Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil

Journal of Microbiology and Biotechnology

Volumn 18, Issue 1, 2008, Pages 5-14

  Von Der Weid, Irene ^a   Korenblum, Elisa ^a   Jurelevicius, Diogo ^a   Rosado, Alexandre Soares ^a   Dino, Rodolfo ^b   Sebastián, Gina Vasquez ^b   Seldin, Lucy ^a  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b PETROBRAS   (Brazil)

Author keywords

16S rRNA gene; Aps gene; Bacterial diversity; Subseafloor biosphere

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; DNA 16S; OXIDOREDUCTASE; RNA 16S; ADENYLYLSULFATE REDUCTASE; PETROLEUM; SEA WATER; SULFATE;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; AMPLICON; ARTICLE; BACTERIUM IDENTIFICATION; BETAPROTEOBACTERIA; BRAZIL; CONTROLLED STUDY; DNA EXTRACTION; DNA LIBRARY; FIRMICUTES; GAMMAPROTEOBACTERIA; GENE AMPLIFICATION; GENE SEQUENCE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OCEAN ENVIRONMENT; OIL INDUSTRY; PHYLOGENY; POLYMERASE CHAIN REACTION; ROCK; SAMPLING; SULFATE REDUCING BACTERIUM; UNINDEXED SEQUENCE; ATLANTIC OCEAN; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; GENE LIBRARY; GENETICS; GRAM NEGATIVE ANAEROBIC BACTERIA; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PROTEOBACTERIA; SEDIMENT;

BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; GAMMAPROTEOBACTERIA;

ATLANTIC OCEAN; BRAZIL; CLONING, MOLECULAR; DNA, BACTERIAL; ECOSYSTEM; GENE LIBRARY; GEOLOGIC SEDIMENTS; OXIDOREDUCTASES ACTING ON SULFUR GROUP DONORS; PETROLEUM; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SULFATES; SULFUR-REDUCING BACTERIA;

EID: 43749116504     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: None     Document Type: Article

References (44)

1. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169.
2. Andreoni, V., L. Cavalca, M. A. Rao, G. Nocerino, S. Bernasconi, E. Dell'Amico, M. Colombo, and L. Gianfreda. 2004. Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere 57: 401-412.
3. Barton, H. A., N. M. Taylor, B. R. Lubbers, and A. C. Pemberton. 2006. DNA extraction from low-biomass carbonate rock: An improved method with reduced contamination and the low-biomass contaminant database. J. Microbiol. Methods 66: 21-31.
4. Boivin-Jahns, V., R. Ruimy, A. Bianchi, S. Daumas, and R. Christen. 1996. Bacterial diversity in a deep-subsurface clay environment. Appl. Environ. Microbiol. 62: 3405-3412.
5. Cunha, C. D., A. S. Rosado, G. V. Sebastián, L. Seldin, and I. von der Weid. 2006. Oil biodegradation by Bacillus strains isolated from the rock of an oil reservoir located in a deepwater production basin in Brazil. Appl. Microbiol. Biotechnol. 73: 949-959.
6. Da Silva, J. E. M., C. A. S. Paulo, A. G. Santos Filho, and E. J. J. Coelho. 2003. Subsea production system. Patent US5192167A.
7. D'Hondt, S. L., S. Rutherford, and A. J. Spivack. 2002. Metabolic activity of subsurface life in deep-sea sediments. Science 15: 2067-2070.
8. D'Hondt, S. L., B. B. Jorgensen, D. J. Miller, A. Batzke, R. Blake, B. A. Cragg, et al. 2004. Distributions of microbial activities in deep sub-seafloor sediments. Science 306: 2216-2221.
9. Egland, P. G., D. A. Pelletier, M. Dispensa, J. Gibson, and C. S. Harwood. 1997. A cluster of bacterial genes for anaerobic benzene ring biodegradation. Proc. Natl. Acad. Sci. USA 94: 6484-6489.
10. Fritsche, K., G. Auling, J. R. Andreesen, and U. Lechner. 1999. Defluvibacter lusatiae gen. nov., sp. nov., a new chlorophenol-degrading member of the alpha-2 subgroup of Proteobacteria. Syst. Appl. Microbiol. 22: 197-204.
11. Haldeman, D. L., P. S. Amy, D. Ringelberg, D. C. White, R. E. Garen, and W. C. Ghiorse. 1995. Microbial growth and resuscitation alter community structure after perturbation. FEMS Microbiol. Ecol. 17: 27-38.
12. Hess, A., B. Zarda, D. Hahn, A. Haner, D. Stax, P. Hohener, and J. Zeyer. 1997. In situ analysis of denitrifying toluene- and m-xylene-degrading bacteria in a diesel fuel-contaminated laboratory aquifer column. Appl. Environ. Microbiol. 63: 2136-2141.
13. Heuer, H. and K. Smalla. 1997. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities, pp. 353-370. In J. D. van Elsas, J. T. Trevors, and E. M. H. Wellington. (eds.), Modern Soil Microbiology. Marcel Dekker, Inc., New York.
14. Hurst, C. J., G. R. Knudsen, M. J. McInerney, L. D. Stetzenbach, and M. V. Walter. 1997. Manual of Environmental Microbiology. American Society for Microbiology.
15. Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, M. Suzuki, K. Takai, M. Delwiche, F. S. Colwell, K. H. Nealson, K. Horikoshi, S. D'Hondt, and B. B. Jorgensen. 2006. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc. Nat. Acad. Sci. USA 103: 2815-2820.
16. Katsivela, E., D. Bonse, A. Kruger, C. Strompl, A. Livingston, and R. M. Wittich. 1999. An extractive membrane biofilm reactor for degradation of 1,3-dichloropropene in industrial waste water. Appl. Microbiol. Biotechnol. 52: 853-862.
17. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5: 150-163.
18. Lee, Y. J., I. D. Wagner, M. E. Brice, V. V. Kevbrin, G. L. Mills, C. S. Romanek, and J. Wiegel. 2005. Thermosediminibacter oceani gen. nov. sp. nov. & Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin. Extremophiles 9: 375-383.
19. Lu, J., Y. Nogi, and H. Takami. 2001. Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1,050 m on the Iheya Ridge. FEMS Microbiol. Lett. 205: 291-297.
20. Meyer, S., R. Moser, A. Neef, U. Stahl, and P. Kampfer. 1999. Differential detection of key enzymes of polyaromatic-hydrocarbon-degrading bacteria using PCR and gene probes. Microbiology 145: 1731-1741.
21. Newberry, C. J., G. Webster, B. A. Cragg, R. J. Parkes, A. J. Weightman, and J. C. Fry. 2004. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ. Microbiol. 6: 274-287.
22. Ogram, A., W. Sun, F. J. Brockman, and J. K. Fredrickson. 1995. Isolation and characterization of RNA from low-biomass deep-subsurface sediments. Appl. Environ. Microbiol. 61: 763-768.
23. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
24. Parkes, R. J., B. A. Cragg, and P. Wellsburry. 2000. Recent studies on bacterial populations and processes in subseafloor sediments: A review. Hydrogeol. J. 8: 11-28.
25. Parkes, R. J., G. Webster, B. A. Cragg, A. J. Weightman, C. J. Newberry, T. G. Ferdelman, J. Kallmeyer, B. B. Jørgensen, I. W. Aiello, and J. C. Fry. 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436: 390-394.
26. Pedersen, K., J. Arlinger, S. Ekendahl, and L. Hallbeck. 1996. 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel to the Aspo hard rock laboratory, Sweden. FEMS Microbiol. Ecol. 19: 249-262.
27. Pineda-Flores, G., G. Boll-Arguello, C. Lira-Galeana, and A. M. Mesta-Howard. 2004. A microbial consortium isolated from a crude oil sample that uses asphaltenes as a carbon and energy source. Biodegradation 15: 145-151.
28. Prince, R. C. 2005. The microbiology of marine oil spill bioremediation, pp. 317-336. In B. Ollivier and M. Magot (eds.), Petroleum Microbiology. ASM Press, Washington, D.C.
29. Ramana, C. V., C. Sasikala, K. Arunasri, P. Anil Kumar, T. N. Srinivas, S. Shivaji, P. Gupta, J. Suling, and J. F. Imhoff. 2006. Rubrivivax benzoatilyticus sp. nov., an aromatic, hydrocarbon-degrading purple betaproteobacterium. Int. J. Syst. Evol. Microbiol. 56: 2157-2164.
30. Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65: 3982-3989.
31. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
32. Schippers, A., L. N. Neretin, J. Kallmeyer, T. G. Ferdelman, B. A. Cragg, R. J. Parkes, and B. B. Jorgensen. 2005. Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433: 861-864.
33. Schippers, A. and L. N. Neretin. 2006. Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environ. Microbiol. 8: 1251-1260.
34. Smirk D., S. Alvey, and D. E. Crowley. 2005. Cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil. FEMS Microbiol. Ecol. 53: 265-273.
35. Teske, A. P. 2005. The deep subsurface biosphere is alive and well. Trends Microbiol. 13: 402-404.
36. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
37. Toffin, L., G. Webster, A. J. Weightman, J. C. Fry, and D. Prieur 2004. Molecular monitoring of culturable bacteria from deep-sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program. FEMS Microbiol. Ecol. 48: 357-367.
38. Tsai, Y.-L. and B. H. Olson. 1992. Detection of low numbers of bacterial numbers in soils and sediments by polymerase chain reaction. Appl. Environ. Microbiol. 58: 754-757.
39. Van Waasbergen, L. G, D. L. Balkwill, F. H. Crocker, B. N. Bjomstad, and R. V. Miller. 2000. Genetic diversity among Arthrobacter species collected across a heterogeneous series of terrestrial deep-subsurface sediments as determined on the basis of 16S rRNA and recA gene sequences. Appl. Environ. Microbiol. 66: 3454-3463.
40. Vrdoljak, G, W. S. Feil, H. Feil, J. C. Defter, and P. Fields. 2005. Characterization of a diesel sludge microbial consortia for bioremediation. Scanning 27: 8-14.
41. Wang, Y. P. and J. D. Gu. 2006. Degradability of dimethyl terephthalate by Variovorax paradoxus T4 and Sphingomanus yanoikuyae DOS01 isolated from deep-ocean sediments. Ecotoxicology 15: 549-557.
42. Webster, G, C. J. Newberry, J. C. Fry, and A. J. Weightman. 2003. Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: A cautionary tale. J. Microbiol. Meth. 55: 155-164.
43. Wilson, I. G. 1997. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63: 3741-3751.
44. Zinkevich, V. and I. B. Beech, 2000. Screening of sulfate-reducing bacteria in colonoscopy samples from healthy and colitic human gut mucosa. FEMS Microbiol. Ecol. 34: 147-155.