Can Bacteria Rescue the Oil Industry?

Can Bacteria Rescue the Oil Industry? Microbes in oil deposits withstand enormous hydrocarbon loads, intense heat, high salt and immense pressure. How can we put them to work for us? By Hans Kristian Kotlar n a cold December day in 1998, I was swimming in my survival suit in the Trondheim-fjord, Norway, practicing for the offshore certificate. The certificate would give me access to one of the oceanic drilling installations of StatoilHydro, among the bigge

By | February 1, 2009

Can Bacteria Rescue the Oil Industry?

Microbes in oil deposits withstand enormous hydrocarbon loads, intense heat, high salt and immense pressure. How can we put them to work for us?

By Hans Kristian Kotlar

n a cold December day in 1998, I was swimming in my survival suit in the Trondheim-fjord, Norway, practicing for the offshore certificate. The certificate would give me access to one of the oceanic drilling installations of StatoilHydro, among the biggest offshore oil and gas companies in the world. As part of the company's research program, we were looking for bacterial strains that could be useful in the oil industry. Obtaining samples of these oil-loving microbes would allow us to start culturing and genetically characterizing the life that survives high temperature oilfields - a venture I hope could one day revolutionize the oil industry.

Until only a few years ago, the majority of researchers doubted the possibility of any living matter in oil reservoirs that were sealed off for 200-500 million years. Despite the discovery of hyperthermophilic life in Yellowstone geysers as early as the 1960s, it wasn't until the early 1990s that a number of researchers started reporting life in oil reserves 3-4 kilometers beneath the surface. Many researchers were skeptical that the found biomatter could be anything but contamination. The capsules we were using in our first foray into the bacterial life of our oil fields were designed to open only once they were deep underground and seal their sample contents within before we retrieved them again. We were hopeful that the microbes we collected would be unique.

Through StatoilHydro's drilling operations, I have had access to underground bacterial communities that is unparalleled anywhere in the world. The samples come up drenched in black, smelly oil of varying consistency. For organisms that are so accustomed to living in extreme environments, they are extraordinarily delicate once brought to the surface: Despite coping with pressures of 200-300 bars (about the force of an elephant standing on the head of a needle), and temperatures often used in disinfection, these organisms do not survive long at the surface. Our goal is two fold: to understand the metabolic processes that extromphiles use to digest oil, and to characterize the genetic blueprint of species that thrive above oil fields. These samples may help us increase oil extraction and identify new underground reserves. The results have surpassed my expectations.

I'm a cancer immunologist by training, which explains my inclination to imagine solutions to improving an oil company's efficiency based on the biological principles I'm most familiar with. Geologists and physicists dominate the science of oil extraction, but the subtle capabilities of microorganisms reveal new approaches to unlocking the full potential of oil reserves - reserves that have been inaccessible using established technology.

© Wesley Allsbrook /

One of our first projects has been to develop bacteria as a scientifically sound dowsing rod to help find new oil reserves around the world. Methods like seismic logging and exploration drilling can have a deleterious impact on sensitive environments such as the Arctic, Antarctica, and jungle ecosystems. But what if we could simply sample surface dirt and test for a bacterial profile that would cue us to underground oil reservoirs?

We've been collecting samples from the surface of wells on the sea floor or on land to try to find a microbial genetic profile that would indicate the underground presence of oil. All oil reservoirs seep small molecules of hydrocarbons to the surface. The microbes that make use of the hydrocarbon seepage as a source of energy will make up a larger percentage of the sample. Therefore the profile of genetic information will be different above an oil field than above areas with no hydrocarbon seepage.

Our samples may increase oil extraction and help identify new underground reserves.

My team has worked on probes that locate a consistent pattern of 16S ribosomal DNA in organisms associated with oil. Printed on microarray plates or developed into lab-on-a-chip systems, these patterns could one day be used in exploration, perhaps even to assess the quality, or other characteristics, of the oil reserves. Already our experiments with direct denaturating gradient gel electrophoresis (DGGE) have shown a pattern that can readily discriminate pockmark areas that show a hydrocarbon gas flux, from areas outside the pockmark (see graphic below).

