Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods

Environmental Microbiology

Volumn 11, Issue 1, 2009, Pages 176-187

  Pham, Vinh D ^a   Hnatow, Linda L ^b   Zhang, Shiping ^b   Fallon, Robert D ^b   Jackson, Scott C ^b   Tomb, Jean Francois ^b   DeLong, Edward F ^a   Keeler, Sharon J ^b  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b DUPONT COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID DERIVATIVE; ARCHAEAL DNA; ARCHAEAL RNA; BACTERIAL DNA; BACTERIAL RNA; PETROLEUM; RIBOSOME DNA; RNA 16S;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA GENE; SEQUENCE HOMOLOGY; UNITED STATES;

ACETATES; ALASKA; ARCHAEA; BACTERIA; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, RRNA; MOLECULAR SEQUENCE DATA; PETROLEUM; PHYLOGENY; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; WATER MICROBIOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS); FIRMICUTES; SYNERGISTES;

EID: 58149216600     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2008.01751.x     Document Type: Article

References (50)

1. Abram, J.W. Nedwell, D.B. (1978) Inhibition of methanogenesis by sulphate reducing bacteria competing for transferred hydrogen. Arch Microbiol 117 : 89 92.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. Lipman, D.J. (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25 : 3389 3402.
3. Bailey, N.J.L., Krouse, H.R., Evans, C.R. Rogers, M.A. (1973) Alteration of crude-oil by waters and bacteria - evidence from geochemical and Isotope studies. Am Assoc Petroleum Geologists Bull 57 : 1276 1290.
4. Barth, T. Riis, M. (1992) Interactions between organic-acid anions in formation waters and reservoir mineral phases. Organic Geochem 19 : 455 482.
5. Bastin, E.S. (1926) Microorganisms in oilfields. Science 63 : 21 24.
6. Beja, O., Suzuki, M.T., Koonin, E.V., Aravind, L., Hadd, A., Nguyen, L.P., et al. (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2 : 516 529.
7. Briee, C., Moreira, D. Lopez-Garcia, P. (2007) Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond. Res Microbiol 158 : 213 227.
8. Cottrell, M.T., Waidner, L.A., Yu, L.Y. Kirchman, D.L. (2005) Bacterial diversity of metagenomic and PCR libraries from the Delaware River. Environ Microbiol 7 : 1883 1895.
9. Dahle, H., Garshol, F., Madsen, M. Birkeland, N.K. (2008) Microbial community structure analysis of produced water from a high-temperature North Sea oil-field. Antonie Van Leeuwenhoek 93 : 37 49.
10. Dojka, M.A., Hugenholtz, P., Haack, S.K. Pace, N.R. (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64 : 3869 3877.
11. Dojka, M.A., Harris, J.K. Pace, N.R. (2000) Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol 66 : 1617 1621.
12. Dolfing, J., Larter, S.R. Head, I.M. (2007) Thermodynamic constraints on methanogenic crude oil biodegradation. ISME J 2 : 442 452.
13. Drake, H.L., Kusel, K. Matthies, C. (2006) Acetogenic prokaryotes. In The Prokaryotes. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H. Stackebrandt, E. (eds). New York, NY, USA : Springer New York, pp. 354 420.
14. Ewing, B., Hillier, L., Wendl, M.C. Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8 : 175 185.
15. 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.
16. Grassia, G.S., McLean, K.M., Glenat, P., Bauld, J. Sheehy, A.J. (1996) A systematic survey for thermophilic fermentative bacteria and archaea in high temperature petroleum reservoirs. FEMS Microbiol Ecol 21 : 47 58.
17. Harris, J.K., Kelley, S.T. Pace, N.R. (2004) New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol 70 : 845 849.
18. Head, I.M., Jones, D.M. Larter, S.R. (2003) Biological activity in the deep subsurface and the origin of heavy oil. Nature 426 : 344 352.
19. Huber, T., Faulkner, G. Hugenholtz, P. (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20 : 2317 2319.
20. Hugenholtz, P., Pitulle, C., Hershberger, K.L. Pace, N.R. (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180 : 366 376.
21. Jannasch, H.W. Jones, G.E. (1959) Bacterial populations in seawater as determined by different methods of enumeration. Limnol Oceanogr 4 : 128 139.
22. Jones, D.M., Head, I.M., Gray, N.D., Adams, J.J., Rowan, A.K., Aitken, C.M., et al. (2008) Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature 451 : 176 180.
23. Kato, T., Haruki, M., Imanaka, T., Morikawa, M. Kanaya, S. (2001) Isolation and characterization of psychotrophic bacteria from oil-reservoir water and oil sands. Appl Microbiol Biotechnol 55 : 794 800.
24. Keller, M. Zengler, K. (2004) Tapping into microbial diversity. Nat Rev Microbiol 2 : 141 150.
