Biodegradation of C7 and C8 iso-alkanes under methanogenic conditions

Environmental Microbiology

Volumn 17, Issue 12, 2015, Pages 4898-4915

  Abu Laban, Nidal ^a   Dao, Anh ^a   Semple, Kathleen ^a   Foght, Julia ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALKANE; CARBON; METHANE; NAPHTHA; PETROLEUM; RNA 16S;

BIOREMEDIATION; CHEMISTRY; EURYARCHAEOTA; GENETICS; METABOLISM; OIL AND GAS FIELD; PEPTOCOCCACEAE; PHYLOGENY;

ALKANES; BIODEGRADATION, ENVIRONMENTAL; CARBON; EURYARCHAEOTA; METHANE; OIL AND GAS FIELDS; PEPTOCOCCACEAE; PETROLEUM; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 84934971617     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12643     Document Type: Article

References (51)

1. Aitken, C.M., Jones, D.M., Maguire, M.J., Gray, N.D., Sherry, A., Bowler, B.F.J., etal. (2013) Evidence that crude oil alkane activation proceeds by different mechanisms under sulfate-reducing and methanogenic conditions. Geochim Cosmochim Ac 109: 162-174.
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. An, D.S., Caffrey, S.M., Soh, J., Agrawal, A., Brown, D., Budwill, K., etal. (2013) Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common. Environ Sci Technol 47: 10708-10717.
4. Axelson, D.E., and Mikula, R.J. (1989) Characterization of oil sands mineral components and clay-organic complexes. Fuel Sci Technol Int 7: 659-673.
5. Bregnard, T., Haner, A., Hohener, P., and Zeyer, J. (1997) Anaerobic degradation of pristane in nitrate-reducing microcosms and enrichment cultures. Appl Environ Microbiol 63: 2077-2081.
6. Callaghan, A.V. (2013) Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins. Front Microbiol 4: 89.
7. Callaghan, A.V., Wawrik, B., Chadhain, S.M.N., Young, L.Y., and Zylstra, G.J. (2008) Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes. Biochem Biophys Res Commun 366: 142-148.
8. Callaghan, A.V., Davidova, I.A., Savage-Ashlock, K., Parisi, V.A., Gieg, L.M., Suflita, J.M., etal. (2010) Diversity of benzyl- and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures. Environ Sci Technol 44: 7287-7294.
9. Callaghan, A.V., Morris, B.E.L., Pereira, I.A.C., McInerney, M.J., Austin, R.N., Groves, J.T., etal. (2012) The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation. Environ Microbiol 14: 101-113.
10. Carmona, M., Zamarro, M., Blazquez, B., Durante-Rodriguez, G., Juarez, J., Valderrama, J., etal. (2009) Anaerobic catabolism of aromatic compounds: a genetic and genomic view. Microbiol Mol Biol Rev 73: 71-133.
11. Fowler, S.J., Dong, X.L., Sensen, C.W., Suflita, J.M., and Gieg, L.M. (2012) Methanogenic toluene metabolism: community structure and intermediates. Environ Microbiol 14: 754-764.
12. Gieg, L.M., and Suflita, J.M. (2002) Detection of anaerobic metabolites of saturated and aromatic hydrocarbons in petroleum-contaminated aquifers. Environ Sci Technol 36: 3755-3762.
13. Grossi, V., Raphel, D., Hirschler-Rea, A., Gilewicz, M., Mouzdahir, A., Bertrand, J.C., and Rontani, J.F. (2000) Anaerobic biodegradation of pristane by a marine sedimentary bacterial and/or archaeal community. Org Geochem 31: 769-772.
14. Hasinger, M., Scherr, K.E., Lundaa, T., Brauer, L., Zach, C., and Loibner, A.P. (2012) Changes in iso- and n-alkane distribution during biodegradation of crude oil under nitrate and sulphate reducing conditions. J Biotechnol 157: 490-498.
15. 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.
16. Heider, J. (2007) Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms. Curr Opin Chem Biol 11: 188-194.
17. Herrmann, S., Kleinsteuber, S., Chatzinotas, A., Kuppardt, S., Lueders, T., Richnow, H.H., and Vogt, C. (2010) Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing. Environ Microbiol 12: 401-411.
18. Holowenko, F.M., MacKinnon, M.D., and Fedorak, P.M. (2000) Methanogens and sulfate-reducing bacteria in oil sands fine tailings waste. Can J Microbiol 46: 927-937.
