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In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

Nature Reviews Microbiology volume 9, pages 39–50 (2011)Cite this article

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An Erratum to this article was published on 16 February 2011

This article has been updated

Key Points

  • 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.

Abstract

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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Figure 1: Iterative and integrated experimental and computational methodology for studying the physiology and metabolism of Geobacter spp.
Figure 2: Model-based insights into acetate and isoleucine metabolism in Geobacter spp.
Figure 3: Alternative mechanisms for maintaining metabolic robustness in microorganisms with different metabolic capabilities.
Figure 4: Proton accumulation during substrate oxidation.
Figure 5: Model-aided metabolic engineering of Geobacter sulfurreducens through the introduction of a futile cycle that leads to increased respiration as well as reduced biomass synthesis.
Figure 6: Genome-scale constraint-based models for the prediction of microbial composition as a function of the environment.
Figure 7: Coupling metabolic models with transport and geochemical models.

Change history

  • 05 January 2011

    In the original article, the Acknowledgements section was omitted; this section has now been included: Acknowledgements: 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. We apologize for this omission.

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Acknowledgements

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.

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Authors and Affiliations

  1. Department of Chemical Engineering and Applied Chemistry, and Institute of Biomaterials and Biomedical Engineering, University of Toronto, 200 College Street, Toronto, M5S 3E5, Ontario, Canada

    Radhakrishnan Mahadevan

  2. Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, 0412, La Jolla, 92093-0412, California, USA

    Bernhard Ø. Palsson

  3. Department of Microbiology, University of Massachusetts, Amherst, 639 North Pleasant Street, Amherst, 01003, Massachusetts, USA

    Derek R. Lovley

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  1. Radhakrishnan Mahadevan
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  2. Bernhard Ø. Palsson
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Correspondence to Radhakrishnan Mahadevan.

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Competing interests

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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Updated list of COBRA reconstructions

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Oxygen-depleted sediment.

Aquifer

An underground, water-saturated, permeable sediment.

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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.

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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.

OptKnock

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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