Fossil Fuel Bioprocessing programs

Souring Systems Biology Program: Microbial Ecology

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.


Microbial community structure, function and distribution in petroleum reservoirs have only recently begun to be described. This is largely due to advances in direct molecular techniques that allow us to detect organisms that cannot be cultivated by normal methods. Many petroleum reservoirs have well-established microbial communities which have had a major long-term impact on the evolution of petroleum in these reservoirs. Using techniques pioneered at Lawrence Berkeley Natural Laboratory, the program has merged the fields of molecular biology and ecology, combined with systems biogeochemistry, to focus on critical controllers of microbial function in reservoir and tar sand environments. Researchers are studying the ecosystem's genetic capacity and the biological or abiotic controls which determine the expression of that capacity.

program Highlights

2014 Highlights

Hydrocarbon reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and to predict roles for specific organisms in biogeochemical transformations in North Slope, Alaska oil fields. Samples were collected from four reservoirs between 1,128 m (~24-27 °C) and 2,743 m (~80 - 83 °C) below the surface. Sample complexity decreased with increasing temperature. We clearly demonstrated the existence of the dissimilatory sulfate reduction pathway regardless of the souring status and conclude factors other than genetic potential appear to control the souring process. This study provided valuable insights into functional roles the individual genomes, especially the candidate phyla, played in these petroleum reservoirs.

2013 Highlights

The overarching aim of our work is to gain a better understanding of key functions carried out by microorganisms in complex microbial communities residing in petroleum reservoirs or laboratory simulations. Our approach has been to use novel technologies and methods developed at LBNL to identify microbial community structure, target selected biogeochemical interactions, and uncover novel functional genes that will aid in the understanding and control of reservoir souring. This involves the direct analysis of DNA, RNA, presence and expression of key functional genes and diagnostic metabolites. We have identified key organisms responsible for H2S production in column studies in collaboration with the Rates and Mechanisms team. Microbial community analysis revealed striking differences in classes of organisms and their mechanisms in prevention or reversal of souring by treatment with nitrate or (per)chlorate. Analysis of produced water from oil reservoirs in Prudhoe Bay and Milne Point Alaska found that as reservoir temperature increased, the microbial community diversity would decrease.  Wells were dominated by different organisms dependent upon geochemical environment.  Cooler reservoirs were dominated by methanogenic Archaea and organisms from the deeply branched phyla OD1, OP9 and WS6, while hotter reservoirs were dominated by fermenters and sulfate reducers. Over 12,000 structural and functional domains were identified, including a high percentage of branched-chain amino acid transporters reflecting the diverse electron donor sources in the reservoirs. We are working with the Modeling team to use the microbial community structure and functional information to develop more accurate models of reservoir souring.

2012 Highlights

We completed analysis of MEHR field samples from Milne Point in Prudhoe Bay, North Slope, Alaska, to identify dominant members of the reservoir microbial community and determine how geochemical parameters shape community structure. The results indicate the communities are dominated by methanogenic archaea as well as the very poorly characterized phyla OD1, OP9 and WS6. The differences in community composition were related to reservoir temperature and oil composition. Identification of a large number of branched-chain amino acid transporter genes indicates active and robust communities.


Diverse sets of hydrocarbon-degrading bacteria were isolated from seawater using oil-baited “bug-traps.” Many of the isolates were similar to those found in the reservoir by 16S rRNA gene analysis. Hydrocarbon degradation studies revealed specificity for different fractions of hydrocarbons, including the C25-C34 alkanes. These preferential substrate utilization capabilities by indigenous microbes may influence oil viscosity and recovery.


We evaluated the use of metal coupons placed directly in the riser of Prudhoe Bay production wells as a proxy for reservoir microbial community composition. In support of a Rates and Mechanisms laboratory study on biosouring of anaerobic sediment, we have identified changes in microbial communities that are highly correlated with specific treatments over multiple sampling times and replicates. Metagenomic studies revealed a high diversity of genes involved with sulfate-reduction (e.g., dissimilatory sulfite reductase, APS reductase). We also investigated population shifts in sulfate-reducing bacteria in soured columns through qPCR of the dsrA gene.


Published in 2014

Temperature and Injection Water Source Influence Microbial Community Structure in Four Alaskan North Slope Hydrocarbon Reservoirs, Y. M. Piceno, F. C. Reid, L. M. Tom, M. E. Conrad, M. Bill, C. G. Hubbard, B. W. Fouke, C. J. Graff, J. Han, W. T. Stringfellow, J. S.Hanlon, P. Hu, T. C. Hazen, G. L. Andersen, Frontiers in Microbiology, V. 5, pp. 409, doi:10.3389/fmicb.2014.00409, August 7, 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, June 26, 2014. 

Published in 2013

Succession of Hydrocarbon-Degrading Bacteria in the Aftermath of the Deepwater Horizon Oil Spill in the Gulf of Mexico, E. A. Dubinsky, M. E. Conrad, R. Chakraborty, M. Bill, S. E. Borglin, J. T. Hollibaugh, O. U. Mason, Y. M. Piceno, F. C. Reid, W. T. Stringfellow, L. M. Tom, T. C. Hazen, G. L. Andersen, Environmental Science & Technology 47, pp. 10860-10867, doi: 10.1021/es401676y, August 14, 2013.

Published in 2012

Metagenome, Metatranscriptome and Single-Cell Sequencing Reveal Microbial Response to Deepwater Horizon Oil Spill, O. U. Mason, T. C. Hazen, S. Borglin, P. S. Chain, E. A. Dubinsky, J. L. Fortney, J. Han, H. Y. Holman, J. Hultman, R. Lamendella, R. Mackelprang, S. Malfatti, L. M. Tom, S. G. Tringe, T. Woyke, J. Zhou, E. M. Rubin, J. K. Jansson, ISME Journal 6 :1715-1727


Deep-Sea Bacteria Enriched by Oil and Dispersant from the Deepwater Horizon Spill, J. Baelum, S. Borglin, R. Chakraborty, J. L. Fortney, R. Lamendella, O. U. Mason, M. Auer, M Zemla, M. Bill, M. E. Conrad, S. A. Malfatti, S. G. Tringe, H. Y. Holman, T. C. Hazen, J. K. Jansson, Environmental Microbiology 14:2405-16.


Microbial Gene Functions Enriched in the Deepwater Horizon Deep-Sea Oil Plume, Z. Lu, Y. Deng, J. D. Van Nostrand,, Z. He, J. Voordeckers, A. Zhou, Y. J. Lee, O. U. Mason, E. A. Dubinsky, K. L. Chavarria, L. M. Tom, J. L. Fortney, R. Lamendella, J. K. Jansson, P. D'haeseleer, T. C. Hazen, J. Zhou, ISME Journal 6 :451-460


Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill, M. J. Beazley, R. J. Martinez, S. Rajan, J. Powell, Y. M. Piceno, L. M. Tom, G. L. Andersen, T. C. Hazen, J. D. Van Nostrand, J. Zhou, B. Mortazavi, P. A. Sobecky, PLoS One 7 :e41305.


Microbial Response to the MC252 Oil and Corexit 9500 in the Gulf of Mexico, R. Chakraborty, S. E. Borglin, E. L. Dubinsky, G. L Andersen, T. C. Hazen, Frontiers in Microbiotechnology 3:357


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