Dominance of Desulfotignum in sulfate-reducing community in high sulfate production-water of high temperature and corrosive petroleum reservoirs

International Biodeterioration and Biodegradation

Volumn 114, Issue , 2016, Pages 45-56

  Li, Xiao Xiao ^a   Liu, Jin Feng ^a   Yao, Feng ^b   Wu, Wei Lin ^b   Yang, Shi Zhong ^a   Mbadinga, Serge Maurice ^a,d   Gu, Ji Dong ^c   Mu, Bo Zhong ^a,d  

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

^b Institute of Petroleum Engineering and Technology   (China)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

^d Shanghai Technology Innovation Center   (China)

Author keywords

Dsr gene; High temperature petroleum reservoirs; Microbial community; Microbiologically influenced corrosion (MIC); Souring; Sulfate reducing prokaryotes (SRP)

Indexed keywords

BACTERIA; BIODEGRADATION; CLONING; GENE ENCODING; HIGH TEMPERATURE CORROSION; INFORMATION MANAGEMENT; OIL FIELDS; PETROLEUM RESERVOIR ENGINEERING; PIPELINE CORROSION; POLYMERASE CHAIN REACTION; RNA; SULFUR COMPOUNDS;

HIGH-TEMPERATURE PETROLEUM RESERVOIRS; MICROBIAL COMMUNITIES; MICROBIOLOGICALLY INFLUENCED CORROSIONS; SOURING; SULFATE REDUCING;

RESERVOIR MANAGEMENT;

BIOLOGICAL METHOD; CLONE; CONCENTRATION (COMPOSITION); CORROSION; GENETIC ANALYSIS; HIGH TEMPERATURE; HYDROCARBON RESERVOIR; MICROBIAL COMMUNITY; OIL PRODUCTION; RESEARCH METHOD; SULFATE-REDUCING BACTERIUM;

CHINA; JIANGSU;

ALPHAPROTEOBACTERIA; ARCHAEOGLOBI; ARCHAEOGLOBUS; BACTERIA (MICROORGANISMS); DESULFOTIGNUM; GAMMAPROTEOBACTERIA; METHANOMICROBIA; PROKARYOTA; THERMOCOCCI; THIOALKALIVIBRIO;

EID: 84973129462     PISSN: 09648305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ibiod.2016.05.018     Document Type: Article

References (79)

