Increasing Agricultural Crop Productivity through the Selective Modification of the Soil Microbiome


Increasing Agricultural Crop Productivity through the Selective Modification of the Soil Microbiome


Project Description


Professor Alex Dumbrell (School of Life Sciences, University of Essex) contact me

Professor Tracy Lawson (School of Life Sciences, University of Essex)

Dr Ruth Bryant (RAGT Seeds Ltd)

Ms Helen Wilson (RAGT Seeds Ltd)

Project Background

Increasing crop productivity in an environmentally sustainable manner is a global challenge of the 21st century. Agronomists have long known that plants modify their local soil microbiome, accumulating species-specific pathogens that suppress that crop’s growth. Rotational cropping practices are used to overcome these negative soil feedbacks. These practices have historically taken a “black box” approach, relying on simple observations of which crops and rotational covers are best suited to follow each other. However, we now have the scientific tools required to open this black box, and provide a mechanistic understanding of how different crops and covers alter the soil microbiome, potentially supporting long-term crop improvement via manipulating plant-microbe interactions. Do you want to be the researcher who uses this new knowledge base to provide novel solutions to improve cropping practices?

Research Methodology

You will establish a series of field trials, targeting different wheat cultivars and cover crops, both grown as monoculture and mixtures, and quantify how these modify the local soil microbiome. Both taxonomic and functional modifications to the soil microbiome will be examined, allowing identification of cultivar/cover-specific positive and negative plant-soil interactions. These plant-soil feedbacks across multiple cropping cycles will be used to develop predictive models that identify how to modify the soil microbiome for improved crop performance.


You will be trained to be a multidisciplinary researcher and emerge from your PhD as a highly employable scientist. Specific training will cover: agricultural field trials and crop rotation practices, Next Generation Sequencing and molecular ecology approaches, automated robotic sample preparation, high-performance computing, bioinformatics, ecoinformatics, modelling and statistics, experimental design and plant physiology. With broad training in scientific skills provided as part of the Continuing Professional Development course at Essex and ARIES-cohort training.

Person Specification

We are looking for an enthusiastic person with a degree in a related subject (e.g. Ecology, Biology, Agronomy, Microbiology) and an interest in plant biology and microbial ecology. You must possess well-developed written and oral communication skills and be able to manage your time effectively. You will be required to do both field and laboratory work.


  • 1. Mommer, L., Cotton, T.E.A., Raaijmakers, J., Termorshuizen, A., van Ruijven, J., Hendriks, M., Rijssel, S.Q., Mortel, J., Paauw, J.W., Schijlen, E., Smit-Tiekstra, A., Berendse, F., de Kroon, H., Dumbrell, A.J. (2018). Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. New Phytologist, 218, 542-553
  • 2. Francioli, D., van Rijssel, S.Q., van Ruijven, J., Termorshuizen, A.J., Cotton, T.E.A., Dumbrell, A.J., Raaijmakers, J.M., Weigelt, A., Mommer, L. (2020). Plant functional group drives the community structure of saprophytic fungi in a grassland biodiversity experiment. Plant and Soil,
  • 3. Ma, H., Pineda, A., Hannula, S.E., Kielak, A.M., Setyarini, S.N., Bezemer, T.M. (2020). Steering root microbiomes of a commercial horticultural crop with plant-soil feedbacks. Applied Soil Ecology,
  • 4. Mariotte, P., Mehrabi, Z., Bezemer, T.M., De Deyn, G.B., Kulmatiski, A., Drigo, B., Veen, G.F., van der Heijden, M.G.A., Kardol, P. (2018). Plant–soil feedback: bridging natural and agricultural sciences. Trends in Ecology and Evolution, 33, 129-142
  • 5. Ma, H., Pineda, A., van der Wurff, A.W.G. Raaijmakers, C., Bezemer, T.M. (2017) Plant–Soil Feedback Effects on Growth, Defense and Susceptibility to a Soil-Borne Disease in a Cut Flower Crop: Species and Functional Group Effects. Frontiers in Plant Science, 8:2127

Key Information

  • This project has been shortlisted for funding by the ARIES NERC DTP and will start on 1st October 2021. The closing date for applications is 23:59 on 12th January 2021.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship, which covers fees, stipend (£15,285 p.a. for 2020-21) and research funding. For the first time in 2021/22 international applicants (EU and non-EU) will be eligible for fully-funded UKRI studentships. Please note ARIES funding does not cover visa costs (including immigration health surcharge) or other additional costs associated with relocation to the UK.
  • ARIES students benefit from bespoke graduate training and ARIES provides £2,500 to every student for access to external training, travel and conferences. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses in the subject area.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside significant relevant non-academic experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis, visa requirements notwithstanding
  • For further information, please contact the supervisor. To apply for this Studentship click on the “Apply now” link below.

Applications are Open

To apply, Send an email to Emma Revill  by 23:59 12th January 2021 with:

  • your CV (including contact details of two academic references)
  • a cover letter explaining your motivation and suitability for the PhD
See other ARIES studentships at University of Essex