Constraint-based in silico modelling of the Fe(III)- reducing bacteria Geobacter sulfurreducens: insights into the subsurface microbial activity

1. Abstract Here we describe the application of the constraint-based modeling approach, coupled in an iterative fashion with experimental studies, to further elucidate the physiology of Geobacter sulfurreducens, a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. The completed reconstructed metabolic network of G. sulfurreducens contained 588 genes (or 17% of a total of 3,467 ORFs), 522 biochemical reactions, and 541 unique metabolites. Examination of the reconstructed metabolic network revealed that G. sulfurreducens has multiple reactions for acetate utilization, the main electron-donor for these bacteria in the subsurface. Simulations fit well with experimental data obtained from chemostat studies, predicting different flux rates and growth yield under a number of growth rates. Evaluation of the rates of proton production and consumption in the extracellular and cytoplasmic compartments revealed the energy conservation with extracellular elelctron acceptors as Fe(III), was limited compared to intracellular acceptors as fumarate. These results demonstrate that iterative modeling coupled with experimentation can accelerate the understanding of the physiology of poorly studied but environmentally relevant organisms and may help optimize their practical applications.