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News Release

The Microbiome of an Oil Reservoir

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Credit: ssuaphoto, iStock

La Jolla, Calif., January 23, 2018 – Researchers at the University of California San Diego Center for Microbiome Innovation have identified the bacteria actively responsible for oil degradation in oil reservoirs, and the metabolic pathways they employ. The findings could help researchers develop targeted strategies to prevent “souring” – a multimillion-dollar problem for the oil industry. The study was published January 9 in Microbiome.  

Crude oil is formed in crevices in the Earth's crust, called oil reservoirs, from the remains of plants and animals that millions of years of heat and pressure changed into oil and natural gas. The presence of microorganisms (bacteria and archaea) in these reservoirs has typically been associated with oil degradation and “souring” – a reduction of oil quality that leads to corrosion of pipes, tankers, and storage containers – which causes costly problems for the oil industry.

“We’ve known for a long time that these bugs are there, and we can study their capacity in the laboratory, but so far, no one has been able to figure out exactly what there are doing in nature,” said UC San Diego professor Karsten Zengler. “Their activity often changes drastically during a process called secondary recovery, when water is pumped into the reservoir to increase the pressure and recover more oil. This process introduces additional nutrients, molecular oxygen, and often a bunch more bugs.”

And not all of them are active participants in the degradation of oil.

For the first time, Zengler and his team have been able to identify the culprits in nature. They obtained samples from an oil reservoir in Jiangsu, China, sequenced the microbial DNA and RNA present in the samples, and looked to see which bacteria had genes that made them capable of breaking down oil and using its molecular components for energy.

“We discovered that there were two types of bacteria present – those that need oxygen to live, and those that don’t,” said Zengler. “While oil reservoirs are typically considered anoxic, an oil reservoir that is undergoing secondary recovery can contain oxygen in abundance. So, it’s not surprising that both communities were present.”

After identifying the species present and the genes involved in the oil degradation process, the researchers were able to identify the active community members by looking at their genes. Then, they were able to propose models for the metabolic pathways employed by both types of bacteria, which could aid in the identification of targeted strategies to prevent souring.

The importance of community

“No bacterial species by itself had all the genes necessary for synthesizing all of the amino acids and vitamins required to sustain population growth,” said Zengler. “However, when taken as a unit, all amino acids and vitamins could be synthesized. This indicates a high level of interdependency among community members – something that could possibly be disrupted to prevent their activity.”

While the researchers were able to elucidate which microbes are there and what they’re doing, they still don’t know how the communities are organized in time and space – something, they say, needs to be investigated in order for methods aimed at disrupting them and preserving oil quality to work.

This work was supported by the National Natural Science Foundation of China (Grant No. 41530318, 41373070) and the NSFC/RGC Joint Research Fund (No. 41161160560), and based in part on work supported by the US Department of Energy (DOE), Office of Science, Office of Biological & Environmental Research Awards DE-SC0012586 and the Frontiers of Innovation Scholars Program at UC San Diego.

About the Center for Microbiome Innovation

The objective of the Center for Microbiome Innovation (CMI) is to accelerate microbiome research and understanding, through partnerships with industry sponsors. Together we will develop novel tools and methods to improve human health and benefit the environment by analyzing and manipulating microbiomes — the distinct and diverse communities of bacteria, viruses and other microorganisms that live within and around us. This is a multidisciplinary center with access to all the latest omics tools (genomics, metagenomics, metatranscriptomics, metabolomics, multiplex proteomics), processing hundreds of thousands of samples each year and analyzing and collecting data for some of the largest microbiome cohorts in the world. Applications range from human disease understanding, ag bio, pharmaceutical, nutraceutical, environmental research, to consumer goods.

Media Contacts

Erin Bateman
Center for Microbiome Innovation