Systems Approach to Environmental Microbiology

Decreasing costs of DNA sequencing and advances in molecular ecology tools have made it feasible to take a systems biology approach to environmental microbiology questions.  Communities in which Geobacter species predominant have been a good testing ground for this environmental systems biology approach because it has also been possible to recover environmentally relevant Geobacter species in pure culture for additional functional genomic studies and genome-scale metabolic modeling.

Studies at the Department of Energy’s uranium bioremediation field study site in Rifle, CO (link to SBR web page on this) have demonstrated that it is possible to diagnose the in situ metabolic status of Geobacter and other organisms important in the bioremediation process, providing a guide to strategies to better promote desired activities.  It has been demonstrated that genome-scale metabolic models can be coupled with hydrogeological models to predict the outcome of uranium bioremediation strategies and to describe the competition between microbial populations for resources under natural attenuation and engineered bioremediation.

Selected Publications with Environmental Focus (for pure culture studies please visit full publication list)

Jiae Yun, Toshiyuki Ueki, Marzia Miletto, and Derek R. Lovley.  2011.  Monitoring the Metabolic Status of Geobacter Species in Contaminated Groundwater by Quantifying Key Metabolic Proteins with Geobacter-Specific Antibodies.  APPLIED AND ENVIRONMENTAL MICROBIOLOGY.  77:4597-4602.

Hila Elifantz, Lucie A. N’Guessan, Paula J. Mouse, Kenneth H. Williams, Michael J. Wilkins, Carla Risso, Dawn E. Holmes, Philip E. Long, and Derek R. Lovley. 2010. Expression of acetate permease-like (apl) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations. FEMS Microbiol Ecol [Epub ahead of print]

Jiao Zhao, Yilin Fang, Timothy D. Scheibe, Derek R. Lovley, and Joern T. Larsen. 2010. Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments. J Contam Hydrol 112(1-4):30-44.

Lucie A. N’Guessan, Hila Elifantz, Kelly P. Nevin, Paula J. Mouse, Barbara Methé, Trevor L. Woodard, Kimberly Manley, Kenneth H. Williams, Michael J. Wilkins, Joern T. Larsen, Philip E. Long, and Derek R. Lovley. 2010. Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer. ISME J 4(2):253-66.

Michael J. Wilkins, N.C. Verberkmoes, Kenneth H. Williams, Stephen J. Callister, Paula J. Mouse, Hila Elifantz, Lucie A. N’Guessan, Brian C. Thomas, Carrie D. Nicora, Manesh B. Shah, Paul Abraham, Mary S. Lipton, Derek R. Lovley, Robert L. Hettich, Philip E. Long, and Jillian F. Banfield. 2009. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol 75(20):6591-6599.

Kai Zhuang, Mounir Izallalen, Paula Mouser, Hanno Richter, Carla Risso, Joern T. Larsen and Derek R Lovley. Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. The ISME Journal5, 305-316 (February 2011) | doi:10.1038/ismej.2010.117

Paula J. Mouser, Dawn E. Holmes, Lorrie A. Perpetua, Raymond DiDonato, Brad Postier, Anna Liu, and Derek R. Lovley. 2009. Quantifying expression of Geobacter spp. oxidative stress genes in pure culture and during in situ uranium bioremediation. ISME J 3(4):454-65.

Paula J. Mouser, Lucie A. N’Guessan, Hila Elifantz, Dawn E. Holmes, Kenneth H. Williams, Michael J. Wilkins, Philip E. Long, and Derek R. Lovley. 2009. Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater. Environ Sci Technol 43(12):4386-92.

Timothy D. Scheibe R. Mahadevan, Yilin Fang, S. Garg, Philip E. Long, and Derek R. Lovley. 2009. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microbial Biotechnology 2(2):274-286.

Dawn E. Holmes, Regina A. O’Neil, Milind A. Chavan, Lucie A. N’Guessan, Helen A. Vrionis, Lorrie A. Perpetua, M. Juliana Larrahondo, Raymond DiDonato, Anna Liu, and Derek R. Lovley. 2009. ISME J 3(2):216-230.

Regina A. O’Neil, Dawn E. Holmes, M.V. Coppi, L.A. Adams, M. Juliana Larrahondo, J.E. Ward, Kelly P. Nevin, Trevor L. Woodard, Helen A. Vrionis, A.L. N'Guessan, and Derek R. Lovley. 2008. Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation. Environ Microbiol 10(5):1218-1230.

Dawn E. Holmes, T. Mester, Regina A. O’Neil, Lorrie A. Perpetua, M. Juliana Larrahondo, R. Glaven, Manju L. Sharma, Joy E. Ward, Kelly P. Nevin, and Derek R. Lovley. 2008. Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes. Microbiology(154):1422-1435.

Derek R. Lovley, R. Mahadevan, and Kelly P. Nevin. 2008. Systems biology approach to bioremediation with extracellular electron transfer. In E. Diaz (ed.), Microbial biodegradation, Genomics and molecular biology. Caister Academic Press, Norfolk, UK. pp. 71-96.

Dawn E. Holmes, Kelly P. Nevin, Regina A. O’Neil, J.E. Ward, L.A. Adams, Trevor L. Woodard, Helen A. Vrionis, and Derek R. Lovley. 2005. Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes. Appl Environ Microbiol 71(11):6870-6877.

Dawn E. Holmes, Kelly P. Nevin, and Derek R. Lovley. 2004. In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol 70(12):7251-7259.

Derek R. Lovley 2003. Cleaning up with genomics: Applying molecular biology to bioremediation. Nature Reviews Microbiology 1(1):36-44.