Q-296. Complete Genome Sequence and Genome-Based In Silico Metabolic Model of Rhodoferax ferrireducens

C. Risso1, B. Methé2, J. Sun3, R. Deboy2, D. R. Lovley1;
1Univ. of Massachusetts, Amherst, MA, 2J. Craig Venter Inst., Rockville, MD, 3Genomatica Inc, San Diego, CA.

Rhodoferax ferrireducens is a subsurface, dissimilatory Fe(III)-reducing microorganism. It has the unusual physiological combination of being able to grow aerobically but also to oxidize a wide range of organic compounds, including sugars, to carbon dioxide with Fe(III) or the anode of a microbial fuel cell serving as the sole electron acceptor. In order to better understand the competitive interactions between R. ferrireducens and Geobacter species that are often abundant in the subsurface, the complete genome sequence of R. ferrireducens, provided by the Department of Energy’s Joint Genome Institute, was annotated in detail. These data were then used to construct an in silico model of the central metabolism of this organism. A total 4770 ORFs have been predicted in the genome of 4.7 Mb, of which 2780 have been assigned a function. The reconstructed R. ferrireducens genome-scale model contains 737 genes and 756 reactions. This metabolic model can simulate growth with a diversity of organic acids, benzoate and glucose. Simulations explained why glucose gives the highest biomass yield of any electron donor, and also helped clarify the experimental results that R. ferrireducens can respire with glucose as the electron donor, but cannot grow fermentatively on glucose. R. ferrireducens was found to grow via fumarate fermentation and all the genes required for this metabolism were located in the genome. Unlike Geobacter species, R. ferrireducens does not contain genes for nitrogen fixation, but has genes for the utilization of a number of forms of fixed nitrogen, including nitrate, ammonia and urea. This reliance on fixed nitrogen may play an important role in the competition with Geobacter species in the subsurface. A putative gene involved in the degradation of cellobiose was found and laboratory studies demonstrated anaerobic growth on this compound. The genome revealed that R. ferrireducens should be able to fix carbon dioxide via the Calvin-Benson-Bassham cycle. This iterative combination of experimental and modeling investigations are aiding in a better understanding the environmental role of R. ferrireducens.