Prokaryotic Community Characterization in a Mesothermic and Water- Flooded Oil Reservoir in Colombia

The prokaryotic community at the “La Cira-Infantas” oil field, located in Colombia's Middle Magdalena Valley Basin, was characterized using 16S rRNA gene sequence analysis. This characterization is a first-step in assessing the dynamics of microbial degradation and defining strategies that may increase oil recovery and quality at the site. Two 16S rRNA gene libraries were generated from the total community DNA extracted from production water using both Eubacterial and Archaea universal primers. Sequence analysis of the libraries indicated that a large percentage of Eubacteria clones were affiliated with class α-, β- and δ-Proteobacteria, Clostridia and Bacteroidetes. Archaea clones were dominated by Methanobacteria and Methanococci. Annotations at these generic levels indicate that the prokaryotic community has the following metabolic capacities: i) reduction of sulfur-compounds and fermentation, ii) nitrate reduction and sulfide oxidation, iii) decomposition of aromatic compounds, and iv) methane production. These results are discussed in the context of the importance of the characterized metabolic capacities for oil biodegradation in the mesothermic and water-flooded environment of this reservoir.

[1]  J. Tomb,et al.  Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. , 2009, Environmental microbiology.

[2]  L. Forney,et al.  Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA , 1997, Applied and environmental microbiology.

[3]  Christoph Wilhelm Sensen,et al.  Contribution of make-up water to the microbial community in an oilfield from which oil is produced by produced water re-injection , 2013 .

[4]  Y. Kamagata,et al.  Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the First Cultured Anaerobe Capable of Degrading Phenol to Acetate in Obligate Syntrophic Associations with a Hydrogenotrophic Methanogen , 2008, Applied and Environmental Microbiology.

[5]  Ian M. Head,et al.  Biological activity in the deep subsurface and the origin of heavy oil , 2003, Nature.

[6]  L. D. Sette,et al.  Bacterial diversity characterization in petroleum samples from Brazilian reservoirs , 2008, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology].

[7]  R. Colwell,et al.  Simple, rapid method for direct isolation of nucleic acids from aquatic environments , 1989, Applied and environmental microbiology.

[8]  G. Bødtker,et al.  Microbial response to reinjection of produced water in an oil reservoir , 2009, Applied Microbiology and Biotechnology.

[9]  E. J. Hsu,et al.  Conversion of Paraffin Oil to Alcohols by Clostridium thermosaccharolyticum , 1995, Applied and environmental microbiology.

[10]  S. Orlicky,et al.  Molecular Characterization of a Toluene-Degrading Methanogenic Consortium , 1999, Applied and Environmental Microbiology.

[11]  Owen P. Ward,et al.  Recent Advances in Petroleum Microbiology , 2003, Microbiology and Molecular Biology Reviews.

[12]  C. Jeanthon,et al.  Characterization of long-chain fatty-acid-degrading syntrophic associations from a biodegraded oil reservoir. , 2005, Research in microbiology.

[13]  B. Logan,et al.  Enzymes responsible for chlorate reduction by Pseudomonas sp. are different from those used for perchlorate reduction by Azospira sp. , 2005, FEMS microbiology letters.

[14]  B. Patel,et al.  Mahella australiensis gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from an Australian oil well. , 2004, International journal of systematic and evolutionary microbiology.

[15]  W. Röling,et al.  The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects. , 2003, Research in microbiology.

[16]  J. Foght,et al.  Effect of nitrate injection on the microbial community in an oil field as monitored by reverse sample genome probing , 1997, Applied and environmental microbiology.

[17]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[18]  C. Jeanthon,et al.  Microbial diversity in production waters of a low-temperature biodegraded oil reservoir. , 2005, FEMS microbiology ecology.

[19]  T. Nazina,et al.  Functional and phylogenetic microbial diversity in formation waters of a low-temperature carbonate petroleum reservoir , 2013 .

[20]  B. Logan,et al.  Effect of O2 exposure on perchlorate reduction by Dechlorosoma sp. KJ. , 2004, Water research.

[21]  G. Bødtker,et al.  Microbial analysis of backflowed injection water from a nitrate-treated North Sea oil reservoir , 2009, Journal of Industrial Microbiology & Biotechnology.

[22]  D. Jones,et al.  Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs , 2004, Nature.

[23]  Bernard Ollivier,et al.  Microbiology of petroleum reservoirs , 2000, Antonie van Leeuwenhoek.

[24]  T. Lien,et al.  Desulfotomaculum thermocisternum sp. nov., a Sulfate Reducer Isolated from a Hot North Sea Oil Reservoir , 1996 .

[25]  Raul Munoz,et al.  Release LTPs104 of the All-Species Living Tree. , 2011, Systematic and applied microbiology.

[26]  Joseph M Suflita,et al.  Methanogenesis, sulfate reduction and crude oil biodegradation in hot Alaskan oilfields. , 2010, Environmental microbiology.

[27]  E. Delong,et al.  Culture-Dependent and Culture-Independent Characterization of Microbial Assemblages Associated with High-Temperature Petroleum Reservoirs , 2000, Applied and Environmental Microbiology.

[28]  K. McLean,et al.  A systematic survey for thermophilic fermentative bacteria and archaea in high temperature petroleum reservoirs , 1996 .

