Nitrous oxide (N₂O) is both a potent greenhouse gas and capable of destroying stratospheric ozone, making it important to understand controls on its production and release from soils. When oxygen is limiting in soils, some microorganisms can use nitrogen-oxides as electron acceptors during denitrification and release N₂O or N₂, contingent on the consumption of N₂O. Nitrous oxide release from soils is thus the net result of both production and consumption by soil microorganisms. To better understand the primary controls on N₂O production versus consumption, we developed a systems biology model of the denitrification gene regulatory network, and then conducted experiments on soils from a mesic grassland where soil organic carbon is relatively plentiful and inorganic N concentrations and denitrification potentials are high.

Results/Conclusions

The structure of our model is based on published regulatory pathways for the genes that code for denitrification enzymes and their associated transcription factors, that are characterized by common biological network motifs. We use the model to study the effects of nitrate and oxygen concentration on gene regulation, particularly the regulation of nitrous oxide reductase, because this enzyme reduces N₂O to N₂ and thus ultimately controls the ratio of N₂O production to consumption. We verify the qualitative network structure and estimate model parameters using rates of N₂O production and consumption in the denitrifying species Pseudomonas fluorescens under different levels of NO­₃^-, O₂ and N₂O. This model allows us to predict the conditions under which production vs. consumption of N₂O will dominate observed net N₂O fluxes from soils. In addition, during soil incubations under anaerobic conditions, we tested the effects of oxygen concentration, carbon availability, and nitrate concentration on N₂O release from soils. We found that nitrate concentration exerts the highest level of control on the magnitude of net N₂O efflux, and appears to be the most important driver of the ratio of N₂O production to consumption. Oxygen concentrations also drive the magnitude of gross N₂O production, but seem to have little influence on ratios of N₂O production versus consumption.