Fossil Fuel Bioprocessing programs

MEHR: Ecogenomics

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

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 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


Back to Top