An overview of the modelled system: batch incubation in a gas-tight vial.

<p>The experiment: The stirred Sistrom's medium <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003933#pcbi.1003933-Lueking1" target="_blank">[27]</a> was inoculated with aerobically grown <i>Pa. denitrificans</i> cells, which were provided with different concentrations of O₂ and (g or aq with a chemical species-name represents gaseous or aqueous, respectively). O₂ is consumed by respiration, driving its transport from the headspace to the liquid. Once the aerobic respiration becomes limited, the cells may switch to denitrification (recruitment), reducing to N₂ via the intermediates NO and N₂O (not shown). For monitoring O₂, CO₂, N₂, NO and N₂O, a robotised incubation system <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003933#pcbi.1003933-Molstad1" target="_blank">[28]</a> was used, which automatically takes samples from the headspace by piercing the rubber septum. Each sampling removes a fraction (3–3.4%) of all gases in the headspace, but it also involves a marginal leakage of O₂ and N₂ into the vial (as indicated by the two-way arrows at the top of the figure). The model: The model operates with two sub-populations: one without and the other with denitrification enzymes ( and , respectively). Both consume O₂ if present, but cannot reduce NO_x. The cells may be recruited to the pool as falls below a critical threshold. The rate of recruitment () is modelled as a probabilistic function: (cells h⁻¹), where represents an O₂ dependent specific-probability (h⁻¹) for any cell to initiate <i>nirS</i> transcription (leading to the synthesis of a full-fledged denitrification proteome).