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.
Overview:
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.
Methodology:
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.
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
For further details about the programme and for information on how to apply please see the following link https://warwick.ac.uk/fac/sci/lifesci/study/pgr/studentships/nerccenta/
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