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Circadian rhythms in plant-microbe-soil interactions

Primary Supervisor: Professor Gary Bending, School of Life Sciences

Secondary supervisor: Professor Isabelle Carre (Warwick), Prof Davey Jones (University of Bangor)

PhD project title: Circadian rhythms in plant-microbe-soil interactions

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 mitigating the threats posed by climate change and land degradation.

Research at Warwick has demonstrated that a variety of factors control the composition of microbial communities which inhabit the root zone, including plant genotype and developmental stage, local environment, and geographical distance. However recently we have shown that there are microbial diurnal cycles in the root zone, involving rhythmic changes in transcriptional activity in diverse groups of bacteria and fungi.

In this project you will derive detailed understanding of diurnal root metatranscriptome dynamics (ie plant and microbial transcriptomes) and investigate the links between plant and microbial gene expression. You will investigate the extent to which diurnal dynamics of microbial community activity and function are linked to diurnal cycles of carbon flow to the root zone and changes in plant gene expression associated with the plant circadian clock. You will also establish the implications of circadian interactions in the root zone for food security.

You will use a variety of experimental resources, including plant mutants with altered circadian clock genes. These will be used together with amplicon, metagenome and metatranscriptome sequencing, and quantitative PCR to profile the structure, abundance and functional characteristics of the microbiome, and key microbial groups with specialized functional traits. Metabolomic analysis of the root zone will also be conducted, together with functional analyses of microbial communities.


  1. Berendsen RL et al. (2012) The rhizosphere microbiome and plant health. Trends in Plant Science 17, 478-486.
  2. Ingle, R., Stoker, C., Stone, W., Adams, N., Smith, R., & Grant, M. et al. (2015). Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogenBotrytis cinerea. The Plant Journal 84, 937-948.
  3. 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.
  4. McKay Fletcher, D., Shaw, R., Sánchez-Rodríguez, A., Daly, K., van Veelen, A., Jones, D., Roose, T. (2019). Quantifying citrate-enhanced phosphate root uptake using microdialysis. Plant And Soil 461, 69-89.
  5. 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.

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