Temperature-dependent differences in community structure of bacteria involved in degradation of petroleum hydrocarbons under sulfate-reducing conditions

Journal of Applied Microbiology

Volumn 110, Issue 1, 2011, Pages 314-322

  Higashioka, Y ^a   Kojima, H ^a   Fukui, M ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Anaerobic biodegradation; bamA gene; Low temperature; p xylene; Petroleum hydrocarbon; Sulfate reducing bacteria

Indexed keywords

BACTERIA; BIODEGRADATION; CLONING; ELECTROPHORESIS; GENES; RNA; SULFUR COMPOUNDS; TEMPERATURE; XYLENE;

ANEROBIC BIODEGRADATION; BAMA GENE; ENRICHMENT CULTURE; LOWS-TEMPERATURES; MICROBIAL COMMUNITIES; MODERATE TEMPERATURE; P-XYLENE; PETROLEUM HYDROCARBON; SULPHATE REDUCING BACTERIA; TEMPERATURE DEPENDENT;

CRUDE OIL;

6 OXOCYCLOHEX 1 ENE 1 CARBONYL COENZYME A HYDROLASE; AROMATIC HYDROCARBON; HYDROLASE; PARA XYLENE; PETROLEUM; RNA 16S; SULFIDE; UNCLASSIFIED DRUG;

ANOXIC CONDITIONS; BIODEGRADATION; CLONE; ELECTROKINESIS; MICROBIAL COMMUNITY; PETROLEUM; POLYMERASE CHAIN REACTION; SULFATE-REDUCING BACTERIUM; TEMPERATURE EFFECT; XYLENE;

ANAEROBIC METABOLISM; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BAMA GENE; COMMUNITY STRUCTURE; DELTAPROTEOBACTERIA; ENRICHMENT CULTURE; ESCHERICHIA COLI; MICROBIAL COMMUNITY; MICROBIAL DEGRADATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SULFATE REDUCING BACTERIUM; TEMPERATURE DEPENDENCE;

BACTERIA (MICROORGANISMS); DESULFOSARCINA;

EID: 78650093772     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2010.04886.x     Document Type: Article

References (37)

