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DNA fingerprinting for reservoir characterization

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DNA fingerprinting (also called DNA typing) involves isolating and creating images of DNA (deoxyribonucleic acid) sequences. In the context of reservoir characterization, DNA samples from microorganisms found living in crude oil are examined.[1]


The process for creating a DNA fingerprint consists of first obtaining a sample of cells containing, extracting the DNA from the sample, and purifying the DNA. [2]Then, the DNA is cut at specific points along the strand with substances called restriction enzymes.

Fragments of different lengths are produced then sorted by placing them on a gel and subjecting the gel to an electric current in a process called electrophoresis: the shorter the fragment, the more quickly it will move toward the positive pole (anode). After electrophoresis, the sorted, double-stranded DNA fragments are subjected to a blotting technique in which they are split into single strands and transferred to a nylon sheet.

Then the fragments are exposed to DNA probes—pieces of synthetic DNA that have been made radioactive and bind to the minisatellites. A piece of X-ray film is then exposed to the fragments, and a dark mark is produced at any point where a radioactive probe has become attached. The resultant pattern of these marks can then be analyzed. Through this procedure, different types of microorganisms can be identified to discover which are beneficial in an oil field (i.e. helping break down oil in cases of site contamination) and which are detrimental (i.e. contributing to pipe corrosion).

Determining effects on formations

Because of the sheer number of bacterial colonies that are fostered within oil reservoirs, a traditional chromatograph is not sufficient in determining each type of bacteria and its significant role within the ecosystem.

Bacterial growth indigenous to a reservoir is due to the abundance of nutrients; whether inorganic, organic, or a combination of the two. To survive, the bacteria have the ability to adapt to the conditions around them. The adaptability process of bacteria to their surroundings (i.e. reservoir rock minerals and fluids as nutrients under reservoir conditions) can and will change all rock petrophysical properties, such as zeta potential; rock wettability; relative permeability; and permeability to water, oil, gas, or other flowing media. Generally, the bacteria in the water phase of petroleum reservoirs possess the ability to modify the surface chemistry of rock minerals and to extract and/or concentrate metal and nonmetal ions such as Fe, Mg, Ca, S, (SRB), etc. In general, all of these mechanisms are referred to as Biopetrophysics™, which may be considered a complementary science to Biostratigraphy when applied to exploration works. More often than not, the bacteria utilize and degrade petroleum compounds and introduce subtle chemical changes which may or may not be detected by routine Chromatography. As a result of these chemo-physical properties changes in pore space, microbial processes have a significant impact on the oil quality or oil recovery mechanisms.

Molecular biology techniques have only recently been used for oil reservoir exploration. Recent achievements in molecular biology have extended the understanding of the role of microbial transformation and maturation of petroleum compounds under certain pressure and temperature windows and have enhanced our ability to investigate the microbial communities in petroleum-impacted ecosystems. Mostly, the analyses have focused on identifying the diversity of microbial species present in the seeps, sea bed, gas vents, reservoir waters, etc., using microbial 16S rRNA, a ribosome, a ribonucleic acid found in all microorganisms since “life” began on our planet. To identify a microorganism, its 16S rRNA sequence information is checked against the 16S rRNA sequence data available in the GenBank database. 16S rRNA gene information is available for microorganisms found in different parts of the world and great distances apart like North Sea oil fields, oil fields in South America and Asia. Using these free gene databases, microorganisms most closely related to those that have been found in oil or gas reservoirs can be identified accurately.

Other than exploration for natural resources, e.g. oil and gas, there are other engineering applications for classifying the bacteria type and their impact on oil field production systems. Driven by the high demands for oil, it is crucial to investigate whether there are any microorganisms in the crude oil, determine their source of living, their original environment, and their effect on the crude oil and reservoir rock properties. For example, industrial research shows most bacteria, either aerobic or anaerobic, have two states: planktonic and sessile. In the first state, bacteria freely float and swim around. In the second state, they attach to any surface, i.e. reservoir rock, reservoir cap rock filled with bacterially produced cements, unconventional shale reservoirs filled with organic matter, etc.

Conversely, because microbial processes have a significant impact on the oil quality and oil recovery, microbially-enhanced oil recovery (MEOR) has been suggested as the fourth stage of oil production, after the implementation of the stages of oil recovery process employing mechanical, physical, and chemical methods.[3]

Corrosion prevention

Corrosion is a leading cause for pipe failure and a main component of the operating and maintenance costs of oil and gas industry pipelines.[4] Basic research to increase the industry’s understanding of the microbial species involved in microbial corrosion, and their interaction with metal surfaces and other microorganisms, can help develop new approaches for the detection, monitoring, and control of microbial corrosion.

