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Open Access Highly Accessed Research article

Constraint-based modeling analysis of the metabolism of two Pelobacter species

Jun Sun1*, Shelley A Haveman23, Olivia Bui1, Tom R Fahland14 and Derek R Lovley2

Author Affiliations

1 Genomatica Inc., 10520 Wateridge Circle, San Diego, CA, USA

2 Department of Microbiology, University of Massachusetts, Amherst, MA, USA

3 Luca Technologies Inc., 500 Corporate Circle, Golden, CO, USA

4 Pathway Genomics Corporation, 4045 Sorrento Valley Blvd., San Diego, CA, USA

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BMC Systems Biology 2010, 4:174  doi:10.1186/1752-0509-4-174

Published: 23 December 2010

Abstract

Background

Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells.

Results

In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models.

Conclusions

We have developed genome-scale metabolic models of P. carbinolicus and P. propionicus. These models of Pelobacter metabolism can now be incorporated into the growing repertoire of genome scale models of the Geobacteraceae family to aid in describing the growth and activity of these organisms in anoxic environments and in the study of their roles and interactions in the subsurface microbial community.