Fossil Fuel Bioprocessing programs

Souring Systems Biology Program: Rates and Mechanisms

MEHR -- Microbially Enhanced Hydrocarbon Recovery --  involves a broad diversity of metabolic processes that act either individually or cooperatively to improve hydrocarbon production and energy yields, and reduce the environmental footprint.  An in-depth understanding of these metabolic processes and the controlling parameters comes from focused interdisciplinary research into model organisms or communities known to perform the relevant functions. 


Systems Biology: This work involves a variety of metabolomic, transcriptomic, proteomic, genomic, and biogeochemical approaches.  A focused aspect of these studies is the development of model organisms or microbial assemblies from members of relevant Petroleum Reservoir microbial populations that have been enhanced in specific functional processes(e.g. biosurfactant production, hydrocarbon biotransformation, hydrocarbon viscosity reduction, biosouring control). Overall these studies provide a basic understanding of the microbiology, biochemistry, molecular biology, and biogeochemistry involved in MEHR relevant metabolic processes and will potentially result in the development of novel strategies to control biosouring, enhance hydrocarbon recovery, and reduce the environmental footprint of oil reservoir processes.

program Highlights

2014 Highlights

In 2014 we continued our investigations of the biogenesis of solid-phase minerals to enhance concretion of unconsolidated matrices and offset worm-holing and bypass events during oil recovery. We investigated the underlying biochemical and genetic mechanisms of phosphorous metabolism and were able to enhance the growth rate of phosphorous metabolizing organisms almost 10-fold. We continued our investigations into the potential for microbial (per)chlorate respiration to control biogenic sulfide production and oil reservoir souring. Hydrogen sulfide (H2S) biogenesis by sulfate reducing microorganisms (SRM) is a potentially deleterious metabolism and is the primary cause of industrial gas inhalation deaths in the U.S. In oil recovery, microbially produced H2S in reservoir gases and fluids has an associated annual cost estimated at $90 billion. Previous studies demonstrated that amendment of active sulfidogenic-packed columns with (per)chlorate resulted in a rapid decrease in H2S production. Over the last year we demonstrated that the mechanism of (per)chlorate inhibition of SRM is multifaceted involving specific interference with SRM biochemistry, thermodynamic preference over sulfate respiration, and sulfide removal through oxidation coupled to (per)chlorate respiration. Our studies involved pure culture models but were confirmed in complex undefined sulfidogenic communities metabolizing multifarious substrates. We continued our investigations of microbial (per)chlorate respiration and identified and characterized several new isolates at both the phenotypic and genome level. We further characterized the genetic basis of (per)chlorate respiration and functionally described new regulatory and stress response genes involved. We investigated the biochemical basis of (per)chlorate respiration and have isolated several of the proteins involved in this unique pathway. We are characterizing these enzymes with a goal of identifying their unique functionality.

2013 Highlights

Over the last year we continued our investigations of microbial processes that produce solid-phase minerals which could be judiciously applied to modify rock porosity with subsequent alteration and improvement of floodwater sweep. As part of these studies we identified the mechanism underlying nitrate-dependent Fe(II) oxidation and demonstrated that the application of this technology to oil saturated columns resulted in an oil recovery enhancement of over 200%. In addition we also investigated the potential for microbial (per)chlorate respiration to control biogenic sulfide production and oil reservoir souring. Hydrogen sulfide (H2S) biogenesis by sulfate reducing microorganisms (SRM) is a potentially deleterious metabolism and is the primary cause of industrial gas inhalation deaths in the US. Anthropogenic H2S sources are dominated by the oil industry but also include pulp and paper manufacture, rayon textile production, chemical manufacture, and waste disposal. In the case of oil recovery, microbially produced H2S in reservoir gases and fluids has an associated annual cost estimated in the order of $90 billion. Our studies demonstrated that amendment of active sulfidogenic packed columns with (per)chlorate resulted in a rapid decrease in H2S production. (Per)chlorate showed distinct effects on microbial community structure compared with nitrate and resulted in a general suppression of the community relative to the untreated control combined with a significant decrease in sulfate reducing species abundance indicating specific toxicity. Furthermore we demonstrated that dissimilatory (per)chlorate reducing bacteria innately oxidize H2S. H2S was preferentially utilized over organic electron donors resulting in an enriched (34S)-elemental sulfur product. Electron microscopy revealed elemental sulfur production in the cytoplasm and on the cell surface. Based on our results we proposed a novel hybrid enzymatic-abiotic mechanism for H2S oxidation similar to that recently proposed for nitrate-dependent Fe(II) oxidation. The results of our studies have implications for the control of biosouring and biocorrosion in a range of industrial environments.

