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


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


Project Description


Dr Laura Lehtovirta-Morley (UEA Biological Sciences)

Prof Matt Hutchings (UEA)

Prof 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 archaea play a critical role in nitrogen cycling in soil ecosystems. 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.

Figure 1. Key players in the global nitrogen cycle: Nitrosotalea devanaterra, one of the model archaea used in this studentship


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 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 Matt Hutchings (UEA) and Colin Murrell (UEA).

Person specification

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


  • Nayak DD, Metcalf WW (2017) Cas9-mediated genome editing in the methanogenic archaeon Methanosarcina acetivorans. PNAS 114:2976-2981.
  • 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.
  • 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.
  • 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.
  • Crombie AT and Murrell JC (2014) Trace gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature 510:148-151.

Application open

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