Bacterial dowsing rods: To find a bacterial profile of surface bacteria that would tip us off to the location of an underground oil reservoir, we sampled from three marine locations. We took two cores from ocean depressions called pockmarks where hydrocarbon seepage was high (B and C), and one core from the periphery (A). We ran samples from various depths of the cores across the wells on a denaturing gradient gel electrophoresis (DGGE), which gives an overall picture of species diversity of the sample. Organisms that use hydrocarbon gas as an energy source will be more abundant above an oil reserve, giving a unique DGGE pattern and revealing the location of oil.

The organisms we find within the oil deposits have also held surprises. At such extreme conditions I had expected to find primarily archaea: Extremophiles that are considered older than bacteria with much more specialized metabolic pathways. However, in most oil reservoirs at the Norwegian Continental Shelf, bacterial species are about five times more diverse and higher in number than archaea. And many of the organisms are genetically quite similar to current, everyday organisms, which is astonishing seeing as these bacteria have been separated and sealed off for many millions of years. It suggests that, contrary to popular belief, there may be exchanges between the underground and the surface, possibly via hydrothermal vents. But the microbes we have found are truly indigenous to the oil deposits: Samples extracted from exploration cores, formation water from the corresponding reservoir section and from the oil itself, give basically the same organisms. In contrast, none of these organisms show up in sea water or outcrop core samples from other locations subjected to the same extraction and analytical procedures. Combined with their ability to tolerate a high load of hydrocarbons, high pressure and high salt concentration, these organisms are likely to exhibit some very exciting properties.

A major challenge to the oil industry is extracting all of the usable oil from an oil field. Two-thirds of the world reserves in fossil hydrocarbons exist as heavy to extra heavy oil. These oils are very viscous, presenting challenges in production, transportation, and refining. On a world average, only 7-8% of the oil in these fields is recovered. Boosting the recovery factor by only a few percent could yield billions of dollars in additional revenue. Just as an example, a moderate size oil field could have about 1.3 billion barrels of oil in reserves. If the recovery rate is increased by 5%, theoretically, the yield increases by some 65 million barrels.

Currently, we are searching for organisms with the ability to convert heavy oil to a lighter version or quality. We aren't limiting this search to microbes found in our oil fields and have been prospecting for oil metabolizing microbes around the globe. Specifically, we're looking for thermophiles that can degrade n-alkanes or open aromatic rings. In other words we want microbes which can bioconvert the heavy components of the oil.

We, the molecular biologists, have always had a small cheering section for microbial solutions to our energy problems.

In our BioThor strain collection - Statoil Hydro's internal collection of more than 5,000 isolates - we have gathered organisms with an exceptional bioconverting activity of heavy oil. Under experimental conditions we see complete conversion to lower oil viscosities as well as effects on distinct compounds within two to three days of the addition of certain bacterial strains. These organisms are currently being analyzed at the genetic level.

Of course it is one thing to prove the concept in a laboratory set up and another to make that concept work under reservoir conditions. To tackle this, we've constructed sand packs and radial reservoir models. The sand packed into columns is soaked with heavy oil and then treated with our experimental strains. Even with the sand impeding the dispersal of bacteria and the flow of oil, we were able to increase the recovery by two-fold. The radial reservoir model is designed to more closely mimic reservoir conditions, in which the characteristics of oil flow into the pipe will reflect the changes in flow-shear forces more accurately. Even in our radial model, recovery was increased. It suggests that the concept is viable even at reservoir conditions (see graphic below).

We hope to test these bacterial strains for the first time in the field in the next several years in combination or in sequence with cold heavy oil production with sand, vapor extraction, or hot water extraction procedures. To make it work, new strategies for reservoir sweep and drainage may have to be developed.

Another impediment to efficient withdrawal of oil is the build-up of wax and salt deposit-scale within pipelines that can drastically reduce oil flow and result in blockages. For several years StatoilHydro has held a patent on a hyperthermophilic organism that is transfected with a gene that encodes a scale inhibitor. These microorganisms secrete a version of the scale inhibitor in situ where it acts as a continuous source of the treatment chemical, inhibiting the scales that choke the pipe, increasing the regularity and efficiency of the production.

