Metabolic Reaction Modeling: A New Approach to Geomicrobial Kinetics
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Date
2015-08-18
Authors
McKernan, Shannon
Journal Title
Journal ISSN
Volume Title
Publisher
University of Oregon
Abstract
Geomicrobial metabolic rates, the speed at which microbes interact and metabolize available substrates from their surroundings, are important parameters in geochemistry and biogeochemistry. Here, I present a new modeling technique to predict geomicrobial rates on the basis of intracellular enzyme reaction networks.
Methanosarcina acetivorans is a marine methanogen capable of disproportioning acetate to methane and carbon dioxide via the acetoclastic pathway. My model uses new developments in biogeochemical and genome-scale metabolic modeling to estimate the rates at which acetoclastic methanogenesis proceeds under a range of acetate concentrations. Based on existing literature, models, and online databases, I constrain enzyme reactions of the model kinetically and thermodynamically.
My results include (1) simulated concentrations of metabolites and enzymes and (2) rates and thermodynamic states of enzyme reactions. From these results, I use a Monod equation to kinetically predict rates of acetoclastic methanogenesis for M. acetivorans within one order of magnitude of experimental results.