Diversity and distribution of sulfate-reducing bacteria in four petroleum reservoirs detected by using 16S rRNA and dsrAB genes

International Biodeterioration and Biodegradation

Volumn 76, Issue , 2013, Pages 58-66

  Guan, Jing ^a   Xia, Li Ping ^a   Wang, Li Ying ^a   Liu, Jin Feng ^a   Gu, Ji Dong ^b   Mu, Bo Zhong ^a  

^a EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

16S rRNA gene; CCA; Corrosion; DsrAB genes; Petroleum microbiology; Sulfate reducing bacteria

Indexed keywords

BACTERIA; BIODEGRADATION; CORROSION; ECOLOGY; GENES; OIL FIELDS; PETROLEUM RESERVOIRS; REDUCTION; RNA; SULFUR COMPOUNDS; VOLATILE FATTY ACIDS;

16S RRNA GENE; CANONICAL CORRESPONDENCE ANALYSIS; ENVIRONMENTAL VARIABLES; MICROBIAL INFLUENCED CORROSIONS; PHYLOGENETIC ANALYSIS; POSITIVE CORRELATIONS; SPECIES DISTRIBUTIONS; SULFATE REDUCING BACTERIA;

PETROLEUM RESERVOIR ENGINEERING;

CLONE; COMMUNITY STRUCTURE; CORROSION; ENZYME ACTIVITY; OIL FIELD; PETROLEUM HYDROCARBON; PHYLOGENETICS; PHYSICOCHEMICAL PROPERTY; RESERVOIR CHARACTERIZATION; RNA; SPECIES DIVERSITY; SULFATE-REDUCING BACTERIUM;

BACTERIA (MICROORGANISMS); DESULFOBACTER; DESULFOBACTERIUM; DESULFOBULBUS; DESULFOMICROBIUM; DESULFOTOMACULUM;

EID: 84871805455     PISSN: 09648305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ibiod.2012.06.021     Document Type: Article

References (64)