To meet the shortfall in raw materials needed for generating world energy, we are also looking at ways to convert different types of biomass waste and raw materials. Extremophiles have unique enzymatic properties that could be useful in increasing the efficiency of many biocatalytic reactions, such as those required in converting biomass into fuel. We've started bioconversion experiments using animal fat, plant oil and fish oil, searching for enzyme systems within thermotolerant species. High thermotolerance is necessary because some fats from animals will not melt below a temperature of 50-60°C. Already, we've found a number of organisms that can split fat and vegetable oils into biofuel components.

Bacteria improve oil extraction: Many oil fields contain a large percentage of heavy oil - a type of oil that is difficult to extract due to its thickness. We tested how well bacteria could degrade heavy oil, first in a free floating solution (A), then in sand columns that more closely mimic conditions in the field (B). Finally, because flow dynamics are different in the field when a pipe is drawing oil from all sides, we tested the recovery in a radial model of sand soaked with heavy oil (C). We were able to see oil recovery increase by approximately two-fold within 2-3 days of culturing with bacteria. The next step will be to try the experiment in the field.

Thermophilic and hyperthermophilic organisms are defined by their ability to live at 50-70°C, and 70°-100°C, respectively. The record reported for living organisms is close to 120°C. We tested three oil reservoirs at around 100°C and found quite a high degree of biodiversity. It is surprising that even at 100°C we see 10 to 15 different species present, together with one or two archaea. While these bacteria are known to live at high temperatures, most geochemists place the traditional boundary for biodegradation of biomass at a maximum of 80°C. Temperatures higher than 80°C, and biodegradation is no longer possible. Our findings argue for an extension to at least 100°C. We plan to use these organisms or simply the enzymes they produce to develop a more efficient conversion of waste oil and biomass into fuel.

With the biotech industry on a constant search for enzymes with high stability and conversion rates, extremophile organisms showcase different strategies to achieving the desired reactions. These organisms build more hydrophobic amino acid residues into their proteins to tolerate the high temperatures, have a broad pH range and high load of organic compounds. And they achieve high salt tolerance by using salt-bridges and/or ionic interactions to stabilize amino acids. These properties could potentially be mined to improve efficiency in many biopharmaceutical applications.

But in order to fully exploit their properties, these organisms must be understood in their "home conditions." Some enzymes will not work unless the protein is pressurized to such a degree that the conformation of the catalytic site will be optimal for the bioconversion (i.e., a change in the entire volume of the enzyme molecule). It may be a few years before we find techniques that allow us to make full use of the potential of these extremophiles. However, these are drawbacks that we plan to overcome with the use of directed enzyme evolution or by genetic engineering of the organisms.

We, the molecular biologists, have always had a small cheering section for microbial solutions to our energy problems. I, for one, would like to see them succeed. But we have yet to see how big a part they will play in improving energy outputs of oil fields and conversion of biomass. As feedstocks and hydrocarbon resources are starting to run short, more sophisticated methods will play an increasingly important role in solving the overall energy demand of the future.

Hans Kristian Kotlar is the R&D manager of biotechnology at StatoilHydro.


Avatar of: anonymous poster

anonymous poster

Posts: 5

February 9, 2009

Keep up the good work!! I can envision hungry, bioconverting bacteria that could be sprayed over layers of landfill, converting them to new "fuel fields".
Avatar of: Philippe Laveaux

Philippe Laveaux

Posts: 5

February 17, 2009

Intriguing. I always figured people have given up on trying to access more oil and are focusing almost exclusively on ethanol and other sources of energy. If these extremophiles truly do increase the output of viable oil that can be extracted won't it only delay the inevitable?\n\nOr perhaps this buys scientists more time to find other alternatives of fuel.
Avatar of: nancy abellard

nancy abellard

Posts: 1

March 26, 2009

- I presume this article is very important to our oil manufacturing industry and economy. If these microbes can better our oil and gas industries then we could be on the verge of finding new ways of having a more abundant supply of fuel and find new ways of conserving our much needed and scarce nonrenewable resources. These bacterial microbes also aid in detecting new oil reserves around the world; by using seismic logging and exploration drilling. This can expand or oil industries internationally and easily reconcile with or demand and consumption of oil and gas products. Statics show that on average oil industries retrieve about 7-8% of the oil on the fields. By boosting the oil recovery factor by only a few percent can yield billions of dollars in additional revenue and boost our economy. These small oil loving microbes can rise or economy to a high and eject the whole world if possible from this dreaded recession. Thank you!

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