PhD Studentship: Developing CRISPR Genome Engineering Tools to Understand Nitrogen Cycling by Novel Archaea

University of East Anglia - School of: Biological Sciences

Start Date: October 2018

Supervisor: Dr Laura Lehtovirta-Morley

Project description: 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.

Training

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.

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 on 12/13 February 2018.

For further information, please visit www.enveast.ac.uk/apply

Person specification:

Minimum entry requirement: 2:1 or equivalent.

This project is suited to candidates with a BSc or MSc degree in Microbiology- and Biochemistry-related disciplines.

EnvEast welcomes applicants from quantitative disciplines who may have limited background in environmental sciences. Excellent candidates will be considered for an award of an additional 3-month stipend to take appropriate advanced-level courses in the subject area.

Funding notes: Successful candidates who meet RCUK’s eligibility criteria will be awarded a NERC studentship - in 2017/18, the stipend is £14,553. 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 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. 

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Type / Role:

PhD

Location(s):

South East England