skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

Abstract

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration withmore » hydrologic flow simulators.« less

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1406754
Report Number(s):
PNNL-SA-129317
Journal ID: ISSN 1664-302X; KP1702030
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Frontiers in Microbiology; Journal Volume: 8
Country of Publication:
United States
Language:
English

Citation Formats

Song, Hyun-Seob, Thomas, Dennis G., Stegen, James C., Li, Minjing, Liu, Chongxuan, Song, Xuehang, Chen, Xingyuan, Fredrickson, Jim K., Zachara, John M., and Scheibe, Timothy D.. Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process. United States: N. p., 2017. Web. doi:10.3389/fmicb.2017.01866.
Song, Hyun-Seob, Thomas, Dennis G., Stegen, James C., Li, Minjing, Liu, Chongxuan, Song, Xuehang, Chen, Xingyuan, Fredrickson, Jim K., Zachara, John M., & Scheibe, Timothy D.. Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process. United States. doi:10.3389/fmicb.2017.01866.
Song, Hyun-Seob, Thomas, Dennis G., Stegen, James C., Li, Minjing, Liu, Chongxuan, Song, Xuehang, Chen, Xingyuan, Fredrickson, Jim K., Zachara, John M., and Scheibe, Timothy D.. Fri . "Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process". United States. doi:10.3389/fmicb.2017.01866.
@article{osti_1406754,
title = {Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process},
author = {Song, Hyun-Seob and Thomas, Dennis G. and Stegen, James C. and Li, Minjing and Liu, Chongxuan and Song, Xuehang and Chen, Xingyuan and Fredrickson, Jim K. and Zachara, John M. and Scheibe, Timothy D.},
abstractNote = {In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators.},
doi = {10.3389/fmicb.2017.01866},
journal = {Frontiers in Microbiology},
number = ,
volume = 8,
place = {United States},
year = {Fri Sep 29 00:00:00 EDT 2017},
month = {Fri Sep 29 00:00:00 EDT 2017}
}