1. 2 by a new type of sulfate-reducing bacterium. Archives of Microbiology 1991, 156:5-14.
2. Altschul S., Madden T., Schaffer A., Zhang J., Zhang Z., Miller W., Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997, 25:3389-3402.
3. Anandkumar B., George R.P., Maruthamuthu S., Palaniswamy N., Dayal R.K. Corrosion behavior of SRB Desulfobulbus propionicus isolated from an Indian petroleum refinery on mild steel. Materials and Corrosion 2011, 62:1-5.
4. Bastin E.S., Greer F.E., Merritt C.A., Moulton G. The presence of sulphate reducing bacteria in oil field waters. Science 1926, 63:21-24.
5. Braak C.J.F. CANOCO-an extension of DECORANA to analyze species-environment relationships. Plant Ecology 1988, 75:159-160.
6. Daly K., Sharp R.J., McCarthy A.J. Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. Microbiology 2000, 146:1693-1705.
7. Dar S.A., Yao L., van Dongen U., Kuenen J.G., Muyzer G. Analysis of diversity and activity of sulfate-reducing bacterial communities in sulfidogenic bioreactors using 16S rRNA and dsrB genes as molecular markers. Applied and Environmental Microbiology 2006, 73:594-604.
8. Dhillon A., Teske A., Dillon J., Stahl D.A., Sogin M.L. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Applied and Environmental Microbiology 2003, 69:2765-2772.
9. Duncan K.E., Gieg L.M., Parisi V.A., Tanner R.S., Tringe S.G., Bristow J., Suflita J.M. Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities. Environmental Science and Technology 2009, 43:7977-7984.
10. Ficker M., Krastel K., Orlicky S., Edwards E. Molecular characterization of a toluene-degrading methanogenic consortium. Applied Environmental Microbiology 1999, 65:5576-5585.
11. Fricke W.F., Martinez-Arias R., Bartels D., Goesmann A., Krause L., Pühler A., Klenk H.P., Richter M., Schüler M., Glöckner F.O., Meyerdierks A., Gottschalk G., Amann R. Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environmental Microbiology 2009, 11:1038-1055.
12. Friedrich M.W. Phylogenetic analysis reveals multiple lateral transfers of adenosine-5'-phosphosulfate reductase genes among sulfate-reducing microorganisms. Journal of Bacteriology 2002, 184:278-289.
13. Gaines R.H. Bacterial activity as a corrosive influence in the soil. Industrial and Engineering Chemistry 1910, 2:128-135.
14. Gardner L.R., Stewart P.S. Action of glutaraldehyde and nitrite against sulfate-reducing bacterial biofilms. Journal of Industrial Microbiology and Biotechnology 2002, 29:354-360.
15. Gieg L.M., Jack T.R., Foght J.M. Biological souring and mitigation in oil reservoirs. Applied Microbiology and Biotechnology 2011, 92:263-282.
16. Gittel A., Mußmann M., Sass H., Cypionka H., Könneke M. Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis. Environmental Microbiology 2008, 10:2645-2658.
17. Green S.J., Leigh M.B., Neufeld J.D. Denaturing gradient gel electrophoresis (DGGE) for microbial community analysis. Handbook of Hydrocarbon and Lipid Microbiology 2010, vol. 60:4137-4158. K.N. Timmis (Ed.).
18. Hippe H., Vainshtein M., Gogotova G.I., Stackebrandt E. Reclassification of Desulfobacterium macestii as Desulfomicrobium macestii comb. nov. International Journal of Systematic and Evolutionary Microbiology 2003, 53:1127-1130.
19. Huber T., Faulkner G., HugenholtzPhilip Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004, 20:2317-2319.
20. Hubert C. Microbial ecology of oil reservoir souring and its control by nitrate injection. Handbook of Hydrocarbon and Lipid Microbiology 2010, vol. 26:2753-2766. K.N. Timmis (Ed.).
21. Hubert C., Voordouw G. Oil field souring control by nitrate-reducing Sulfurospirillum spp. that outcompete sulfate-reducing bacteria for organic electron donors. Applied and Environmental Microbiology 2007, 73:2644-2652.
22. Imachi H., Sekiguchi Y., Kamagata Y., Loy A., Qiu Y.L., Hugenholtz P., Kimura N., Wagner M., Ohashi A., Harada H. Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum Cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology 2006, 72:2080-2091.
23. Ito T., Nielsen J.L., Okabe S., Watanabe Y., Nielsen P.H. Phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm determined by combining microautoradiography and fluorescent in situ hybridization. Applied and Environmental Microbiology 2002, 68:356-364.
