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A multidisciplinary approach to unlock soil organic nitrogen transformations

Principal Supervisor: Dr Yin Chen, School of Life Sciences, University of Warwick

Co-supervisors: Professor Alex Cameron, School of Life Sciences; Professor Timothy Bugg, Department of Chemistry; Dr Corrine Smith, School of Life Sciences

PhD project title:  A multidisciplinary approach to unlock soil organic nitrogen transformations

University of Registration: University of Warwick

Project outline:

A steadily increasing population demands more food production from agricultural crops, which in turn drives the increased demand for nitrogen fertilisers. Ammonium and nitrate are the predominant inorganic forms of nitrogen applied to crops. These not only increase the cost of food production but also have considerable environmental consequences such as the release of greenhouse gases (NOX). An important yet overlooked source of nitrogen for crops is organic nitrogen. Recent evidence suggests that up to 50% of the soil nitrogen pool consists of methylated ammonium compounds, such as choline, carnitine and trimethylamine oxide (CR Warren, New Phytologist 198: 476-485). Understanding the re-mineralization of such methylated ammoniums to inorganic nitrogen is vital for future cost-effective management of nitrogen fertilization in the field.

Soil microbes are largely responsible for the transformation of organic nitrogen species to inorganic nitrogen, which can then be utilized by plants. However, our knowledge on the key microbes involved in the remineralization of methylated ammoniums to ammonium is very limited: the main players remain un-established; the key enzymes remain poorly understood, the underpinning catalytic mechanisms are unknown. Recent research at Warwick has established that certain soil rhizobial species are capably of methylated ammonium remineralisation (e.g. Chen et al., 2010 Applied and environmental microbiology 76: 4102-4104). The aim of the project is therefore twofold: 1) to characterise the transformation and regulation of methylated ammonium remineralisation to ammonium by these soil rhizobia, and 2) to study a key known enzyme, Tdm (Zhu et al., 2016 FEBS Journal), involved in ammonium remineralisation by these soil microbes using molecular, biochemical and structural approaches.


  1. CR Warren, New Phytologist 198: 476-485;
  2. Chen et al., 2010 Applied and environmental microbiology 76: 4102-4104
  3. Zhu et al., 2016 FEBS Journal 283:3979-3993

BBSRC Strategic Research Priority: Food Security

Techniques that will be undertaken during the project:

  • Isolation and cultivation of soil rhizobia
  • Targeted gene mutagenesis and complementation
  • Protein expression and biochemical characterization
  • Stopped flow enzyme kinetics
  • Inductively coupled plasma mass spectrometry
  • Homology modelling and X-ray crystallization
  • High resolution cryo-electron microscopy (cryo-EM)
Contact: Dr Yin Chen, University of Warwick