1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
2. Barton L.L., Fauque G.D. Biochemistry, physiology and biotechnology of sulfate-reducing bacteria. Adv. Appl. Microbiol. 2009, 68:41-98.
3. Bass C., Lappin-Scott H. The bad guys and the good guys in petroleum microbiology. Oilfield Rev. 1997, 9:17-25.
4. Batista J.F., Pereira R.F.C., Lopes J.M., Carvalho M.F.M., Feio M.J., Reis M.A.M. In situ corrosion control in industrial water systems. Biodegradation 2000, 11:441-448.
5. Beeder J., Nilsen R.K., Rosnes J.T., Torsvik T., Lien T. Archaeoglobus fulgidus isolated from Hot North Sea oil field waters. Appl. Environ. Microbiol. 1994, 60:1227-1231.
6. Blanco Y., Rivas L.A., Garcia-Moyano A., Aguirre J., Cruz-Gil P., Palacin A., van Heerden E., Parro V. Deciphering the prokaryotic community and metabolisms in South African deep-mine biofilms through antibody microarrays and graph theory. PloS one 2014, 9:e114180.
7. Broda D.M., Saul D.J., Bell R.G., Musgrave D.R. Clostridium algidixylanolyticum sp. nov., a psychrotolerant, xylan-degrading, spore-forming bacterium. Int. J. Syst. Evol. Microbiol. 2000, 50:623-631.
8. Carlson H.K., Kuehl J.V., Hazra A.B., Justice N.B., Stoeva M.K., Sczesnak A., Mullan M.R., Iavarone A.T., Engelbrektson A., Price M.N. Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per) chlorate and nitrate. ISME J. 2015, 9:1295-1305.
9. Cha I.T., Min U.G., Kim S.J., Yim K.J., Roh S.W., Rhee S.K. Methanomethylovorans uponensis sp. nov., a methylotrophic methanogen isolated from wetland sediment. Antonie Van Leeuwenhoek 2013, 104:1005-1012.
10. Chao A. Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 1984, 11:265-270.
11. Chao A., Yang M.C.K. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 1993, 80:193-201.
12. Cheng L., He Q., Ding C., Dai L.R., Li Q., Zhang H. Novel bacterial groups dominate in a thermophilic methanogenic hexadecane-degrading consortium. FEMS Microbiol. Ecol. 2013, 85:568-577.
13. Chin K.J., Sharma M.L., Russell L.A., O'Neill K.R., Lovley D.R. Quantifying expression of a dissimilatory (bi)sulfite reductase gene in petroleum-contaminated marine harbor sediments. Microb. Ecol. 2008, 55:489-499.
14. Colwell R.K., Chao A., Gotelli N.J., Lin S.Y., Mao C.X., Chazdon R.L., Longino J.T. Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages. J. Plant Ecol. 2012, 5:3-21.
15. Davidova I.A., Duncan K.E., Perez-Ibarra B.M., Suflita J.M. Involvement of thermophilic archaea in the biocorrosion of oil pipelines. Environ. Microbiol. 2012, 14:1762-1771.
16. Dinh H.T., Kuever J., Muszmann M., Hassel A.W., Stratmann M., Widdel F. Iron corrosion by novel anaerobic microorganisms. Nature 2004, 427:829-832.
17. Enning D., Venzlaff H., Garrelfs J., Dinh H.T., Meyer V., Mayrhofer K., Hassel A.W., Stratmann M., Widdel F. Marine sulfate-reducing bacteria cause serious corrosion of iron under electroconductive biogenic mineral crust. Environ. Microbiol. 2012, 14:1772-1787.
18. Geets J., Borremans B., Diels L., Springael D., Vangronsveld J., van der Lelie D., Vanbroekhoven K. DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria. J. Microbiol. Methods 2006, 66:194-205.
19. Gittel A., Sorensen K.B., Skovhus T.L., Ingvorsen K., Schramm A. Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment. Appl. Environ. Microbiol. 2009, 75:7086-7096.
20. Guan J., Zhang B.L., Mbadinga S.M., Liu J.F., Gu J.D., Mu B.Z. Functional genes (dsr) approach reveals similar sulphidogenic prokaryotes diversity but different structure in saline waters from corroding high temperature petroleum reservoirs. Appl. Microbiol. Biotechnol. 2014, 98:1871-1882.
21. Habe H., Kobuna A., Hosoda A., Kosaka T., Endoh T., Tamura H., Yamane H., Nojiri H., Omori T., Watanabe K. Identification of the electron transfer flavoprotein as an upregulated enzyme in the benzoate utilization of Desulfotignum balticum. Biosci. Biotechnol. Biochem. 2009, 73:1647-1652.