24. Javaherdashti R. A review of some characteristics of MIC caused by sulfate-reducing bacteria. Anti-Corrosion Methods and Materials 1999, 46:173-180.
25. Jayaraman A., Hallock P.J., Carson R.M., Lee C.C., Mansfeld F.B., Wood T.K. Inhibiting sulfate-reducing bacteria in biofilms on steel with antimicrobial peptides generated in situ. Applied Microbiology and Biotechnology 1999, 52:267-275.
26. Kaksonen A.H., Plumbb J.J., Robertsonb W.J., Franzmannb P.D., Gibsonc J.A.E., Puhakka J.A. Culturable diversity and community fatty acid profiling of sulfate-reducing fluidized-bed reactors treating acidic, metal-containing wastewater. Geomicrobiology Journal 2004, 21:469-480.
27. Kengen S.W.M., Breidenbach C.G. Reductive dechlorination of tetrachloroethene to cis-1,2-dichloroethene by a thermophilic anaerobic enrichment culture. Applied and Environmental Microbiology 1999, 65:2312-2316.
28. Klein M., Friedrich M., Roger A.J., Hugenholtz P., Fishbain S., Abicht H., Blackall L.L., Stahl D.A., Wagner M. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. Journal of Bacteriology 2001, 183:6028-6035.
29. Lee A.K., Newman D.K. Microbial iron respiration impacts on corrosion processes. Applied Microbiology and Biotechnology 2003, 62:132-139.
30. Lefebvre O., Ha Nguyen T., Al-Mamun A., Chang I., Ng H. T-RFLP reveals high β-Proteobacteria diversity in microbial fuel cells enriched with domestic wastewater. Journal of Applied Microbiology 2010, 109:839-850.
31. Leu J.Y., Traa C.P.M., Porter A.J.R., Hamilton W.A. The same species of sulphate-reducing Desulfomicrobium occur in different oil field environments in the North Sea. Letters in Applied Microbiology 1999, 29:246-252.
32. Lewandowski Z., Beyenal H. Mechanisms of microbially influenced Corrosion. Springer Series on Biofilms 2008, 35-37.
33. Li H., Chen S., Mu B.Z., Gu J.-D. Molecular detection of anaerobic ammonium-oxidizing (Anammox) bacteria in high-temperature petroleum reservoirs. Microbial Ecology 2010, 60:771-783.
34. Lien T., Beeder J. Desulfobacter vibrioformis sp. nov., a sulfate reducer from a water-oil separation system. International Journal of Systematic Bacteriology 1997, 47:1124-1128.
35. Lien T., Madsen M., Steen I.H., Gjerdevik K. Desulfobulbus rhabdoformis sp. nov., a sulfate reducer from a water-oil separation system. International Journal of Systematic Bacteriology 1998, 48:469-474.
36. Lin S., Krause F., Voordouw G. Transformation of iron sulfide to greigite by nitrite produced by oil field bacteria. Applied Microbiology and Biotechnology 2009, 83:369-376.
37. Little B.J., Lee J.S. Microbiologically influenced corrosion. Kirk-Othmer Encyclopedia of Chemical Technology 2009, 1-42.
38. Magot M. Desulfovibrio bastinii sp. nov. and Desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water. International Journal of Systematic and Evolutionary Microbiology 2004, 54:1693-1697.
39. Magot M., Ravot G., Campaignolle X., Ollivier B., Patel B.K.C., Fardeau M.L., Thomas P., Crolet J.L., Garcia J.L. Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a new anaerobic, slightly halophilic, thiosulfate-reducing bacterium from corroding offshore oil wells. International Journal of Systematic and Evolutionary Microbiology 1997, 47:818-824.
40. Mansfeld F.B., Wood T.K., Zuo R., Ornek D., Syrett B.C., Green R.M., Hsu C.H. Inhibiting mild steel corrosion from sulfate-reducing bacteria using antimicrobial-producing biofilms in Three-Mile-Island process water. Applied Microbiology and Biotechnology 2004, 64:275-283.
41. Meyer B., Kuever J. Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes - origin and evolution of the dissimilatory sulfate-reduction pathway. Microbiology 2007, 153:2026-2044.
42. 2S production in an oil reservoir model column by nitrate injection. Applied Microbiology and Biotechnology 2002, 58:400-408.
43. Nazina T.N., Grigor'yan A.A., Xue Y.F., Sokolova D.Sh, Novikova E.V., Tourova T.P., Poltaraus A.B., Belyaev S.S., Ivanov M.V. Phylogenetic diversity of aerobic saprotrophic bacteria isolated from the Daqing Oil Field. Microbiology 2002, 71:103-110.
44. Nemati M., Jenneman G.E., Voordouw G. Mechanistic study of microbial control of hydrogen sulfide production in oil reservoirs. Biotechnology and Bioengineering 2001, 74:424-434.
