Microbial biodiversity in a Malaysian oil Weld and a systematic comparison with oil reservoirs worldwide

Archives of Microbiology

Volumn 194, Issue 6, 2012, Pages 513-523

  Li, Dongmei ^a   Midgley, David J ^a   Ross, Jason P ^a   Oytam, Yalchin ^a   Abell, Guy C J ^a   Volk, Herbert ^a   Daud, Wan Ata Wan ^b   Hendry, Philip ^a  

^a CSIRO   (Australia)

^b PETRONAS CARIGALI SDN BHD   (Malaysia)

Author keywords

Biodiversity; Formation water; Oil; Petroleum; Primer

Indexed keywords

PETROLEUM; RIBOSOME DNA;

ALPHAPROTEOBACTERIA; AMPLICON; ARTICLE; BACTEROIDETES; BETAPROTEOBACTERIA; BIODIVERSITY; CONTROLLED STUDY; DELTAPROTEOBACTERIA; DNA EXTRACTION; DNA RESTRICTION; FIRMICUTES; GAMMAPROTEOBACTERIA; MALAYSIA; MARINOBACTER; METHANOCOCCUS; MICROBIAL BIODIVERSITY; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; OIL FIELD; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOMONAS; TAXONOMY; UNINDEXED SEQUENCE; WATER ANALYSIS; WATER SAMPLING;

ARCHAEA; BIODIVERSITY; COMPUTATIONAL BIOLOGY; DNA PRIMERS; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; MALAYSIA; MARINOBACTER; OIL AND GAS FIELDS; PHYLOGENY; POLYMERASE CHAIN REACTION; PSEUDOMONAS; RNA, RIBOSOMAL, 16S;

ARCHAEA; BACTERIA (MICROORGANISMS); DEFERRIBACTERACEAE; MARINOBACTER; MARINOBACTERIUM; METHANOCOCCI; PSEUDOMONAS;

EID: 84865863877     PISSN: 03028933     EISSN: 1432072X     Source Type: Journal    
DOI: 10.1007/s00203-012-0788-z     Document Type: Article

References (46)

