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Microbial biogeochemistry in agricultural landscapes: An investigation of reactive nitrogen oxide fluxes from soil

Primary Supervisor: Dr Ryan M Mushinski, School of Life Sciences

Secondary supervisor: Professor Gary Bending

PhD project title: Microbial biogeochemistry in agricultural landscapes: An investigation of reactive nitrogen oxide fluxes from soil.

University of Registration: University of Warwick

Project outline:


A range of pollutant gases, and especially nitrogen (N) compounds (N2O, NO, NO2, etc.) are emitted to the atmosphere from agricultural activities.1 These gases are extremely important for a myriad of reason including their contribution to climate change, urban air pollution, and N-deposition. Common agricultural practices such as fertilization will continue to increase, likely resulting in high emissions. However, N-gas forecasts from agricultural lands are hampered by (1) a lack of field-based measurements and (2) an incomplete understanding of the processes associated with production and consumption of these gases.2 Additionally, efforts are currently being made to increase carbon (C) storage in soil, which may have direct consequences on emissions of atmospherically-relevant gases. This project aims to better quantify N-gas fluxes from agricultural systems as well as map the connectedness of microbial soil C and N cycling in relation to gas emissions. 

Aims and Objectives

  • Quantify reactive N-gas emissions along gradients of soil N and C in agricultural systems.
  • Use culture-independent methods to identify agricultural soil microbiomes, specifically focusing on heterotrophic microbes that produce extracellular reactive oxygen (H2O2) as well as N-cycle taxa.
  • Explore how N-cycle intermediates and products (e.g, NO and NH2OH) react extracellularly with reactive oxygen produced by heterotrophic bacteria and fungi to form various reactive N products.

Background and Context

The N-cycle is a significant source of atmospheric N-gases; however, the conditions leading to both emission and consumption are extremely complex. This is particularly true for the suite of NOz gases (HONO, HNO3, organic nitrates, and particulate nitrates), which are much less studied than N2O, NO, and NO2, but represent an important driver of climate via their contribution to the oxidizing capacity of the atmosphere. Additionally, there are potential intersections between N-cycling microbes and those involved in carbon-cycling, which may affect transformations of N in the soil. For example, N-cycle products (e.g., NH2OH and NO) can react extracellularly with reactive oxygen species (ROS = OH, O2¯, HO2, H2O2) generated by heterotrophic microbes to produce reactive N compounds such as nitrite and NO2. These types of understudied reactions in soil represent a major gap in our understanding of the N-cycle which prevents us from scaling these processes to the regional and global scales. This proposed study will explore how agricultural practices found throughout the UK influence N-gas emissions and systematically evaluate the responsible mechanisms.

Project Description

The approach will be to couple microbiological analysis (culture-independent) to field-based measurements taken from the University of Warwick – Wellesbourne Campus.3 Various crops will be planted under differing soil nitrogen and carbon concentrations. Field-based fluxes of NO, NO2, and NOz will be measured, while soil ROS and N-cycle rates will be quantified from sampled soil to allow for the establishment of predictive relationships between these variables and to provide evidence for the role of ROS in reactive N production. Results will allow the student to establish correlations between gas flux potentials on specific crops, fertilizer, soil carbon, ROS production rates, and microbial assemblages.


  1. Robertson GP, Paul EA, Harwood RR. 2000. Greenhouse Gases in Intensive Agriculture:
  2. Contributions of Individual Gases to the Radiative Forcing of the Atmosphere. Science 289: 1922-1925.
  3. Hudman, R. C. et al. 2012. Steps towards a mechanistic model of global soil nitric oxide
  4. emissions: implementation and space based-constraints. Atmospheric Chemistry & Physics 12: 7779-7795.
  5. University of Warwick – Wellesbourne Campus:

BBSRC Strategic Research Priority: Sustainable Agriculture and Food, Plant and Crop Science

Techniques that will be undertaken during the project:

Training during this fellowship includes a wide range of molecular techniques and analyses (microbial culturing, DNA extraction from soil, PCR, sequencing, and bioinformatics) as well as analytical chemistry (nitrogen oxide quantification, reactive oxygen extraction from soil and subsequent quantification, and building sampling microcosms). Field-based cultivation and management of agricultural crops will also be emphasized.

Typical pattern of working hours:

  • 35 hrs per week with flexible working arrangements

Contact: Dr Ryan Mushinski, University of Warwick