22. Habe H., Kobuna A., Hosoda A., Kouzuma A., Yamane H., Nojiri H., Omori T., Watanabe K. Subtractive hybridization and random arbitrarily primed PCR analyses of a benzoate-assimilating bacterium, Desulfotignum balticum. Appl. Microbiol. Biotechnol. 2008, 79:87-95.
23. Harwati T.U., Kasai Y., Kodama Y., Susilaningsih D., Watanabe K. Characterization of diverse hydrocarbon-degrading bacteria isolated from Indonesian seawater. Microbes Environ. 2007, 22:412-415.
24. Hesham A.E.-L., Ahmad A., Daqiang C., Khan S. PCR-DGGE and real-time PCR dsrB-based study of the impact of heavy metals on the diversity and abundance of sulfate-reducing bacteria. Biotechnol. Bioprocess Eng. 2014, 19:703-710.
25. Huber T., Faulkner G., Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004, 20:2317-2319.
26. Hubert C., Voordouw G. Oil field souring control by nitrate-reducing Sulfurospirillum spp. that outcompete sulfate-reducing bacteria for organic electron donors. Appl. Environ. Microbiol. 2007, 73:2644-2652.
27. Hughes J.B., Hellmann J.J., Ricketts T.H., Bohannan B.J.M. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 2001, 67:4399-4406.
28. Iino T., Ito K., Wakai S., Tsurumaru H., Ohkuma M., Harayama S. Iron corrosion induced by nonhydrogenotrophic nitrate-reducing Prolixibacter sp. strain MIC1-1. Appl. Environ. Microbiol. 2015, 81:1839-1846.
29. Janssen A.J.H., Lens P.N.L., Stams A.J.M., Plugge C.M., Sorokin D.Y., Muyzer G., Dijkman H., Van Zessen E., Luimes P., Buisman C.J.N. Application of bacteria involved in the biological sulfur cycle for paper mill effluent purification. Sci. Total Environ. 2009, 407:1333-1343.
30. Jetten M.S.M., Stams A.J.M., Zehnder A.J.B. Methanogenesis from acetate-a comparison of the acetate metabolism in Methanothrix-soehngenii and Methanosarcina spp. FEMS Microbiol. Rev. 1992, 708:181-197.
31. 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. J. Bacteriol. 2001, 183:6028-6035.
32. Klok J.B.M., van den Bosch P.L.F., Buisman C.J.N., Stams A.J.M., Keesman K.J., Janssen A.J.H. Pathways of sulfide oxidation by haloalkaliphilic bacteria in limited-oxygen gas lift bioreactors. Environ. Sci. Technol. 2012, 46:7581-7586.
33. Kuever J., Könneke M., Galushko A., Drzyzga O. Reclassification of Desulfobacterium phenolicum as Desulfobacula phenolica comb. nov. and description of strain SaxT as Desulfotignum balticum gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 2001, 51:171-177.
34. LeChevallier M.W., Cawthon C.D., Lee R.G. Factors promoting survival of bacteria in chlorinated water supplies. Appl. Environ. Microbiol. 1988, 54:649-654.
35. Lenhart T.R., Duncan K.E., Beech I.B., Sunner J.A., Smith W., Bonifay V., Biri B., Suflita J.M. Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces. Biofouling 2014, 30:823-835.
36. Li C.Y., Zhang D., Li X.X., Mbadinga S.M., Yang S.Z., Liu J.F., Gu J.D., Mu B.Z. The biofilm property and its correlationship with high-molecular-weight polyacrylamide degradation in a water injection pipeline of Daqing oilfield. J. Hazard. Mater. 2016, 304:388-399.
37. Li C.Y., Li J.Y., Mbadinga S.M., Liu J.F., Gu J.D., Mu B.Z. Analysis of bacterial and archaeal communities along a high-molecular-weight polyacrylamide transportation pipeline system in an oil field. Int. J. Mol. Sci. 2015, 16:7445-7461.
38. Li D., Midgley D.J., Ross J.P., Oytam Y., Abell G.C., Volk H., Daud W.A., Hendry P. Microbial biodiversity in a Malaysian oil field and a systematic comparison with oil reservoirs worldwide. Arch. Microbiol. 2012, 194:513-523.
39. Li H., Yang S.Z., Mu B.Z., Rong Z.F., Zhang J. Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield. FEMS Microbiol. Ecol. 2007, 60:74-84.
