Acidophilic microbial communities associated with a natural, biodegraded hydrocarbon seepage

Journal of Applied Microbiology

Volumn 101, Issue 2, 2006, Pages 290-299

  Roling W F M ^a,c   Ortega Lucach, S ^a   Larter, S R ^a,b   Head, I M ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF CALGARY   (Canada)

^c VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

16S rRNA genes; Acidophilic communities; Outcrop oil seep; PCR DGGE; Petroleum biodegradation

Indexed keywords

BACTERIA; BIODEGRADATION; ELECTROPHORESIS; GASOLINE; GENES; HYDROCARBONS; POLYMERASE CHAIN REACTION; RNA;

16S RRNA GENE; ACIDOPHILIC COMMUNITY; HYDROCARBON SEEPAGE; INDEPENDENT ANALYSIS; MICROBIAL COMMUNITIES; NATURAL SURFACE; OIL SEEPS; OUTCROP OIL SEEP; PCR-DGGE; PETROLEUM BIODEGRADATIONS;

BIOREMEDIATION;

PETROLEUM;

BIODEGRADATION; DNA FINGERPRINTING; HYDROCARBON; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PETROLEUM; SEEPAGE;

ALPHAPROTEOBACTERIA; ARCHAEBACTERIUM; ARTICLE; BACTERIUM DETECTION; BIODEGRADATION; DNA EXTRACTION; FUNGUS; MICROFLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; SPECIES DOMINANCE;

ACIDIPHILIUM; ACIDOCELLA; ALPHAPROTEOBACTERIA; FUNGI;

EID: 33745933713     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2006.02926.x     Document Type: Article