1. Beller, H.R., Spormann, A.M., Sharma, P.K., Cole, J.R. and Reinhard, M. (1996) Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium. Appl Environ Microbiol 62, 1188-1196.
2. Chakraborty, R. and Coates, J.D. (2004) Anaerobic degradation of monoaromatic hydrocarbons. Appl Microbiol Biotechnol 64, 437-446.
3. Cline, J.D. (1969) Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol Oceanogr 14, 454-458.
4. Cozzarelli, I.M., Herman, J.S. and Baedecker, M.J. (1995) Fate of microbial metabolites of hydrocarbons in a coastal plain aquifer: the role of electron acceptors. Environ Sci Technol 29, 458-469.
5. Finster, K. (2008) Anaerobic bacteria and archaea in cold ecosystems. In Psychrophiles: From Biodiversity to Biotechnology eds Margesin, R, Schinner, F, Marx, JC, and Gerrrday, C. pp. 103-119. Springer-Verlag Berlin Heidelberg: New York.
6. Harms, G., Zengler, K., Rabus, R., Aeckersberg, F., Minz, D., Rossello-Mora, R. and Widdel, F. (1999) Anaerobic oxidation of o-xylene, m-xylene and homologous alkylbenzenes by new types of sulfate-reducing bacteria. Appl Environ Microbiol 65, 999-1004.
7. Head, I.M. and Swannell, R.P.J. (1999) Bioremediation of petroleum hydrocarbon contaminants in marine habitats. Curr Opin Biotechnol 10, 234-239.
8. Higashioka, Y., Kojima, H., Nakagawa, T., Sato, S. and Fukui, M. (2009) A novel n-alkane-degrading bacterium as a minor member of p-xylene-degrading sulfate-reducing consortium. Biodegradation 20, 383-390.
9. Kirchman, D.L. (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39, 91-100.
10. Kleikemper, J., Schroth, M.H., Sigler, W.V., Schmucki, M., Bernasconi, S.M. and Zeyer, J. (2002) Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer. Appl Environ Microbiol 68, 1516-1523.
11. Kleinsteuber, S., Schleinitz, K.M., Breitfeld, J., Harms, H., Richnow, H.H. and Vogt, C. (2008) Molecular characterization of bacterial communities mineralizing benzene under sulfate-reducing conditions. FEMS Microbiol Ecol 66, 143-157.
12. 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.
13. Koizumi, Y., Kelly, J.J., Nakagawa, T., Urakawa, H., El-Fantroussi, S., Al-Muzaini, S., Fukui, M., Urushigawa, Y. et al. (2002) Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Appl Environ Microbiol 68, 3215-3225.
14. Kube, M., Beck, A., Meyerdierks, A., Amann, R., Reinhardt, R. and Rabus, R. (2005) A catabolic gene cluster for anaerobic benzoate degradation in methanotrophic microbial Black Sea mats. Syst Appl Microbiol 28, 287-294.
15. Kumar, S., Tamura, K. and Nei, M. (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
16. Kuntze, K., Shinoda, Y., Moutakki, H., Mclnerney, M.J., Vogt, C., Richnow, H.H. and Boll, M. (2008) 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes. Environ Microbiol 10, 1547-1556.
17. Küver, J., Könneke, M., Galushko, A. and Drzyzga, O. (2001) Reclassification of Desulfobacterium phenolicum as Desulfobacula phenolica comb. nov. and description of strain Sax (T) as Desulfotignum balticum gen. nov., sp. nov. Int J Syst Evol Microbiol 51, 171-177.
18. Laban, N.A., Selesi, D., Jobelius, C. and Meckenstock, R.U. (2009) Anaerobic benzene degradation by Gram-positive sulfate-reducing bacteria. FEMS Microbiol Ecol 68, 300-311.
19. Lane, D.J. (1991) 16S/23S rRNA sequencing. in Nucleic Acid Techniques in Bacterial Systematics ed. Stackebrandt, E. and Goodfellow, M. pp. 115-175. New York: Wiley.
20. Lovley, D.R. (2001) Bioremediation. Anaerobes to rescue. Science 293, 1444-1446.
21. Morasch, B. and Meckenstock, R.U. (2005) Anaerobic degradation of p-xylene by a sulfate-reducing enrichment culture. Curr Microbiol 51, 127-130.
22. Morasch, B., Schink, B., Tebbe, C.C. and Meckenstock, R.U. (2004) Degradation of o-xylene and m-xylene by a novel sulfate-reducer belonging to the genus Desulfotomaculum. Arch Microbiol 181, 407-417.
23. Musat, F. and Widdel, F. (2008) Anaerobic degradation of benzene by a marine sulfate-reducing enrichment culture, and cell hybridization of the dominant phylotype. Environ Microbiol 10, 10-19.
24. 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 rRNA. Appl Environ Microbiol 59, 695-700.
25. Muyzer, G., Hottenträger, S., Teske, A. and Wawer, C. (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA - a new molecular approach to analyse the genetic diversity of mixed microbial communities In Molecular Microbial Ecology Manual ed. Akkermans, A.D.L., Van Elsas, J.D. and De Bruijn, F. pp. 3.4.4:1-23. Dordrecht: Kluwer Academic Publishers.
26. Nakagawa, T., Sato, S., Yamamoto, Y. and Fukui, M. (2002) Successive changes in community structure of an ethylbenzene-degrading sulfate-reducing consortium. Water Res 36, 2813-2823.
27. Nakagawa, T., Sato, S. and Fukui, M. (2008) Anaerobic degradation of p-xylene in sediment-free sulfate-reducing enrichment culture. Biodegradation 19, 909-913.
28. Phelps, C.D., Kerkhof, L.J. and Young, L.Y. (1998) Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol Ecol 27, 269-279.
29. Purdy, K.J., Nedwell, D.B. and Embley, T.M. (2003) Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting Antarctic sediments. Appl Environ Microbiol 69, 3181-3191.
30. Rabus, R., Nordhaus, R., Ludwig, W. and Widdel, F. (1993) Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. Appl Environ Microbiol 59, 1444-1451.
31. Rabus, R., Fukui, M., Wilkes, H. and Widdel, F. (1996) Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Appl Environ Microbiol 62, 3605-3613.
32. Strittmatter, A.W., Liesegang, H., Rabus, R., Decker, I., Amann, J., Andres, S., Henne, A., Fricke, W.F. et al. (2009) Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ Microbiol 11, 1038-1055.
33. Tabuchi, K., Kojima, H. and Fukui, M. (2010) Seasonal changes in organic matter mineralization in a sublittoral sediment and temperature-driven decoupling of key processes. Microb Ecol 60, 551-560.
34. Tarpgaard, I.H., Boetius, A. and Finster, K. (2006) Desulfobacter psychrotolerans sp. nov., a new psychrotolerant sulfate-reducing bacterium and descriptions of its physiological response to temperature changes. Antonie Van Leeuwenhoek 89, 109-124.
35. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmongin, F. and Higgins, D.G. (1997) The clustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 24, 4876-4882.
36. Widdel, F. and Bak, F. (1992) Gram-negative mesophilic sulfate-reducing bacteria In The Prokaryotes, vol IV, 2nd edn, ed. Balows, A, Truper, H.G, Dworkin, M, Harder, W and Schleifer, K.H. pp. 3352-3378. New York: Springer-Verlag.
37. Wilson, K. (1990) Miniprep of bacterial genomic DNA. In Short Protocols in Molecular Biology, 2nd edn, ed. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidmann, J.G., Smith, J.A. and Struhl, K. pp. 2.4.1-2.4.2. New York: Wiley.