differentiation

School of Natural and Environmental Sciences

Dr Catherine Tétard Jones , Dr W Dawson , Dr Lionel Duphy , Prof W Willats Friday, January 22, 2021 Competition Funded PhD Project (Students Worldwide)
Newcastle United Kingdom Biochemistry Microbiology Molecular Biology Plant Biology

About the Project

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 an unprecedented level of 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 bioimaging 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.

Informal enquiries may be made to


Applications should be made by emailing with a CV and a covering letter, 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. We will also require electronic copies of your degree certificates and transcripts.

In addition to the CV and covering letter, please email a completed copy of the Newcastle-Liverpool-Durham (NLD) BBSRC DTP Studentship Application Details Form (Word document) to , noting the additional details that are required for your application which are listed in this form. A blank copy of this form can be found at:

Funding Notes

Studentships are funded by the Biotechnology and Biological Sciences Research Council (BBSRC) for 4 years. Funding will cover tuition fees at the UK rate only, a Research Training and Support Grant (RTSG) and stipend. We aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.


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2. Mechanisms of early microbial establishment on growing root surfaces. Vadose Zone Journal, 15(2), 2016.
3. 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.
4. Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo. Plant Signalling and Behavior, 9, Article No. E29878, 2014.
5. Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis. Plant, Cell and Environment, 38, 1213-1232, 2015.
6. A new versatile microarray-based method for high throughput screening of carbohydrate-active enzymes. The Journal of Biological Chemistry, 290(14), 9020-9036, 2015.
7. A small number of low-abundance bacteria dominate plant species-specific responses during rhizosphere colonization. Frontiers in Microbiology, 8: 975, 2017.
8. Quantitative Trait Loci mapping of phenotypic plasticity and genotype – environment interactions in plant and insect performance. Philosophical Transactions of the Royal Society B: Biological Sciences 2011, 366(1569), 1368-1379.
9. Identifying the role of soil microbes in plant invasions. Journal of Ecology 104: 1211-1218, 2016.
10. New live screening of plant-nematode interactions in the rhizosphere. Scientific Reports, 8, Article No. 1440, 2018.

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