40. Liu X.-Z., Zhang L.-M., Prosser J.I., He J.-Z. Abundance and community structure of sulfate reducing prokaryotes in a paddy soil of southern China under different fertilization regimes. Soil Biol. Biochem. 2009, 41:687-694.
41. Lomans B.P., Maas R., Luderer R., den Camp H.J.O., Pol A., van der Drift C., Vogels G.D. Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl. Environ. Microbiol. 1999, 65:3641-3650.
42. Mand J., Park H.S., Jack T.R., Voordouw G. The role of acetogens in microbially influenced corrosion of steel. Front. Microbiol. 2013, 5:268.
43. Mayumi D., Mochimaru H., Yoshioka H., Sakata S., Maeda H., Miyagawa Y., Ikarashi M., Takeuchi M., Kamagata Y. Evidence for syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis in the high-temperature petroleum reservoir of Yabase oil field (Japan). Environ. Microbiol. 2011, 13:1995-2006.
44. Mbadinga S.M., Li K.P., Zhou L., Wang L.Y., Yang S.Z., Liu J.F., Gu J.D., Mu B.Z. Analysis of alkane-dependent methanogenic community derived from production water of a high-temperature petroleum reservoir. Appl. Microbiol. Biotechnol. 2012, 96:531-542.
45. Musat F., Widdel F. Anaerobic degradation of benzene by a marine sulfate-reducing enrichment culture, and cell hybridization of the dominant phylotype. Environ. Microbiol. 2008, 10:10-19.
46. Muyzer G., Sorokin D.Y., Mavromatis K., Lapidus A., Clum A., Ivanova N., Pati A., d'Haeseleer P., Woyke T., Kyrpides N.C. Complete genome sequence of "Thioalkalivibrio sulfidophilus" HL-EbGr7. Stand. Genomic Sci. 2011, 4:23-35.
47. Nazina T.N., Shestakova N.M., Grigor'yan A.A., Mikhailova E.M., Tourova T.P., Poltaraus A.B., Feng C.X., Ni F.T., Belyaev S.S. Phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the Dagang oil field (P.R. China). Microbiology 2006, 75:55-65.
48. Page S., Gaylarde C. Biocide activity against Legionella and Pseudomonas. Int. Biodeterior. 1990, 26:139-148.
49. Parks D.H., Beiko R.G. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 2010, 26:715-721.
50. Perez-Jimenez J.R., Kerkhof L.J. Phylogeography of sulfate-reducing bacteria among disturbed sediments, disclosed by analysis of the dissimilatory sulfite reductase genes (dsrAB). Appl. Environ. Microbiol. 2005, 71:1004-1011.
51. Pham V.D., Hnatow L.L., Zhang S., Fallon R.D., Jackson S.C., Tomb J.F., DeLong E.F., Keeler S.J. Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. Environ. Microbiol. 2009, 11:176-187.
52. Quillet L., Besaury L., Popova M., Paisse S., Deloffre J., Ouddane B. Abundance, diversity and activity of sulfate-reducing prokaryotes in heavy metal-contaminated sediment from a salt marsh in the Medway Estuary (UK). Mar. Biotechnol. 2012, 14:363-381.
53. Ren H.Y., Zhang X.J., Song Z.Y., Rupert W., Gao G.J., Guo S.X., Zhao L.P. Comparison of microbial community compositions of injection and production well samples in a long-term water-flooded petroleum reservoir. PloS one 2011, 6:e23258.
54. Savage K.N., Krumholz L.R., Gieg L.M., Parisi V.A., Suflita 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 Microbiol. Ecol. 2010, 72:485-495.
55. Shen Y., Voordouw G. Primers for dsr genes and most probable number method for detection of sulfate-reducing bacteria in oil reservoirs. Springer Protoc. Handb. 2015, 1-9.
56. Sooknah R., Papavinasam S., Revie R.W. Monitoring microbiologically influenced corrosion: a review of techniques. CORROSION 2007 2007, NACE International, Nashville, Tennessee.
57. Sorokin D.Y., Antipov A.N., Kuenen J.G. Complete denitrification in coculture of obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria from a hypersaline soda lake. Archives Microbiol. 2003, 180:127-133.
58. Sorokin D.Y., Berben T., Melton E.D., Overmars L., Vavourakis C.D., Muyzer G. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 2014, 18:791-809.
