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


About the Project

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 population, including both closely related or more distant organisms. This project aims to analyse the microevolutionary mechanisms responsible for the creation and maintenance of diversity across several terrestrial ecosystems.

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 sequencing technology (such as Illumina NovaSeq) 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.

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. This project will also involve some in vivo experimental environmental perturbations (1) to determine the effect of several environmental changes on the existing standing variation in the native and perturbed populations as well as their consequences for ecosystem services, processes, function and resilience.

The PhD student will join a dynamic team of researchers headed by Dr Gubry-Rangin (University of Aberdeen). This well-established group with a world-wide reputation in microbial ecology and a high-impact track record focuses on ecology and evolution of microbial populations in various ecosystems (2,3). The student will also strongly interact with the research group of Prof. Creevey (Queen’s University Belfast), widely renowned for ecological theory and bioinformatics approaches and with the one of Prof. Hallett (University of Aberdeen), expert in soil science. All required training (including on bioinformatics) will be provided.

The PhD student will be part of 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 to the student, with training on several state-of-the-art technological facilities, including genomic platforms and cutting-edge molecular and environmental facilities. The PhD student 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.

More project details are available here:

How to apply:

Funding Notes

QUADRAT studentships are open to UK and international candidates (EU and non-EU). Funding will cover UK tuition fees/stipend/research & training support grant only.

Before applying please check full funding and eligibility information: View Website


Zhao J, Meng Y, Drewer J, Skiba UM, Prosser JI, Gubry-Rangin C. (2020) Differential ecosystem function stability of ammonia oxidising archaea and bacteria upon short-term environmental perturbation. MSystems 5 (3) e00309-20.

Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ. (2015) Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proc Natl Acad Sci USA 112(30):9370-5.

Sheridan PO, Raguideau S, Quince C, Holden J, Zhang L, Thames Consortium, Williams TA, Gubry-Rangin C. (2020) Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat Com (in press).

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