Applications are invited for a fully funded, 42 month PhD studentship commencing in October 2022 at the University of Aberdeen, as part of The newly established Anthony & Margaret Johnston Centre for Doctoral Training in Plant Sciences enabled by a generous legacy gift.

Project Description

Plants are intimately associated with a diverse set of soil microorganisms including mycorrhizal fungi and a wide range of bacterial and fungal decomposers. These belowground interactions drive aboveground ecosystem function through their influence on plant productivity, nutrient cycling and carbon sequestration. Arbuscular mycorrhizal fungi (AMF) rely on their hosts as their primary source of carbon, receiving up to 20% of plant photosynthates.

In return, AMF can promote plant growth by enhancing the uptake of otherwise inaccessible soil nutrients. There is significant potential to promote symbioses between AMF and crops in agricultural environments to enhance soil nutrient uptake, in turn reducing crop dependency on heavy fertilisation rates1,2. Plant-AMF symbioses are also known to improve soil structure, increase soil water holding capacity and sequester more carbon, thereby improving soil health and crop productivity.

AMF cannot decompose organic matter themselves. Instead, they use their extraradical hyphal network to scavenge for nutrients, including those liberated by microbial decomposers. Root exudation can stimulate the activity of rhizosphere decomposer communities, enhancing microbial mineralization and the release of nutrients from organic matter, which in turn improves nutrient availability for AMF and plants.

The extraradical hyphae of AMF acts as extensions of plant roots allowing them to indirectly access a greater soil volume. The region of soil influenced by hyphal exudates, often referred to as the hyphosphere, possesses a microbiome that is distinct from the bulk soil and rhizosphere3. While the direct exchange of plant-fixed carbon for AMF-acquired soil nutrients is well studied, the critical tripartite interaction between plants, AMF and hyphosphere microbiome and their impact on carbon and nutrient (nitrogen and phosphorous) dynamics remain unexplored.

Two hypotheses will be tested in this exciting PhD project:

(1) AMF presence promotes hyphosphere decomposer community activity through additional exudation beyond the nutrient depletion zone, thereby increasing the extent of carbon-nutrient exchange.

(2) Application of inorganic nitrogen and phosphorous will lower AMF infection of plants and alter soil decomposer communities to have lower expression of traits linked to nutrient mining from organic matter.

The project will use lab and pot experiments to test these hypotheses, both involving fully cross-factorial designs with and without AMF inoculation and nutrient additions. The in-vitro experiment will involve growing plantlets in association with AMF in bi-compartmented systems, such that the plant and AMF grow in the root compartment and the fungal mycelia extend into the root-free compartment4. Such a system will enable us to characterise the plant-AMF exudation patterns and the microbial community that develops in the root compartment (rhizosphere microbiome) and in the hyphae-only compartment (hyphosphere microbiome).

A similar scaled-up experiment will be performed in the greenhouse to ascertain the implications of these interactions in soils. This will involve the use of soil ingrowth cores to create hyphae-only compartments and isotope tracers to quantify the movement of carbon, nitrogen and phosphorous5,6. Student will be trained in using metabolomics to characterise root exudates and metagenomics to measure microbiome traits and community assembly.

Informal enquiries would be welcomed for a discussion. Please contact Dr Ashish Malik ( for further information.

Essential background of student:

Applicants are expected to hold (or be about to achieve) at least a 2:1 UK Honours degree (or Equivalent) in a relevant subject. Applicants with a 2:2 Honours degree (or Equivalent) may be considered providing they have a Distinction or Commendation at Master’s level.

Funding Notes

This 42 Month PhD project is part of the Anthony & Margaret Johnston Centre for Doctoral Training in Plant Sciences at the University of Aberdeen.
This opportunity is open to UK and International students and includes full funding to cover tuition fees and a stipend at the UKRI rate (£16,062 For the 22/23 academic year).
Funding for international students does not cover visa costs (either for yourself or for accompanying family members), immigration health surcharge or any other additional costs associated with relocation to the UK.
The expected start date is October 2022.


  • Formal applications can be completed online:
  • You should apply for Biological Sciences (PhD) to ensure your application is passed to the correct team.
  • Please clearly note the name of the supervisor and project title on the application form. If you do not mention the project title and the supervisor on your application, it will not be considered for the studentship.
  • Please include: a cover letter specific to the project you are applying for, an up-to-date copy of your academic CV, and relevant educational certificates and transcripts.
  • Please note: you DO NOT need to provide a research proposal with this application.
  • General application enquiries can be made to


1. Ryan, M. H. & Graham, J. H. Little evidence that farmers should consider abundance or diversity of arbuscular mycorrhizal fungi when managing crops. New Phytologist 220, 1092–1107 (2018).
2. Berruti, A., Lumini, E., Balestrini, R. & Bianciotto, V. Arbuscular Mycorrhizal Fungi as Natural Biofertilizers: Let’s Benefit from Past Successes. Frontiers in Microbiology 6, (2016).
3. Zhang, L., Zhou, J., George, T. S., Limpens, E. & Feng, G. Arbuscular mycorrhizal fungi conducting the hyphosphere bacterial orchestra. Trends in Plant Science (2022) doi:10.1016/j.tplants.2021.10.008.
4. Le Pioufle, O. & Declerck, S. Reducing Water Availability Impacts the Development of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis MUCL 41833 and Its Ability to Take Up and Transport Phosphorus Under in Vitro Conditions. Frontiers in Microbiology 9, (2018).
5. Chowdhury, S. et al. Nutrient Source and Mycorrhizal Association jointly alters Soil Microbial Communities that shape Plant-Rhizosphere-Soil Carbon-Nutrient Flows. bioRxiv 2020.05.08.085407 (2020) doi:10.1101/2020.05.08.085407.
6. Malik, A. A., Dannert, H., Griffiths, R. I., Thomson, B. C. & Gleixner, G. Rhizosphere bacterial carbon turnover is higher in nucleic acids than membrane lipids: implications for understanding soil carbon cycling. Frontiers in microbiology 6, 268–268 (2015).

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