45. Okabe S., Odagiri M., Ito T., Satoh H. Succession of sulfur-oxidizing bacteria in the microbial community on corroding concrete in sewer systems. Applied and Environmental Microbiology 2006, 73:971-980.
46. Plugge C.M., Balk M., Stams A.J.M. Desulfotomaculum thermobenzoicum subsp. nov., a thermophilic, syntrophic, propionate-oxidizing, spore-forming bacterium. International Journal of Systematic and Evolutionary Microbiology 2002, 52:391-399.
47. Rees G.N., Grassia G.S., Sheehy A.J., Dwived P.P., Patel B.K.C. Desulfacinum infernum gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a petroleum reservoir. International Journal of Systematic Bacteriology 1995, 45:85-89.
48. Riviere, D., Desvignes, V., Pelletier, E., Chaussonnerie, S., Guermazi, S., Weissenbach, J., Li, T., Camacho, P., Sghir, A., 2009. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. 3, 700-714.
49. Sass H., Cypionka H. Isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of Desulfovibrio cavernae sp. nov. Systematic and Applied Microbiology 2004, 27:541-548.
50. Savage K.N., Krumholz L.R., Gieg L.M., Parisi V.A., Suflita J.M., Allen J., Philp R.P., Strittmatter A.W., Liesegang H., Rabus R., Decker I., Amann J., Andres S., Henne A., Suflita J.M., Duncan K.E. Problems caused by microbes and treatment strategies anaerobic hydrocarbon biodegradation and biocorrosion: a case study. Applied Microbiology and Molecular Biology in Oilfield Systems 2010, vol. 17:141-149. C. Whitby, T.L. Skovhus (Eds.).
51. Savage K.N., Krumholz L.R., Gieg L.M., Parisi V.A., Sufl{ligature}ita J.M., Allen J., Philp R.P., Elshahed M.S. Biodegradation of low-molecular-weight alkanes under mesophilic, sulfate-reducing conditions: metabolic intermediates and community patterns. FEMS Microbiology Ecology 2010, 72:485-495.
52. Schauder R., Widdel F., Fuchs G. Carbon assimilation pathways in sulfate-reducing bacteria II. Enzymes of a reductive citric acid cycle in the autotrophic Desulfobacter hydrogenophilus. Archives of Microbiology 1987, 148:218-225.
53. Shan D., Fang M., Wang C., Wei L., Guo J.b. Repressing sulfate-reducing bacteria growth in the affusion system of oil field by changing ecological factors. Journal of Harbin Institute of Technology 2008, 15:167-171.
54. Stams A.J.M., Kremer D.R.K., Nicolay K., Weenk G.H., Hansen T.A. Pathway of propionate formation in Desulfobulbus propionicus. Archives of Microbiology 1984, 139:167-173.
55. Surkov A.V., Dubinina G.A., Lysenko A.M., Glockner F.O., Kuever J. Dethiosulfovibrio russensis sp. nov.,Dethiosulfovibrio marinus sp. nov. and Dethiosulfovibrio acidaminovorans sp. nov., novel anaerobic, thiosulfate- and sulfur-reducing bacteria isolated from 'Thiodendron' sulfur mats in different saline environments. International Journal of Systematic and Evolutionary Microbiology 2001, 51:327-337.
56. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 2011, 85:9247-9248.
57. Tang Y.Q., Matsui T., Morimura S., Wu X.L., Kida K. Effect of temperature on microbial community of a glucose-degrading methanogenic consortium under hyperthermophilic chemostat cultivation. Journal of Bioscience and Bioengineering 2008, 106:180-187.
58. Taylor J., Parkes R.J. The cellular fatty acids of the sulphate-reducing bacteria, Desulfobacter sp., Desulfobulbus sp. and Desulfovibvio, Desulfuvicans. Journal of General Microbiology 1983, 129:3303-3309.
59. Teske A. Sulfate-reducing and methanogenic hydrocarbon-oxidizing microbial communities in the marine environment. Handbook of Hydrocarbon and Lipid Microbiology 2010, vol. 43:2203-2223. K.N. Timmis (Ed.).
60. Wagner M., Roger A.J., Flax J.L., Brusseau G.A., Stahl D.A. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. Journal of Bacteriology 1998, 180:2975-2982.
61. Warren Y.A., Citron D.M., Merriam C.V., Goldstein E.J.C. Biochemical differentiation and comparison of Desulfovibrio species and other phenotypically similar genera. Journal of Clinical Microbiology 2005, 43:4041-4045.
62. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology 1991, 173:697-703.
63. Widdel F., Boetius A., Rabus R. Anaerobic biodegradation of hydrocarbons including methane. The Prokaryotes 2006, 2:1028-1049.
64. Youssefa N., Elshahed M.S., McInerney M.J. Microbial processes in oil fields: culprits, problems, and opportunities. Advances in Applied Microbiology 2009, 66:141-251.