[29]  V. M. Oliveira,et al.  Diversity analyses of microbial communities in petroleum samples from Brazilian oil fields , 2013 .

[30]  Y. Hattori,et al.  Diversity of Indigenous Anaerobes and Methane Conversion System from Reservoir Oil by Indigenous Anaerobes in Depleted Oil Fields , 2009 .

[31]  C. A. Thomas,et al.  Molecular cloning. , 1977, Advances in pathobiology.

[32]  K. Jakobsen,et al.  High coverage sequencing of DNA from microorganisms living in an oil reservoir 2.5 kilometres subsurface. , 2011, Environmental microbiology reports.

[33]  T. Tourova,et al.  Characterization of the aerobic hydrocarbon-oxidizing enrichments from a high-temperature petroleum reservoir by comparative analysis of DNA- and RNA-derived clone libraries , 2011, Microbiology.

[34]  W. Hamilton,et al.  Identification and Phylogenetic analysis of thermophilic sulfate-reducing bacteria in oil field samples by 16S rDNA gene cloning and sequencing. , 1998, Anaerobe.

[35]  G. Voordouw,et al.  Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria , 1996, Applied and environmental microbiology.

[36]  H. Penning,et al.  DNA-SIP identifies sulfate-reducing Clostridia as important toluene degraders in tar-oil-contaminated aquifer sediment , 2010, The ISME Journal.

[37]  E. Stackebrandt,et al.  Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckelii sp. nov. , 2002, Archives of Microbiology.

[38]  Bozhong Mu,et al.  Microbial communities involved in anaerobic degradation of alkanes , 2011 .

[39]  Geert M. van der Kraan,et al.  Microbial diversity of an oil-water processing site and its associated oil field: the possible role of microorganisms as information carriers from oil-associated environments. , 2010, FEMS microbiology ecology.

[40]  Guven Ozdemir,et al.  Heavy metal biosorption by biomass of Ochrobactrum anthropi producing exopolysaccharide in activated sludge. , 2003, Bioresource technology.

[41]  B. Patel,et al.  Fusibacter paucivorans gen. nov., sp. nov., an anaerobic, thiosulfate-reducing bacterium from an oil-producing well. , 1999, International journal of systematic bacteriology.

[42]  K. Kersters,et al.  Ochrobactrum anthropi gen. nov., sp. nov. from Human Clinical Specimens and Previously Known as Group Vd , 1988 .

[43]  J. Heider,et al.  Anaerobic Toluene Catabolism of Thauera aromatica: the bbs Operon Codes for Enzymes of β Oxidation of the Intermediate Benzylsuccinate , 2000, Journal of bacteriology.

[44]  A. Schramm,et al.  Prokaryotic Community Structure and Sulfate Reducer Activity in Water from High-Temperature Oil Reservoirs with and without Nitrate Treatment , 2009, Applied and Environmental Microbiology.

[45]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[46]  L. D. Sette,et al.  Analysis of the composition of bacterial communities in oil reservoirs from a southern offshore Brazilian basin , 2007, Antonie van Leeuwenhoek.

[47]  A. Gieseke,et al.  Identification of Bacteria Potentially Responsible for Oxic and Anoxic Sulfide Oxidation in Biofilters of a Recirculating Mariculture System , 2005, Applied and Environmental Microbiology.

[48]  Bozhong Mu,et al.  Characterization of an alkane-degrading methanogenic enrichment culture from production water of an oil reservoir after 274 days of incubation , 2011 .

[49]  K. Yamane,et al.  Diversity and Similarity of Microbial Communities in Petroleum Crude Oils Produced in Asia , 2008, Bioscience, biotechnology, and biochemistry.

[50]  F. Widdel,et al.  Methane formation from long-chain alkanes by anaerobic microorganisms , 1999, Nature.

[51]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[52]  T. Hansen.  Bergey's Manual of Systematic Bacteriology , 2005 .

[53]  B. Patel,et al.  Description of Thermoanaerobacter brockii subsp. lactiethylicus subsp. nov., isolated from a deep subsurface French oil well, a proposal to reclassify Thermoanaerobacter finnii as Thermoanaerobacter brockii subsp. finnii comb. nov., and an emended description of Thermoanaerobacter brockii. , 1995, International journal of systematic bacteriology.

[54]  M. Caldwell,et al.  Anaerobic Biodegradation of Long-Chain n-Alkanes under Sulfate-Reducing Conditions , 1998 .

[55]  O. Brakstad,et al.  Characterisation of culture-independent and -dependent microbial communities in a high-temperature offshore chalk petroleum reservoir , 2009, Antonie van Leeuwenhoek.

[56]  P. Jin,et al.  Bacterial communities in a crude oil gathering and transferring system (China). , 2009, Anaerobe.

[57]  F. Widdel,et al.  Microbial nitrate-dependent cyclohexane degradation coupled with anaerobic ammonium oxidation , 2010, The ISME Journal.

[58]  A. K. Rowan,et al.  Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs , 2008, Nature.

[59]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[60]  R. Amann,et al.  Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms , 1992, Applied and environmental microbiology.

[61]  Xiuzhu Dong,et al.  Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater. , 2005, International journal of systematic and evolutionary microbiology.

[62]  G. Voordouw.  Production-related petroleum microbiology: progress and prospects. , 2011, Current opinion in biotechnology.