The regulation of microbial nitrogen-transforming pathways: an enzyme-explicit modeling approach

Nitrogen is an essential component of all living organisms. Though atmospheric dinitrogen gas serves as the vast inventory of nitrogen source, it is only biologically available to a few nitrogen-fixing microorganisms and plants. Most organisms rely on reactive forms of nitrogen whose availability depends on diverse nitrogen-transforming reactions that are carried out by complex networks of metabolically versatile microorganisms in both cooperative and competitive ways. To elucidate critical regulation points in microbial nitrogen transforming pathways, we constructed an enzyme-explicit nitrogen reaction network model consisting of 14 redox reactions involving 6 nitrogen species of different oxidation states. By coupling microbial growth with paired energy-yielding redox reactions, we were able to simultaneously predict biochemical transformations and reaction paths that display microbial community changes without having to directly parameterize microbial species guilds, which makes our enzyme-explicit model highly scalable to microbial communities with varying complexity. The regulation of nitrogen reaction networks is formulated using two distinct modeling approaches: (1) The enzyme kinetics-based approach in which enzymatic regulation is described based on competitive inhibitions on top of Michaelis-Menten kinetics. (2) The cybernetic approach in which the regulation is formulated with cybernetic control variables determined by accounting for optimal resource allocation. Both approaches for formulating microbial regulations provide proper descriptions of selected pathways within the complete nitrogen reaction work during model calibrations with simplified batch reactions. However, the cybernetic approach provides more robust and stable simulations for complex systems under dynamic environmental conditions. The dynamic interplay among various nitrogen substrates, enzyme responses and partitioning of carbon resources captured using the cybernetic approach is critical for elucidating the microbial regulation of biogeochemical transformations. With the increasing availability of high throughput -omics data, our enzyme-explicit model with cybernetic regulation provides a reasonable basis for incorporating microbial metabolism numerically across scales.