References (39)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215, 403-410.
2. Amann, R.I., Ludwig, W. and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59, 143-169.
3. Atlas, R.M. and Cerniglia, C.E. (1995) Bioremediation of petroleum pollutants - diversity and environmental aspects of hydrocarbon biodegradation. Bioscience 45, 332-338.
4. Baker, B.J. and Banfield, J.F. (2003) Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44, 139-152.
5. Barns, S.M., Fundyga, R.E., Jeffries, M.W. and Pace, N.R. (1994) Remarkable archaeal diversity detected in a Yellowstone national park hot spring environment. Proc Natl Acad Sci U S A 91, 1609-1613.
6. Cornford, R., Astin, T.R., Marshall, J.E.A., Gabbott, S. and Jenkins, C.D. (1988) Source rock and seep oil maturity in Dorset, southern England. Org Geochem 13, 399-409.
7. Dojka, M.A., Hugenholtz, P., Haack, S.K. and Pace, N.R. (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64, 3869-3877.
8. Dore, S.Y., Laursen, A.E. and Kulpa, C.F. (2003) Polycyclic aromatic hydrocarbon degradation in soil surrounding an outdoor coal storage pile. J Environ Eng Sci 2, 227-231.
9. Edwards, U., Rogall, T., Blöcker, H., Emde, M. and Böttger, E.C. (1988) Isolation and complete nucleotide determination of entire genes. Characterisation of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17, 7843-7853.
10. van Elsas, J.D., Duarte, G.F., Keijzer-Wolters, A. and Smit, E. (2000) Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Methods 43, 133-151.
11. Felsenstein, J. (1989) PHYLIP-phylogeny inference package. Cladistics 5, 164-166.
12. Good, I.J. (1953) The population frequencies of species and the estimation of the population parameters. Biometrika 40, 237-264.
13. Green, P. (2000) Methylobacterium. In The Prokaryotes, 3rd edn. URL http://141.150.157.117:8080/prokPUB/chaprender/ jsp/showchap.jsp?chapnum= 302&initsec=02_00.
14. Gemmell, R.T. and Knowles, C.J. (2000) Utilisation of aliphatic compounds by acidophilic heterotrophic bacteria. The potential for bioremediation of acidic wastewaters contaminated with toxic organic compounds and heavy metals. FEMS Microbiol Lett 192, 185-190.
15. Hamamura, N., Olson, S.H., Ward, D.M. and Inskeep, W.P. (2005) Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park. Appl Environ Microbiol 71, 5943-5950.
16. Head, I.M., Jones, D.M. and Larter, S.R. (2003) Biological activity in the deep subsurface and the origin of heavy oil. Nature 426, 344-352.
17. Johnson, D.B. (1998) Biodiversity and ecology of acidophilic microorganisms. FEMS Microbiol Ecol 27, 307-317.
18. Johnson, D.B. and Bridge, T.A.M. (2002) Reduction of ferric iron by acidophilic heterotrophic bacteria: evidence for constitutive and inducible enzyme systems in Acidiphilium spp. J Appl Microbiol 92, 315-321.
19. Johnson, D.B. and Hallberg, K.B. (2003) The microbiology of acidic mine waters. Res Microbiol 154, 466-473.
20. Johnson, D.B., Okibe, N. and Roberto, F.F. (2003) Novel thermo-acidophilic bacteria isolated from geothermal sites in Yellowstone National Park: physiological and phylogenetic characteristics. Arch Microbiol 180, 60-68.
21. Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules. In Mammalian Protein Metabolism ed. Munro, H.N. pp. 21-132. New York: Academic Press.
22. Kniemeyer, O., Fischer, T., Wilkes, H., Glöckner, F.O. and Widdel, F. (2003) Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl Environ Microbiol 69, 760-768.
23. Lees, G.M. and Cox, P.T. (1937) The geological basis of the present search for oil in Great Britain by the D'Arcy Exploration Company, Limited. Q J Geol Soc 93, 156-194.
24. Magot, M., Ollivier, B. and Patel, B.K.C. (2000) Microbiology of petroleum reservoirs. Antonie Van Leeuwenhoek 77, 103-116.
25. Marchand, E.A. and Silverstein, J. (2002) Influence of heterotrophic microbial growth on biological oxidation of pyrite. Environ Sci Technol 36, 5483-5490.
26. Marchand, E.A. and Silverstein, J. (2003) The role of enhanced heterotrophic bacterial growth on iron oxidation by Acidithiobacillus ferrooxidans. Geomicrobiol J 20, 231-244.
27. Muyzer, G., de Waal, E.C. and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S ribosomal RNA. Appl Environ Microbiol 59, 695-700.
28. Ovreas, L., Forney, L., Daae, F.L. and Torsvik, V. (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63, 3367-3373.
29. Quentmeier, A. and Friedrich, C.G. (1994) Transfer and expression of degradative and antibiotic resistance plasmids in acidophilic bacteria. Appl Environ Microbiol 60, 973-978.
30. Raskin, L., Poulsen, L.K., Noguera, D.R., Rittmann, B.E. and Stahl, D.A. (1994) Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl Environ Microbiol 60, 1241-1248.
31. Röling, W.F.M., Van Breukelen, B.M., Braster, M., Goeltom, M.T., Groen, J. and Van Verseveld, H.W. (2000) Analysis of microbial communities in a landfill leachate polluted aquifer using a new method for anaerobic physiological profiling and 16S rDNA based fingerprinting. Microb Ecol 40, 177-188.
32. Röling, W.F.M., Milner, M.G., Jones, D.M., Lee, K., Daniel, F., Swannell, R.J.P. and Head, I.M. (2002) Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl Environ Microbiol 68, 5537-5548.
33. Röling, W.F.M., Head, I.M. and Larter, S.R. (2003) The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects. Res Microbiol 154, 321-328.
34. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
35. Scotchman, I.C. (1991) The geochemistry of concretions from the Kimmeridge Clay Formation of southern and eastern England. Sedimentology 38, 79-106.
36. Stapleton, R.D., Savage, D.C., Sayler, G.S. and Stacey, G. (1998) Biodegradation of aromatic hydrocarbons in an extremely acidic environment. Appl Environ Microbiol 64, 4180-4184.
37. Teske, A., Hinrichs, K.U., Edgcomb, V., Gomez, A.D., Kysela, D., Sylva, S.P., Sogin, M.L. and Jannasch, H.W. (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68, 1994-2007.
38. Van de Peer, Y. and de Wachter, R. (1994) Treecon for windows-a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10, 569-570.
39. Watson, D.F., Hindle, A.D. and Farrimond, P. (2000) Organic geochemistry of petroleum seepages within the Jurassic Bencliff Grit, Osmington Mills, Dorset, UK. Petrol Geosci 6, 289-297.