Advances in sequencing technologies have enabled the detailed characterization of microbial genomes and environmental metagenomes.
These genomes have been the basis for the reconstruction of detailed metabolic networks and models for several microorganisms.
Geobacter spp., with their unique ability for extracellular electron transfer, are examples of such organisms and have important applications in bioremediation and microbial fuel cells.
In addition to helping to derive an in-depth understanding of the physiology and metabolism of Geobacter spp., genome-scale modelling was valuable in helping to describe microbial ecology and, in particular, the competition of these species with other Fe III reducers.
Integration of the recently developed automated pipeline for metabolic modelling with physiology experiments will allow researchers to use the modelling approaches described here for the characterization of other environmentally relevant microorganisms.
There is a wide diversity of unexplored metabolism encoded in the genomes of microorganisms that have an important environmental role. Genome-scale metabolic modelling enables the individual reactions that are encoded in annotated genomes to be organized into a coherent whole, which can then be used to predict metabolic fluxes that will optimize cell function under a range of conditions. In this Review, we summarize a series of studies in which genome-scale metabolic modelling of Geobacter spp. has resulted in an in-depth understanding of their central metabolism and ecology. A similar iterative modelling and experimental approach could accelerate elucidation of the physiology and ecology of other microorganisms inhabiting a diversity of environments, and could guide optimization of the practical applications of these species.
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We acknowledge the US Department of Energy's Genomic Science Program (cooperative agreement DE-FC02-02ER63446) and Subsurface Biogeochemical Research Program (grant DE-FG02-07ER64367) for funding, and C. O'Connell for help with the illustrations.
Bernhard Ø. Palsson has a financial interest in Genomatica Inc., although the findings reported in this publication do not directly relate to the interests of Genomatica, Inc.
Radhakrishnan Mahadevan and Derek R. Lovely declare no competing financial interests.
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- Humic substances
The fraction of the dark organic matter that is stable and can serve as electron carriers.
- Anoxic submerged soil
An underground, water-saturated, permeable sediment.
- Dissimilatory metal reduction
An enzymatic reaction in which a metal is reduced but is not assimilated or incorporated into cells for the purposes of biosynthesis during, for example, respiration.
- Tricarboxylic acid cycle
The reaction cycle that serves as the primary source of reduced carriers in metabolism.
- ACK–POR pathway
The acetate kinase (ACK)–pyuvate oxidoreductase (POR) pathway for the generation of pyruvate from acetate in anaerobes.
- Anapleurotic reaction
A reaction that replenishes metabolites that are removed from the tricarboxylic acid cycle.
- Glyoxylate bypass
An alternative pathway (instead of the tricarboxylic acid cycle) for the use of acetate through the generation of glyoxalate.
- Metabolite connectivity
The number of reactions in which a metabolite participates.
- ATP synthase
An enzyme that synthesizes ATP using the electrochemical gradient across the membrane.
A model-based optimization algorithm for metabolic engineering.
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Mahadevan, R., Palsson, B. & Lovley, D. In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nat Rev Microbiol 9, 39–50 (2011). https://doi.org/10.1038/nrmicro2456
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