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Unravelling the global microbiome of crop plants to improve sustainability and food security

Primary Supervisor: Professor Gary Bending, School of Life Sciences

Secondary supervisor: Dr Ryan Mushinski, SLS, Chris Quince, Earlham Institute

PhD project title: Unravelling the global microbiome of crop plants to improve sustainability and food security

University of Registration: University of Warwick

Project outline:

Plants live in close association with complex communities of microbes which together constitute their ‘microbiome’. The microbiome interacts with the plant in numerous ways; some microbes are beneficial and promote plant growth, while others are pathogens which reduce crop yields. Understanding and harnessing interactions within the microbiome has enormous importance for devising net zero carbon emission sustainable agricultural systems while ensuring food and energy security, and also mitigating the threats posed by climate change and land degradation.

In collaboration with an international team of scientists you will use molecular approaches to investigate the composition of crop microbiomes, the factors which shape the assembly of microbiomes, and specific functional traits within microbiomes that impact crop growth and yield. The programme will be part of a major initiative to profile microbiomes from key crops including wheat, maize and rice from agricultural systems from across the planet.

You will use a range of methods including amplicon and metagenome sequencing, and quantitative PCR to profile the structure, abundance and functional characteristics of the microbiome, and key microbial groups with specialized functional traits. There will also be scope to assemble and characterize microbial genomes using metagenomic sequences, to isolate and characterize microbes, and investigate plant-microbe interactions under controlled environment conditions.


  1. Hilton, S., Picot, E., Schreiter, S., Bass, D., Norman, K., Oliver, A., Moore, J.D., Mauchline, T.H.,Mills, P.R., Teakle, G.R., Clark, I.M., Hirsch, P.R., van der Gast, D.J., Bending, G.D. (2021)Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale. Microbiome 9, 1-15.

  2. Lidbury, I.D.E.A., Borsetto, C., Murphy, A.R.J., Botrtill, A., Jones, A.M.E., Bending, G.D. et al. (2021) Niche-adaptation in plant-associated Bacteroidetes favours specialization in organic phosphorus mineralization. ISME J 15, 1040-1050.

  3. Picot, E., Hale, C.C., Hilton, S., Teakle, G.R., Schäfer, H., Huang, Y., Perryman, S., West, J.S.,Bending, G.D. (2021) Contrasting responses of rhizosphere bacterial, fungal, protist and nematode communities to nitrogen fertilization and crop genotype in field grown oilseed rape (Brassica napus). Frontiers in Sustainable Food Systems 5, 88.

  4. Albornoz, F.E., Orchard, S., Standish, R.J., Dickie, I.A., Bending, G.D. et al. (2021) Evidence for niche differentiation in the environmental responses of co-occurring mucormycotinian fine rootendophytes and glomeromycotinian arbuscular mycorrhizal fungi. Microbial Ecology 81, 864-873.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science

Techniques that will be undertaken during the project:

  • PCR-amplicon sequencing
  • Metagenomic sequencing
  • Quantitative PCR
  • Network analysis
  • Multivariate statistical analysis
  • Microbial isolation and characterization
  • Plant growth trials under controlled environmental conditions

Contact: Professor Gary Bending, University of Warwick