2012 Highlights

Our research over the last year has continued to investigate microbial processes that produce solid-phase minerals which could be judiciously applied to modify rock porosity with subsequent alteration and improvement of floodwater sweep. To date, there has been little investigation of these processes to enhanced oil recovery. We investigated a unique approach to altering reservoir petrology through the biogenesis of iron-based authigenic rock minerals. This process is mediated by chemolithoautotrophic nitrate-dependent Fe(II)-oxidizing microorganisms which precipitate iron minerals from the metabolism of soluble ferrous iron (Fe2+). This mineral biogenesis can result in pore restriction and reduced pore throat diameter.


Advantageously, and unlike biomass plugs, these biominerals are not susceptible to pressure or thermal degradation. Furthermore, they do not require continual substrate addition for maintenance. Our studies demonstrated the biogenesis of various insoluble iron minerals in packed bed columns resulted in effective hydrology alteration and homogenization of heterogenous flowpaths upon stimulated microbial Fe2+ biooxidation.


Oil saturated column studies demonstrated an effective enhancement in oil recovered of over 100%. We characterized the organisms responsible for this metabolism and identified an underlying biochemical mechanism. As a positive benefit of this metabolism, we demonstrated that these organisms produce excess amounts of nitrogen oxyanions (NO2-, NO, N2O), all of which are known to have beneficial effects by inhibiting microbial sulfate reduction in oil reservoirs. These studies indicate the potential for nitrate-dependent Fe2+ biooxidation to improving sweep efficiency and enhancing oil recovery.

2011 Highlights

In 2011 Coates' group demonstrated that selective microbial precipitation of iron minerals can successfully eradicate flowpath preference and normalize total flow. They developed a novel phosphite-based medium to prevent uncontrolled chemical precipitation of iron minerals and optimize the biological triggering of iron precipitation. They also characterized the novel thermophilic iron-reducing organism Thermincola potens, which dissolves solid iron minerals, and identified the biochemical and genetic basis of this process. Biosouring, the unwelcome presence of hydrogen sulfide in oil reservoirs, is another target of Coates’s research. The team is working on a novel method to biologically control the sulfate-reducing microbial community using chlorate control of sulfidogenesis.

2010 Highlights

Coates group efforts focused on hydrocarbon biotransformation and lithology alteration by model organism Dechloromonas aromatica, a beta-proteobacterium that oxidizes a diverse range of monoaromatic hydrocarbons. Researchers characterized its aerobic benzene oxidation pathway and investigated mechanisms involved in the respiration of the insoluble Fe(III) oxyhydroxides by Thermincola potens. These findings provide the first study to implicate direct extracellular electron transfer by Gram-positive bacteria and identify c-type cytochromes as a potential molecular conduit for charge transport.



Published in 2014

Isotopic Insights into Microbial Sulfur Cycling in Oil Reservoirs, C. G. Hubbard, Y. Cheng, A. Engelbrekston, J. L. Druhan, L. Li, J. B. Ajo-Franklin, J. D. Coates and M.E. Conrad, Frontiers in Microbiology, doi: 10.3389/fmicb.2014.00480, 2014.


Inhibition of Microbial Sulfate Reduction in a Flow-Through Column System by (Per)chlorate Treatment, A. Engelbrektson, C. G. Hubbard, L.M. Tom, A. Boussina, Y. T. Jin, H. Wong, Y. M. Piceno, H. K. Carlson, M. E. Conrad, G. Andersen and J. D. Coates, Frontiers in Microbiology, doi: 10.3389/fmicb.2014.00315, 2014. 


