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Klier, C.

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

Environ. Sci. Technol. 46, 2790-2798 (2012)
DOI PMC
Open Access Green möglich sobald Postprint bei der ZB eingereicht worden ist.
The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter FLUX BALANCE ANALYSIS; STABLE-ISOTOPE FRACTIONATION; PSEUDOMONAS-PUTIDA KT2440; GEOBACTER-SULFURREDUCENS; ESCHERICHIA-COLI; METABOLIC RECONSTRUCTION; IN-SILICO; BIOAVAILABILITY RESTRICTIONS; BIODEGRADATION KINETICS; CATABOLITE REPRESSION
ISSN (print) / ISBN 0013-936X
e-ISSN 1520-5851
Zeitschrift Environmental Science & Technology
Quellenangaben Band: 46, Heft: 5, Seiten: 2790-2798 Artikelnummer: , Supplement: ,
Verlag ACS
Verlagsort Washington, DC
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Groundwater Ecology (IGOE)