Cleaning oil spills

Just as bacteria can be useful in the oil recovery process, they can help break down bacteria after the occurrence of oil spills in a process called biodegredation.After the use of tools like spades, brooms, and chemicals, bacteria can help clean up oil in water and soil.[5] Through DNA isolation, the most efficient strains of bacteria can be selected and, as a 2014 study conducted by a group of Norwegian scientists concluded, when those bacteria are provided with proper nutrients, they can produce cleanup results that go beyond those of chemical treatments. Microbes were essential in cleanup efforts after the Deepwater Horizon incident and can be instrumental for efficiently cleaning up spill sites in the future.[6]


  1. Encyclopedia Brittanica. 2014. DNA fingerprinting. (Accessed 1 December 2014).
  2. Zhu, X., Kilbane, J.J. 2005. Faster and More Accurate Data Collection for Microbiologically Influenced Corrosion. Presented at the SPE International Symposium on Oilfield Chemistry, The Woodlands, Texas, 2-4 February. SPE-93089-MS.
  3. Hayatdavoudi, A., Chegenizadeh, N., Christoserdov, A., et al. 2013.Application of Bacterial DNA Fingerprinting in Crude Oil for Evaluating the Reservoir-Part I. Search and Discovery 17 June.
  4. Hayatdavoudi, A., Chegenizadeh, N., Chistoserdov, A., et al. 2013. Application of New Fingerprinting Bacteria DNA in Crude Oil for Reservoir Characterization-Part II. SPE Annual Technical Conference and Exhibition, New Orleans, 30 September-2 October. SPE-166087-MS.
  5. Benjaminsen, C. 'Super bacteria' clean up after oil spills. 2014. Science Daily 10 March. (Accessed 1 December 2014)
  6. Biello, D. 2010. Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill. Scientific American 25 May.

Noteworthy papers in OnePetro

Alabbas, F.M., Kakpovbia, A.E., Spear, J.R. , et al. 2014. Utilization of 454 Pyrosequencing of 16S rRNA for Biodiversity Investigations of Crude Oil Systems. Presented at CORROSION 2014, San Antonio, Texas, USA, 9-13 March. NACE-2014-3827.

Almahamedh, H.H., Williamson, C., Spear, J.R., et al. 2011. Identification of Microorganisms And Their Effects On Corrosion of Carbon Steels Pipelines. Presented at CORROSION 2011, Houston, 13-17 March. NACE-11231.

Allison, P.W., Sahar, R.N.R.R., Guan, O.H., et al. 2008. The Investigation Of Microbial Activity In An Offshore Oil Production Pipeline System And The Development Of Strategies To Manage The Potential For Microbially Influenced Corrosion. Presented at CORROSION 2008, New Orleans, 16-20 March. NACE-08651.

Gu, T., Xu, D. 2013. Why Are Some Microbes Corrosive And Some Not? Presented at CORROSION 2013, Orlando, Florida, 17-21 March. NACE-2013-2336.

Haiying, C., Weidong, W. 2007. 16S rRNA: Genes Comparative Analysis of Microbial Communities in Oil Reservoir With Nutrients Injection by Terminal Restriction Fragment Length Polymorphism Method. Presented at the International Symposium on Oilfield Chemistry, Houston, 28 February-2 March. SPE-106398-MS.

Jahagirdar, S.R. 2008. Oil-Microbe Detection Tool Using Nano Optical Fibers. Presented at the SPE Western Regional and Pacific Section AAPG Joint Meeting, Bakersfield, California, USA, 29 March-4 April. SPE-113357-MS.

Kadarwati, S., Udiharto, M., Hadi, N. 1999.Selected Indonesian Microbes Potentials for MEOR. Presented at the SPE Asia Pacific Improved Oil Recovery Conference, Kuala Lumpur, Malaysia, 25-26 October. SPE-57316-MS.

Kilbane, J. 2014. Forensic Analysis of Failed Pipe: Microbiological Investigations. NACE Presented at CORROSION 2014, San Antonio, Texas, USA, 9-13 March. NACE-2014-3789.

Kilbane, J., Zhu, X., Lubeck, J., et al. 2004. Improved Method for Monitoring Microbial Communities in Gas Pipelines. Presented at CORROSION 2004, New Orleans, 28 March-1 April. NACE-04592.

Larsen, J., Holmkvist, L., Sørensen, K., et al. 2011. Identification And Quantification of Microorganisms Involved In Downhole MIC In a Dan Oil Producing Well. Presented at CORROSION 2011, Houston, 13-17 March. NACE-11223.

Larsen, J., Sørensen, K., Højris, B., et al. 2009. Significance Of Troublesome Sulfate-Reducing Prokaryotes (Srp) In Oil Field Systems. Presented at CORROSION 2009, Atlanta, Georgia, 22-26 March. NACE-09389.

Machuca, L.L. , Bailey, S.I., Gubner, R. 2011. Microbiologically Influenced Corrosion of High Resistance Alloys In Seawater. Presented at CORROSION 2011, Houston, 13-17 March. NACE-11230.

Skovhus, T.L., Højris, B., Saunders, A.M., et al. 2009. Practical Use of New Microbiology Tools in Oil Production. SPE Production & Operations 24 (1): 180–186. SPE-109104-PA.

Zhu, X., Kilbane, J.J. 2005. Faster and More Accurate Data Collection for Microbiologically Influenced Corrosion. Presented at the SPE International Symposium on Oilfield Chemistry, The Woodlands, Texas, USA, 2-4 February. SPE-93089-MS.

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