25. Kogure, K., Simidu, U. Taga, N. (1979) Tentative direct microscopic method for counting living marine - bacteria. Can J Microbiol 25 : 415 420.
26. Li, H., Yang, S.-Z., Mu, B.-Z., Rong, Z.-F. Zhang, J. (2006) Molecular analysis of the bacterial community in a continental high-temperature and water-flooded petroleum reservoir. FEMS Microbiol Lett 257 : 92 98.
27. Li, H., Yang, S.-Z., Mu, B.-Z., Rong, Z.-F. Zhang, J. (2007) Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield. FEMS Microbiol Ecol 60 : 74 84.
28. Liles, M.R., Manske, B.F., Bintrim, S.B., Handelsman, J. Goodman, R.M. (2003) A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69 : 2684 2691.
29. Lozupone, C. Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71 : 8228 8235.
30. McInerney, M.J., Bryant, M.P. Pfennig, N. (1979) Anaerobic bacterium that degrades fatty-acids in syntrophic association with methanogens. Arch Microbiol 122 : 129 135.
31. McInerney, M.J., Nagle, D.P. Knapp, R.M. (2005) Microbially enhanced oil recovery: past, present, and future. In Petroleum Microbiology. Ollivier, B. Magot, M. (eds). Washington, DC, USA : American Society for Microbiology Press, pp. 215 237.
32. Magot, M. 2005) Indigenous microbial communities in oil fields. In Petroleum Microbiology. Ollivier B. Magot, M. (eds). Washington DC, USA : American Society for Microbiology Press, pp. 21 33.
33. Marchesi, J.R., Sato, T., Weightman, A.J., Martin, T.A., Fry, J.C., Hiom, S.J., et al. (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64 : 795 799.
34. Meredith, W., Kelland, S.J. Jones, D.M. (2000) Influence of biodegradation on crude oil acidity and carboxylic acid composition. Org Geochem 31 : 1059 1073.
35. Nazina, T.N., Griror'yan, A.A., Feng, Q.X., Shestakova, N.M., Babich, T.L., Pavlova, N.K., et al. (2007) Microbiological and production characteristics of the high-temperature Kongdian petroleum reservoir revealed during field trial of biotechnology for the enhancement of oil recovery. Microbiology 76 : 297 309.
36. Nunoura, T., Oida, H., Masui, N., Inagaki, F., Takai, K., Hirano, S., et al. (2006) Culture-dependent and independent analyses of subsurface microbial communities in oil-bearing strata of the Sagara oil reservoir. Island Arc 15 : 328 337.
37. Orphan, V.J., Taylor, L.T., Hafenbradl, D. Delong, E.F. (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microbiol 66 : 700 711.
38. Pace, N.R. 1997) A molecular view of microbial diversity and the biosphere. Science 276 : 734 740.
39. Pham, V.D., Konstantinidis, K.T., Palden, T. DeLong, E.F. (2008) Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ Microbiol 10 : 2313 2330.
40. Röling, W.F., Head, I.M. Larter, S.R. (2003) The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects. Res Microbiol 154 : 321 328.
41. Sambrook, J. Russell, D.W. (2006) Purification of bacteriophage λ particles by isopycnic centrifugation through CsCl gradients. Cold Spring Harb Protoc 2006. doi:10.1101/pdb.prot3968.
42. Schink, B. (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61 : 262 280.
43. Smalley, P.C., Goodwin, N.S., Dillon, J.F., Bidinger, C.R. Drozd, R.J. (1997) New tools target oil-quality sweetspots in viscous-oil accumulations. Spe Res Eng 12 : 157 161.
44. Suzuki, M.T., Preston, C.M., Beja, O., de la Torre, J.R., Steward, G.F. DeLong, E.F. (2004) Phylogenetic screening of ribosomal RNA gene-containing clones in Bacterial Artificial Chromosome (BAC) libraries from different depths in Monterey Bay. Microb Ecol 48 : 473 488.
45. Thauer, R.K. (1982) Dissimilatory sulphate reduction with acetate as electron donor. Philos Trans R Soc Lond B Biol Sci 298 : 467 471.
46. Voordouw, G., Armstrong, S.M., Reimer, M.F., Fouts, B., Telang, A.J., Shen, Y. Gevertz, D. (1996) Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria. Appl Environ Microbiol 62 : 1623 1629.
47. Wang, Q., Garrity, G.M., Tiedje, J.M. Cole, J.R. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73 : 5261 5267.
48. Warren, E., Bekins, B.A., Godsy, E.M. Smith, V.K. (2004) Inhibition of acetoclastic methanogenesis in crude oil- and creosote-contaminated groundwater. Bioremediat J 8 : 1 11.
49. Webster, G., Parkes, R.J., Fry, J.C. Weightman, A.J. (2004) Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ Microbiol 70 : 5708 5713.
50. Wilhelms, A., Larter, S.R., Head, I., Farrimond, P., di-Primio, R. Zwach, C. (2001) Biodegradation of oil in uplifted basins prevented by deep-burial sterilization. Nature 411 : 1034 1037.