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Title: Dynamic Metabolic Modeling of Denitrifying Bacterial Growth: The Cybernetic Approach

Denitrification is a multistage reduction process converting nitrate ultimately to nitrogen gas, carried out mostly by facultative bacteria. Modeling of the denitrification process is challenging due to the complex metabolic regulation that modulates sequential formation and consumption of a series of nitrogen oxide intermediates, which serve as the final electron acceptors for denitrifying bacteria. In this work, we examined the effectiveness and accuracy of the cybernetic modeling framework in simulating the growth dynamics of denitrifying bacteria in comparison with kinetic models. In four different case studies using the literature data, we successfully simulated diauxic and triauxic growth patterns observed in anoxic and aerobic conditions, only by tuning two or three parameters. In order to understand the regulatory structure of the cybernetic model, we systematically analyzed the effect of cybernetic control variables on simulation accuracy. The results showed that the consideration of both enzyme synthesis and activity control through u- and v-variables is necessary and relevant and that uvariables are of greater importance in comparison to v-variables. In contrast, simple kinetic models were unable to accurately capture dynamic metabolic shifts across alternative electron acceptors, unless an inhibition term was additionally incorporated. Therefore, the denitrification process represents a reasonable example highlighting themore » criticality of considering dynamic regulation for successful metabolic modeling.« less
Publication Date:
OSTI Identifier:
Report Number(s):
Journal ID: ISSN 0888-5885; KP1601010
DOE Contract Number:
Resource Type:
Journal Article
Resource Relation:
Journal Name: Industrial and Engineering Chemistry Research; Journal Volume: 54; Journal Issue: 42
American Chemical Society (ACS)
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
Sponsoring Org:
Country of Publication:
United States
denitrification process; cybernetic model; kinetic model; metabolism; regulation