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Circadian rhythms in plant-microbe interactions

School of Life Sciences

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Prof G Bending , Dr I A Carré No more applications being accepted Competition Funded PhD Project (European/UK Students Only)

About the Project

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 due to diurnal cycles of carbon flow to the root zone, changes in plant gene expression associated with the plant circadian clock, or because rhizosphere microbes themselves have circadian clocks. 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.
Techniques that will be undertaken during the project:
- PCR-amplicon sequencing
- Metagenomic and metatranscriptomic sequencing
- Quantitative PCR
- Network analysis
- Multivariate statistical analysis
- Plant growth trials under controlled environmental conditions

Funding Notes

Studentship includes: fees, a tax-free stipend of at least £15,009 p.a (to rise in line with UKRI recommendation); a travel allowance in year 1; a travel / conference budget; a generous consumables budget and use of a MacBook Pro for the duration of the programme. In order to apply you must ensure that you are eligible.


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

Adams and Carre (2011) Downstream of the plant circadian clock: output pathways for the control of physiology and development. Essays in Biochemistry, 49, 53–69.
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