Integrating genome-scale metabolic modeling of a microbial community into simulations of subsurface flow and biogeochemical reactive transport.
EMSL Project ID
47984
Abstract
The goal of this project is to develop a mechanistic, quantitative, and predictive simulation capability for coupled flow and biogeochemical reactive transport that accounts for: - genome-specific networks of metabolic reactions ("in silico" models) for microbial species (Geobacter metallireducens (Sun et al., 2009), Geobacter bemedjiensis, Desulfobacter postgatei)
- single reaction TEAPs (Fe(III), U(VI), sulfate) and thermodynamically-constrained Monod-type rate laws for microbial guilds representing specific ecological niches (Yabusaki et al., 2011)
- multicomponent geochemical reaction networks for major ion chemistry, surface complexation (H+, Fe(II), U(VI)), ion exchange (Ca++, Mg++, K+, N+), mineral reactions (goethite, FeS, calcite, siderite) (Fang et al., 2009a)
- dynamic water table and hydraulic gradients in a physically and geochemically heterogeneous, variably-saturated aquifer (e.g., Yabusaki et al. (2011)).
A key component of this project is the use of proteomic data from groundwater samples to assess and refine the magnitude of individual intracellular reaction fluxes predicted by the fundamentally detailed in silico models (> 700 intracellular and exchange reactions per species). Advanced computing is necessary to provide the high performance and large memory to simulate the comprehensively detailed models of coupled processes (e.g., geology, hydrology, biology, chemistry) in the context of three-dimensional multiscale variability in material properties. eSTOMP, a massively parallel processing multifluid flow and biogeochemical reactive transport subsurface simulator is the principal enabling technology that addresses the aforementioned complexity of process and property detail during field experiments in the Rifle (Colorado) IFRC flood plain aquifer. The potential impact of this approach is the engineering of electron donor (e.g., acetate), terminal electron acceptor [e.g., U(VI)], nutrient and/or biogeochemical conditions that enhance metabolic pathways of target microorganism(s) to effect desirable biological transformations, such as reduction in greenhouse gas production and atmospheric release, contaminant destruction and/or immobbilization.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2013-10-01
End Date
2015-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Team Members