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

Lead Research Organisation: University of East Anglia
Department Name: Biological Sciences

Abstract

Nitrification is a core process in the global biogeochemical nitrogen cycle and a major player in climate change. Ammonia oxidation is the first and rate-limiting step in nitrification and performed by distinct groups of archaea and bacteria. Archaea are the most important nitrifiers in unfertilised natural soil ecosystems, environments comprising >60% of the world's land area, which are generally unfavourable for ammonia oxidising bacteria. Ammonia oxidising archaea (AOA) are among the most numerous living organisms on the planet, but their mechanisms of adaptation to low nitrogen environments are not understood. Recent genomic analyses revealed that ammonium uptake (Amt) and ammonium sensing (PII) genes are highly conserved in AOA, and absent in many ammonia oxidising bacteria.

The overarching hypothesis of this project is that the recently predicted ammonia uptake pathway underpins the adaptation of AOA to low nitrogen environments. The aim of the studentship is to characterise this pathway and link it to the ecology of ammonia oxidising microorganisms, major players in the global nitrogen cycle.

The nitrification research field is dynamic and exciting, and given how little is known about archaea, this studentship provides an excellent opportunity to make a major contribution to the field. The hypothesis and the research methodology are novel, providing excellent scope for publications and independent thinking through method development and data analyses. This project uses a unique collection of AOA strains which are key players in the global nitrogen cycle, but poorly understood. This project will develop a novel genetic system for AOA and provide a significant advance in understanding their molecular physiology.

All necessary infrastructure is in place at UEA and collectively the supervisors have outstanding expertise in the techniques involved. This is a unique opportunity as the applicant has some of the few pure cultures of AOA in the world and strong knowledge and experience in handling them. The project will have a major impact in environmental microbiology and the development of the archaeal genetic system will open up a plethora of future research opportunities.

PhD students registered at UEA undertake both subject specific and Personal and Professional Development (PPD) training during their degrees. The student will receive advanced training in cutting-edge techniques in molecular biology. Student will be based in the ELSA lab (Murrell, Lehtovirta-Morley, Crombie) and members of both the ELSA lab and Hutchings lab can offer the student advice on microbiology and molecular biology. S/he will attend the weekly Environmental Microbiology lab meetings (comprising ~25 researchers, including PIs Murrell, Lehtovirta-Morley, Crombie, Todd) and present their work regularly in lab meetings. Students give at least one seminar annually in an internal research colloquium and are expected to speak in at least one national and one international research conference during their PhD. Students are encouraged to supervise undergraduate lab classes, attend conferences, seminars and workshops and participate in enterprise and engagement. This project will therefore provide the student with a well-rounded research and transferable skill set, and prepare them for a career either within or out of academia.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
NE/S007334/1 01/10/2019 30/09/2027
2287390 Studentship NE/S007334/1 01/10/2019 31/03/2023 Timothy Matsiko Klein