Healthy soils underpin life on Earth. They recycle nutrients, store carbon, support biodiversity, and drive crop productivity. Yet, despite soils harbouring the most diverse microbial communities on the planet, we still know remarkably little about which microbes are actually active and contributing to these vital processes at any given moment. Identifying active microbes, the ones “alive and kicking” is crucial for understanding how soils respond to climate change, land-use pressures, and agricultural management.
This PhD project will pioneer a direct comparison of three of the most exciting methods currently available for detecting microbial activity in soils:
By systematically comparing these approaches across soils and plant rhizospheres, the student will establish how different methods complement or contradict each other, and how they can be used together to build a robust picture of microbial activity. Importantly, this project will connect activity data with forthcoming metatranscriptomic datasets from the DECODing Biodiversity project, enabling novel insights into which microbes are not just present, but contributing functionally at ecosystem scales.
Research Aims
This project is a CENTA Flagship Project.
This project is not suitable for CASE funding
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All applications must include the CENTA application form.
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DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.
The student will gain:
This project will be delivered in collaboration with the Defra Centre of Excellence (CoE), providing a strong policy and stakeholder interface. The CoE will act as the CASE partner, offering access to policy-relevant datasets, perspectives on soil monitoring, and opportunities to engage with decision-makers. UKCEH provides world-leading expertise in microbial ecology, isotope labelling, and environmental bioinformatics, while academic partners contribute specialist knowledge in soil and plant–microbe interactions. The collaboration ensures the student gains experience in both cutting-edge research and policy-relevant applications, strengthening pathways from discovery science to evidence-based decision-making on soil health and microbial activity.
Over three years, this PhD will focus on both research and professional development. In Year 1, the student will complete an in-depth literature review and build laboratory and computational skills, piloting SIP, BONCAT, and D₂O labelling approaches in controlled soils. Year 2 will centre on full-scale laboratory experiments, data generation (including integration with metatranscriptomics from the DECODing Biodiversity project), and presentation of initial findings at conferences. In Year 3, the focus will shift to advanced data analysis, cross-method comparison, ecological synthesis, and preparation of manuscripts and the thesis. Across all years, personal and professional development will be prioritised, including networking, society memberships, teaching opportunities, leadership activities, and workshops on grant writing, project management, and career planning. Together, these activities will ensure that the candidate develops into a skilled, confident researcher ready for a successful post-PhD career, while delivering cutting-edge insights into active soil microbiomes.
For any enquiries related to this project please contact Susheel Bhanu Busi, [email protected].
The successful applicant would be registered at the University of Warwick.
To apply to this project:
Applications must be submitted by 23:59 GMT on Wednesday 7th January 2026.