59. Sorokin D.Y., Kuenen J., Jetten M. Denitrification at extremely alkaline conditions in obligately autotrophic alkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio denitrificans strain ALJD. Archi. Microbiol. 2001, 175:94-101.
60. Sorokin D.Y., Tat'yana P.T., Antipov A.N., Muyzer G., Kuenen J.G. Anaerobic growth of the haloalkaliphilic denitrifying sulfur-oxidizing bacterium Thialkalivibrio thiocyanodenitrificans sp. nov. with thiocyanate. Microbiology 2004, 150:2435-2442.
61. Stott J., Dicken G., Rizk T., Gamble C., Saul S., Granli T., Haegh T. Corrosion inhibition in PWRI Systems That use Nitrate Treatment to Control SRB Activity and Reservoir Souring. CORROSION 2008 2008, NACE International, New Orleans, Louisiana.
62. Sun J., Hu S., Sharma K.R., Ni B.-J., Yuan Z. Stratified microbial structure and activity in sulfide-and methane-producing anaerobic sewer biofilms. Appl. Environ. Microbiol. 2014, 80:7042-7052.
63. Sun W., Li J., Jiang L., Sun Z., Fu M., Peng X. Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation. Appl. Microbiol. Biotechnol. 2015, 99:8751-8764.
64. 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. Mol. Biol. Evol. 2011, 28:2731-2739.
65. Tang Y.Q., Li Y., Zhao J.Y., Chi C.Q., Huang L.X., Dong H.P., Wu X.L. Microbial communities in long-term, water-flooded petroleum reservoirs with different in situ temperatures in the Huabei oilfield, China. PloS one 2012, 7:e33535.
66. Uchiyama T., Ito K., Mori K., Tsurumaru H., Harayama S. Iron-corroding methanogen isolated from a crude-oil storage tank. Appl. Environ. Microbiol. 2010, 76:1783-1788.
67. Usher K.M., Kaksonen A.H., Cole I., Marney D. Critical review: microbially influenced corrosion of buried carbon steel pipes. Int. Biodeterior. Biodegradation 2014, 93:84-106.
68. Venzlaff H., Enning D., Srinivasan J., Mayrhofer K.J.J., Hassel A.W., Widdel F., Stratmann M. Accelerated cathodic reaction in microbial corrosion of iron due to direct electron uptake by sulfate-reducing bacteria. Corros. Sci. 2013, 66:88-96.
69. Voordouw G. The genus Desulfovibrio: the centennial. Appl. Environ. Microbiol. 1995, 61:2813.
70. 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. J. Bacteriol. 1998, 180:2975-2982.
71. Wang L.Y., Li W., Mbadinga S.M., Liu J.F., Gu J.D., Mu B.Z. Methanogenic microbial community composition of oily sludge and its enrichment amended with alkanes incubated for over 500 days. Geomicrobiol. J. 2012, 29:716-726.
72. Williamson C.H.D., Jain L.A., Mishra B., Olson D.L., Spear J.R. Microbially influenced corrosion communities associated with fuel-grade ethanol environments. Appl. Microbiol. Biotechnol. 2015, 99:6945-6957.
73. Yakimov M.M., Timmis K.N., Golyshin P.N. Obligate oil-degrading marine bacteria. Curr. Opin. Biotechnol. 2007, 18:257-266.
74. Yu Y., Lee C., Kim J., Hwang S. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol. Bioeng. 2005, 89:670-679.
75. Zengler K., Richnow H.H., Rossello-Mora R., Michaelis W., Widdel F. Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 1999, 401:266-269.
76. Zhang T., Fang H.H.P., Ko B.C.B. Methanogen population in a marine biofilm corrosive to mild steel. Appl. Microbiol. Biotechnol. 2003, 63:101-106.
77. Zhou L., Li K.P., Mbadinga S.M., Yang S.Z., Gu J.D., Mu B.Z. Analyses of n-alkanes degrading community dynamics of a high-temperature methanogenic consortium enriched from production water of a petroleum reservoir by a combination of molecular techniques. Ecotoxicology 2012, 21:1680-1691.
78. Zhu X.Y., Lubeck J., Kilbane J.J. Characterization of microbial communities in gas industry pipelines. Appl. Environ. Microbiol. 2003, 69:5354-5363.
79. Zrafi-Nouira I., Guermazi S., Chouari R., Safi N.D., Pelletier E., Bakhrouf A., Saidane-Mosbahi D., Sghir A. Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil. Biodegradation 2009, 20:467-486.