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Applications are now open for PhD studentships starting in October 2018. 

Please read the recruitment introduction for more information about eligibility, how to apply, and possibilities for further funding.

The deadline for applications is 8 January 2018.

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LEHTOVIRTA-MORLEY_UBIO18EE - Developing CRISPR genome engineering tools to understand nitrogen cycling by novel archaea

Project description

Selected other project supervisors
Professor Matthew Hutchings (UEA)
Professor Colin Murrell (UEA)

Scientific background
Nitrification is a central step in the global nitrogen cycle and a key driver of environmental change through its role in greenhouse gas emission and eutrophication. Distinct groups of microorganisms (archaea and bacteria) perform ammonia oxidation, the first step of nitrification. Ammonia oxidising microbial communities are shaped by environmental factors including soil nitrogen content, but the mechanistic basis underpinning this selection is unclear. This makes it hard to protect the resilience of ecosystem services and manage nitrogen losses from agricultural ecosystems, a major challenge to global food security.

The project
This studentship will determine the mechanisms of environmental adaptation in ammonia oxidising archaea. This project will characterise the archaeal ammonia uptake pathway, which is absent in ammonia oxidising bacteria, and link archaeal cell physiology to their ecological niche in soil.

Research methodology
This project uses novel archaea discovered by the applicant, which represent a missing link in the global nitrogen cycle. These strains represent a unique resource, and it is vital to develop a genetic system to understand their physiology. This project will use a powerful and innovative CRISPR-Cas9 mutagenesis approach to delete the genes encoding the ammonia uptake pathway and analyse mechanisms of ammonia transport in our unique collection of archaeal strains.

The student will receive training in cutting-edge techniques in environmental molecular microbiology, including DNA extraction, cloning, PCR, mutagenesis and characterisation of mutants through oxygen uptake and colorimetric inorganic nitrogen assays. S/he will present their data at departmental seminars, at national and international conferences and at the annual Norwich Science Festival. The student will join the cohort of PhD students at UEA and attend training courses for research and transferable skills.

The student will join the thriving molecular microbiology theme at UEA with >40 scientists whose research spans the biogeochemical cycles of nitrogen, carbon and sulphur. The project will be co-supervised by Professors Matt Hutchings and Colin Murrell.
Person specification
This project is suited to candidates with a BSc or MSc degree in Microbiology- and Biochemistry-related disciplines.

This project has been shortlisted for funding by the EnvEast NERC Doctoral Training Partnership, comprising the Universities of East Anglia, Essex and Kent, with over twenty other research partners. Undertaking a PhD with the EnvEast DTP will involve attendance at mandatory training events throughout the course of the PhD.

Shortlisted applicants will be interviewed by EnvEast on 12/13 February 2018.

Selected candidates who meet RCUK’s eligibility criteria will be awarded a NERC studentship - in 2017/18, the stipend is £14,553. Ordinarily, EnvEast studentships are for 3.5 years, although longer awards may be made to applicants from quantitative disciplines who have limited experience in the environmental sciences, to allow them to take appropriate advanced-level courses in the subject area.

In most cases, UK and EU nationals who have been resident in the UK for 3 years are eligible for a stipend. For non-UK EU-resident applicants NERC funding can be used to cover tuition fees, RTSG and training costs, but not any part of the stipend. Individual institutes may, however, elect to provide a stipend from their own resources.

This PhD studentship is expected to begin in September/October 2018. Both full-time and part-time study are possible (those planning to study part-time may wish to discuss this with the supervisor before applying).


  1. Nayak DD, Metcalf WW (2017) Cas9-mediated genome editing in the methanogenic archaeon Methanosarcina acetivorans. PNAS 114:2976-2981.
  2. Lehtovirta-Morley LE, Sayavedra-Soto L, Gallois N, Schouten S, Stein LY, Prosser JI, Nicol GW (2016) Identifying potential mechanisms enabling acidophily in the ammonia-oxidizing archaeon 'Candidatus Nitrosotalea devanaterra'. Appl Environ Microbiol 82:2608-2619.
  3. Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW (2011) Cultivation of an obligately acidophilic ammonia oxidizer from a nitrifying acid soil. PNAS 108:15892-15897.
  4. Qin Z, Munnoch, JT, Devine R, Holmes N, Seipke RF, Wilkinson B and Hutchings MI (2017). Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Chem Sci 8:3218-27.
  5. Crombie AT and Murrell JC (2014) Trace gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature 510:148-151.