1. Allen EE, BanWeld JF (2005) Community genomics in microbial ecology and evolution. Nat Rev Microbiol 3:489-498 (Pubitemid 40716175)
2. Antunes A et al (2007) Marinobacter salsuginis sp. nov., isolated from the brine-seawater interface of the Shaban Deep, Red Sea. Int J Syst Evol Microbiol 57:1035-1040 (Pubitemid 46796480)
3. Bastin ES (1926) The problem of the natural reduction of sulphates. AAPG Bull 10:1270-1299
4. Bonch-Osmolovskaya EA et al (2003) Radioisotopic, culture-based, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir. Appl Environ Microbiol 69:6143-6151 (Pubitemid 37280340)
5. Chouari R, Paslier DL, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ Microbiol 7:1104-1115 (Pubitemid 41026511)
6. Colwell RK (1997) EstimateS: statistical estimation of species richness and shared species from samples. Version 8.0.0. User's Guide and application published at: http://purl.oclc.org/estimates
7. Dahle H, Garshol F, Madsen M, Birkeland N-K (2008) Microbial community structure analysis of produced water from a hightemperature North Sea oil-Weld. Antonie van Leeuwenhoek 93:37-49
8. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685-5689
9. DeLong EF (2004) Microbial population genomics and ecology: the road ahead. Environ Microbiol 6:875-878
10. Edgar R (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797 (Pubitemid 38832724)
11. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) Version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, p 5
12. Fuhrman JA, Davis AA (1997) Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar Ecol Prog Ser 150:275-285
13. Gonzalez JM, Mayer F, Moran MA, Hodson RE, Whitman WB (1997) Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 47:369-376 (Pubitemid 27163900)
14. Grabowski A, Nercessian O, Fayolle F, Blanchet D, Jeanthon C (2005) Microbial diversity in production waters of a low-temperature biodegraded oil reservoir. FEMS Microbiol Ecol 54:427-443 (Pubitemid 41416859)
15. Hall C, Tharakan P, Hallock J, Cleveland C, JeVerson M (2003) Hydrocarbons and the evolution of human culture. Nature 426:318-322 (Pubitemid 37463154)
16. Head IM, Jones DM, Larter SR (2003) Biological activity in the deep subsurface and the origin of heavy oil. Nature 426:344-352 (Pubitemid 37463157)
17. Head IM, Jones DM, Roling WFM (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4:173-182
18. Ibrahim Z (2004) Simulation analysis of microbial well treament of Bokor Weld, Malaysia. In: SPE Asia PaciWc oil and gas conference and exhibition. Paper number SPE 88453, Perth, Australia
19. Iino T, Nakagawa T, Mori K, Harayama S, Suzuki K-I (2008) Calditerrivibrio nitroreducens gen. nov., sp. nov., a thermophilic, nitratereducing bacterium isolated from a terrestrial hot spring in Japan. Int J Syst Evol Microbiol 58:1675-1679
20. Karim MGA, Salim MAH (2001) Microbial enhanced oil recovery (MEOR) technology in Bokor Weld, Sarawak. In: SPE Asia Paci-Wc improved oil recovery conference. Paper number SPE 72125
21. Lake LW (1989) Enhanced oil recovery. Prentice Hall, Englewood CliVs
22. Li D, Hendry P (2008) Microbial diversity in petroleum reservoirs. Microbiol Aust 29:25-27
23. Li H, Yang SZ, Mu BZ, Rong ZF, Zhang J (2006) Molecular analysis of the bacterial community in a continental high-temperature and water-Xooded petroleum reservoir. FEMS Microbiol Lett 257:92-98
24. Li H, Yang SZ, Mu BZ (2007a) Phylogenetic diversity of the archaeal community in a continental high-temperature, water-Xooded petroleum reservoir. Curr Microbiol 55:382-388 (Pubitemid 47536821)
25. Li H, Yang SZ, Mu BZ, Rong ZF, Zhang J (2007b) Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an oVshore oilWeld. FEMS Microbiol Ecol 60:74-84 (Pubitemid 46426574)
26. Ludwig W et al (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371 (Pubitemid 38854737)
27. Magot M, Ollivier B, Patel BKC (2000) Microbiology of petroleum reservoirs. Antonie van Leeuwenhoek 77:103-116 (Pubitemid 30160411)
28. Midgley DJ et al (2010) Characterisation of a microbial community associated with a deep, coal seam methane reservoir in the Gippsland Basin, Australia. Int J Coal Geol 82:232-239
29. Nemati M, Jenneman GE, Voordouw G (2001) Impact of nitrate-mediated microbial control of souring in oil reservoirs on the extent of corrosion. Biotechnol Progress 17:852-859 (Pubitemid 32972647)
30. Oliveira VMD, Sette LD, Simioni KCM, Santos Neto EVD (2008) Bacterial diversity characterization in petroleum samples from Brazilian reservoirs. Braz J Microbiol 39:445-452
31. Orphan VJ, Taylor LT, Hafenbradl D, Delong EF (2000) Culturedependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microbiol 66:700-711 (Pubitemid 30082762)
32. Palleroni NJ (2005) Genus I. Pseudomonas In: Brenner NRK DJ, T. Staley J, Garrity GM (ed) Bergey's manual of systematic bacteriology, 2nd edn. Springer, East Lansing, pp 323-379
33. Pham VD et al (2009) Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. Environ Microbiol 11:176-187
34. R Development Core Team (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org
35. Raes J, Bork P (2008) Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol 6:693-699
36. Reardon CL et al (2004) Composition and diversity of microbial communities recovered from surrogate minerals incubated in an acidic uranium-contaminated aquifer. Appl Environ Microbiol 70:6037-6046 (Pubitemid 39471851)
37. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for deWning operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501-1506 (Pubitemid 40396689)
38. Sette L, Simioni K, Vasconcellos S, Dussan L, Neto E, Oliveira V (2007) Analysis of the composition of bacterial communities in oil reservoirs from a southern oVshore Brazilian basin. Antonie van Leeuwenhoek 91:253-266 (Pubitemid 46431841)
39. She Y et al (2008) Analysis on the microbial diversity of qinghai high salt content oil reservoirs. In: 2nd International conference on bioinformatics and biomedical engineering, ICBBE 2008, pp 780-783
40. Sorensen KB, CanWeld DE, Teske AP, Oren A (2005) Community composition of a hypersaline endoevaporitic microbial mat. Appl Environ Microbiol 71:7352-7365 (Pubitemid 43194230)
41. Takai K et al (2005) Marinobacter alkaliphilus sp. nov., a novel alkaliphilic bacterium isolated from subseaXoor alkaline serpentine mud from Ocean Drilling Program Site 1200 at South Chamorro Seamount, Mariana Forearc. Extremophiles 9:17-27 (Pubitemid 40306923)
42. Van Der Kraan GM, Bruining J, Lomans BP, Van Loosdrecht MCM, Muyzer G (2009) Microbial diversity of an oil-water processing site and its associated oil Weld: the possible role of microorganisms as information carriers from oil-associated environments. FEMS Microbiol Ecol 71:428-443
43. van Elsas JD, Mäntynen V, Wolters AC (1997) Soil DNA extraction and assessment of the fate of Mycobacterium chlorophenolicum strain PCP-1 in diVerent soils by 16S ribosomal RNA gene sequence based most-probable-number PCR and immunoXuorescence. Biol Fertil Soils 24:188-195
44. Voordouw G et al (1996) Characterization of 16S rRNA genes from oil Weld microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulWde-oxidizing bacteria. Appl Environ Microbiol 62:1623-1629
45. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classiWer for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261-5267 (Pubitemid 47326658)
46. Yamane K et al (2008) Diversity and similarity of microbial communities in petroleum crude oils produced in Asia. Biosci Biotechnol Biochem 72:2831-2839