Methane Oxidation Linked to Chlorite Dismutation, L. G. Miller, S. M. Baesman, C. I. Carlstrom, J. D. Coates, R. S. Oremland, Frontiers in Microbiology, V. 5, doi: 10.3389/fmicb.2014.00275, 2014. 


Chlorate Reduction in Shewanella Algae ACDC is a Recently Acquired Metabolism Characterized by Gene Loss, Suboptimal Regulation and Oxidative Stress, I. C. Clark, R. A. Melnyk, A. T. Iavarone, P. S. Novichkov, J. D. Coates, Molecular Microbiology, doi:10.1111/mmi.12746.


Control of Sulfidogenesis Through Bio-oxidation of H2S Coupled to (Per)chlorate Reduction, P. A. Gregoire, A. Engelbrektson, C. G. Hubbard, Z. Metlagel, R. Csencsits, M. Auer, M. E. Conrad, J. Thieme, P. Northrup and J.D. Coates, Environmental Microbiology, doi: 10.1111/1758-2229.12156, December 2014. 


Published in 2013

Applicability of Anaerobic Nitrate-Dependent Fe(Ii) Oxidation to Microbial Enhanced Oil Recovery (MEOR), H. Zhu, J. D. Coates, Environmental Science & Technology, doi: 10.1021/es401838b, 2013/06/27 2013.


Physiological and Genetic Description of Dissimilatory Perchlorate Reduction by the Novel Marine Bacterium Arcobacter Sp. Strain Cab, C. I. Carlstrom, O. Wang, R. A. Melnyk, S. Bauer, J. Lee, A. Engelbrektson, J. D. Coates, mBio, doi: 10.1128/mBio.00217-13, May 2013.


Surfaceomics and Surface-Enhanced Raman Spectroscopy of Environmental Microbes: Matching Cofactors with Redox-Active Surface Proteins, H. K. Carlson, A. T. Lavarone, J. D. Coates, Proteomics, doi: 10.1002/pmic.201300010, April 2013.


Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions, Hans K. Carlson, Iain C. Clark, Steven J. Blazewicz, Anthony T. Lavarone, John D. Coates, Journal of Bacteriology, doi: 10.1128/JB.00058-13, May 2013.

Published in 2012

Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002, Kathryne Byrne-Bailey, Karrie Weber, John D. Coates, Journal of Bacteriology, 194(9), pp. 2400-2401, doi: 10.1128/JB.00214-12, May 2012.


Bioelectrical Redox Cycling of Anthraquinone-2,6-Disulfonate Coupled to Perchlorate Reduction, Iain Clark, Hans Carlson, Anthony Iavarone, John D. Coates, Energy & Environmental Science, doi: 10.1039/c0xx00000x, Accepted Manuscript, May 2012.


Towards a Mechanistic Understanding of Anaerobic Nitrate Dependent Iron Oxidation: Balancing Electron Uptake and Detoxification, Hans Karl Carlson, Iain Clark, Ryan Melnyk, John D. Coates, Frontiers in Microbiology 3:57, doi: 10.3389/fmicb.2012.00057, February 20, 2012.


Pseudomonas syringae Coordinates Production of a Motility-Enabling Surfactant with Flagellar Assembly, Adrien Burch, Briana K. Shimada, Sean W. A. Mullin, Christopher Dunlap, Michael Bowman, Steven Lindow, Journal of Bacteriology194(4), doi: 10.1128/JB.06058-11, February 2012.


Surface Multiheme C-Type Cytochromes from Thermincola potens and Implications for Dissimilatory Metal Reduction by Gram-Positive Bacteria, Hans Carlson, Anthony Iavarone, Amita Gorur, Boon Siang Yeo, Rosalie Tran, Ryan Melnyk, Richard Mathies, Manfred Auer, John D. Coates, Proceedings of the National Academy of Sciences 109(5), pp. 1702-1707, doi: 10.1073/pnas.1112905109, January 31, 2012.

Published in 2011

Identification of a Perchlorate Reduction Genomic Island with Novel Regulatory and Metabolic Genes, Ryan Melnyk, Anna Engelbrektson, Iain Clark, Hans Carlson, Kathy Byrne-Bailey, John D. Coates, Applied and Environmental Microbiology, doi: 10.1128/AEM.05758-11, August 2011.



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