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QUADRAT DTP: Ecological and evolutionary processes associated with environmental change in microbial populations

   School of Biological Sciences

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  Prof Cecile Gubry-Rangin, Prof C Creevey, Prof P Hallett  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

This project aims to analyse the microevolutionary mechanisms responsible for the creation and maintenance of microbial diversity across several terrestrial ecosystems. Understanding how biological diversity is created and maintained has been a key challenge for biologists for more than a century. Diversity is greatest in bacteria and archaea and its description has been dramatically improved by high-throughput sequencing which has been applied to a large range of land-use ecosystems. Large public genomic repositories now provide a fantastic opportunity to move beyond description and to solve some of the mysteries concerning the physiological and evolutionary mechanisms involved in biological diversification. Lateral gene transfer has been proposed as a key mechanism driving prokaryotic adaptation and this mechanism occurs within microbial  populations, including both closely related or more distant organisms.  

Microevolutionary mechanisms within microbial populations have been largely ignored by microbiologists partly due to the species concept debate and to the previously poor genetic diversity recovered from highly diverse natural microbial populations. However, the release of ultra-deep metagenomic sequencing technology now opens new opportunities for microbial population analyses, such as population metagenomics, which allows exploration and interpretation of the myriad of individual haplotypes that provide the population-level diversity of natural microbiomes (Nicholls et al., 2020). 

The proposed research will therefore use available deep metagenomics sequencing from a range of soils to establish a population metagenomics bioinformatics pipeline. Once established, the student will generate some novel deep metagenomics sequencing across a range of soil ecosystems to test specific hypotheses relating to the physiological and evolutionary microbial adaptation required in different land-use soils and across several environmental gradients (either pH, temperature, moisture or other abiotic factors) (e.g. Sheridan et al., 2022). In particular, soils of different structural complexity (including diverse pore sizes, moisture content) will be analysed as such complexity impact microbial diversity (Hallett et al., 2022). This project will also involve some in vivo experimental environmental perturbations to determine the effect of several environmental changes (including drought and rewetting treatments) on the existing standing variation in the native and perturbed populations as well as their consequences for ecosystem services, processes, function and resilience. 

The supervisory and project team will provide support and training in microbial ecology, bioinformatics, evolutionary ecology, population ecology and soil science. The project will combine molecular genetics, bioinformatics analyses, and empirical work (microcosms and fieldwork), to explain how microbial communities are affected and respond to climate change. There will be ample opportunity for the student to develop their own project directions in line with the overall project objectives. 

You will join a cohort of PhD students interested in environmental management, biodiversity and earth systems science, and will collaborate with a broad network of end-users and stakeholders. An excellent scientific environment will be provided, with training on several state-of-the-art technological facilities, including genomic platforms and cutting-edge molecular and environmental facilities. You will therefore benefit from excellence in environmental science research with specific knowledge on research impact and policies critical for achieving Sustainable Development Goals, while gaining a diverse range of transferable and generic skills to ensure their competitive future career paths. 

Candidate Background: The candidate should have a strong interest in bioinformatics and ecological theory, in addition to a motivation to deliver new insight in global change ecology. A student holding an MSc in bioinformatics, microbial ecology and/or evolutionary biology is desirable, but not essential.

More project details are available here: https://www.quadrat.ac.uk/quadrat-projects/

How to apply: https://www.quadrat.ac.uk/how-to-apply/ 

Funding Notes

QUADRAT studentships are open to UK and overseas candidates. Funding covers:
• A monthly stipend for accommodation and living costs, based on UKRI rates (currently £17,668 pa for 2022/23, updated annually)
• Fees (home rate tuition fees and/or fee waiver for overseas fees, where applicable)
• Research and training costs
For further information before applying please check full funding and eligibility information: https://www.quadrat.ac.uk/funding-and-eligibility/


1. Nicholls SM, Aubrey W, Edwards A, de Grave K, Huws S, Schietgat L, Soares A, Creevey CJ, Clare A (2020) Recovery of gene haplotypes from a metagenome. BioArxiv, https://doi.org/10.1101/223404
2. Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. (2022) Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat Com 13:1-13. https://doi.org/10.1038/s41467-022-31847-7
3. Hallett, P.D., Marin, M., Bending, G.D., George, T.S., Collins, C.D. & Otten, W. 2022. Building soil sustainability from root–soil interface traits. Trends in Plant Science. 27. https://doi.org/10.1016/j.tplants.2022.01.010
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