Clarifying the regulation of NO/N2O production in Nitrosomonas europaea during anoxic–oxic transition via flux balance analysis of a metabolic network model

• Stoichiometric network modelling was used to analyse NO and N2O production.
• FBA was used to quantify the rates of NO and N2O producing pathways in AOBs.
• N2O is produced due to electron flow imbalances in the cell.
• Cytochromes play a key role in N2O production by directing electron flow.
• The cytochrome P460 reaction can potentially mitigate N2O emissions.

The metabolic mechanism regulating the production of nitric and nitrous oxide (NO, N2O) in ammonia oxidizing bacteria (AOB) was characterized by flux balance analysis (FBA) of a stoichiometric metabolic network (SMN) model. The SMN model was created using 51 reactions and 44 metabolites of the energy metabolism in Nitrosomonas europaea, a widely studied AOB. FBA of model simulations provided estimates for reaction rates and yield ratios of intermediate metabolites, substrates, and products. These estimates matched well, deviating on average by 15% from values for 17 M yield ratios reported for non-limiting oxygen and ammonium concentrations. A sensitivity analysis indicated that the reactions catalysed by cytochromes aa3 and P460 principally regulate the pathways of NO and N2O production (hydroxylamine oxidoreductase mediated and nitrifier denitrification). FBA of simulated N. europaea exposure to oxic–anoxic–oxic transition indicated that NO and N2O production primarily resulted from an intracellular imbalance between the production and consumption of electron equivalents during NH3 oxidation, and that NO and N2O are emitted when the sum of their production rates is greater than half the rate of NO oxidation by cytochrome P460.

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