Project highlights

  • Circadian clocks represent adaptations to the rhythmic nature of our environment because they allow organisms to adjust their physiology ahead of predictable daily changes in light and temperature conditions linked to the rotation of the earth
  • The soil proximal to plant roots, termed the rhizosphere, is a zone of particularly intense microbial activity. These microbial communities are key determinants of plant health and are dominant drivers of carbon, nitrogen and phosphorus biogeochemical cycling processes in terrestrial ecosystems
  • We have shown that rhizosphere microbiota exhibit diurnal cycles of abundance, linked to functioning of the plant circadian clock. You will use a range of cutting edge molecular and biogeochemical approaches to investigate the significance of rhizosphere microbial circadian rhythmicity for the cycling and bioavailability of nutrients, and its significance for plant health.


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, particularly nutrient cycling processes, are linked to diurnal cycles of carbon flow to the root zone and changes in plant gene expression associated with the plant circadian clock.


University of Warwick


  • Climate and Environmental Sustainability
  • Organisms and Ecosystems


Project investigator

Professor Gary Bending, University of Warwick ([email protected])


How to apply


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, and the relationship between diurnal rhythmicity of microbial communities and the cycling and bioavailabiity of nutrients within the root zone will be determined using biogeochemical approaches.

Training and skills

Students will be awarded CENTA2 Training Credits (CTCs) for participation in CENTA2-provided and ‘free choice’ external training. One CTC equates to 1⁄2 day session and students must accrue 100 CTCs across the three years of their PhD.

Training will be provided in a range of chemical analyses as appropriate (e.g. C and N biogeochemistry, metabolomics), molecular techniques (DNA extraction, PCR, sequencing), metagenome and metatranscriptomic sequencing, and bioinformatics.

Further details


Professor Gary Bending
School of Life Sciences
University of Warwick


[email protected]

Information and links at the following webpage:

If you wish to apply to the project, applications should include:

  • A CV with the names of at least two referees (preferably three and who can comment on your academic abilities)

Applications to be received by the end of the day on Wednesday 11th January 2023. 

Possible timeline

Year 1

Investigate diurnal rhythmicity of rhizosphere microbiome biodiversity.

Year 2

Characterise diurnal rhythmicity of rhizosphere biogeochemistry, focussing on the nitrogen or phosphorus cycle.

Year 3

Determine diurnal rhythmicity of key microbial functional signatures related to nitrogen or phosphorus cycling.

Further reading

  • Berendsen RL et al. (2012) The rhizosphere microbiome and plant health. Trends in Plant Science 17, 478-486.
  • 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.
  • 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.
  • 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.
  • 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.


The project will comprise a mix of field work, laboratory work and desk based bioinformatic analysis. During any lockdown periods, bioinformatic components of the project will become the focus of the programme.