19. Imachi, H., Sekiguchi, Y., Kamagata, Y., Loy, A., Qiu, Y., Hugenholtz, P., etal. (2006) Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl Environ Microbiol 72: 2080-2091.
20. Jarling, R., Sadeghi, M., Drozdowska, M., Lahme, S., Buckel, W., Rabus, R., etal. (2012) Stereochemical investigations reveal the mechanism of the bacterial activation of n-alkanes without oxygen. Angew Chem Int Edit 51: 1334-1338.
21. Kleinsteuber, S., Schleinitz, K.M., and Vogt, C. (2012) Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers. Appl Microbiol Biotechnol 94: 851-873.
22. Kropp, K.G., Davidova, I.A., and Suflita, J.M. (2000) Anaerobic oxidation of n-dodecane by an addition reaction in a sulfate-reducing bacterial enrichment culture. Appl Environ Microbiol 66: 5393-5398.
23. Kunapuli, U., Lueders, T., and Meckenstock, R.U. (2007) The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation. ISME J 1: 643-653.
24. Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogint, M.L., and Pace, N.R. (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82: 6955-6959.
25. Lueders, T., Kindler, R., Miltner, A., Friedrich, M.W., and Kaestner, M. (2006) Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl Environ Microbiol 72: 5342-5348.
26. Penner, T.J., and Foght, J.M. (2010) Mature fine tailings from oil sands processing harbour diverse methanogenic communities. Can J Microbiol 56: 459-470.
27. Prince, R., and Suflita, J. (2007) Anaerobic biodegradation of natural gas condensate can be stimulated by the addition of gasoline. Biodegradation 18: 515-523.
28. Qiu, Y., Sekiguchi, Y., Hanada, S., Imachi, H., Tseng, I., Cheng, S., etal. (2006) Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Arch Microbiol 185: 172-182.
29. Rabus, R., Wilkes, H., Behrends, A., Armstroff, A., Fischer, T., Pierik, A.J., and Widdel, F. (2001) Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism. J Bacteriol 183: 1707-1715.
30. Rabus, R., Jarling, R., Lahme, S., Kuhner, S., Heider, J., Widdel, F., and Wilkes, H. (2011) Co-metabolic conversion of toluene in anaerobic n-alkane-degrading bacteria. Environ Microbiol 13: 2576-2585.
31. Schütte, U.M., Abdo, Z., Bent, S.J., Shyu, C., Williams, C.J., Pierson, J.D., and Forney, L.J. (2008) Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol 80: 365-380.
32. Selesi, D., Jehmlich, N., von Bergen, M., Schmidt, F., Rattei, T., Tischler, P., etal. (2010) Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47. J Bacteriol 192: 295-306.
33. Siddique, T., Fedorak, P.M., and Foght, J.M. (2006) Biodegradation of short-shain n-alkanes in oil sands tailings under methanogenic conditions. Environ Sci Technol 40: 5459-5464.
34. Siddique, T., Fedorak, P., MacKinnon, M., and Foght, J. (2007) Metabolism of BTEX and naphtha compounds to methane in oil sands tailings. Environ Sci Technol 41: 2350-2356.
35. Siddique, T., Gupta, R., Fedorak, P.M., MacKinnon, M.D., and Foght, J.M. (2008) A first approximation kinetic model to predict methane generation from an oil sands tailings settling basin. Chemosphere 72: 1573-1580.
36. Siddique, T., Penner, T., Semple, K., and Foght, J.M. (2011) Anaerobic biodegradation of longer-chain n-alkanes coupled to methane production in oil sands tailings. Environ Sci Technol 45: 5892-5899.
37. Siddique, T., Penner, T., Klassen, J., Nesbo, C., and Foght, J.M. (2012) Microbial communities involved in methane production from hydrocarbons in oil sands tailings. Environ Sci Technol 46: 9802-9810.
38. Siddique, T., Kuznetsov, P., Kuznetsova, A., Li, C., Young, R., Arocena, J.M., and Foght, J.M. (2014a) Microbially-accelerated consolidation of oil sands tailings. Pathway II: solid phase biogeochemistry. Front Microbiol 5: 107.
39. Siddique, T., Kuznetsov, P., Kuznetsova, A., Arkell, N., Young, R., Li, C., etal. (2014b) Microbially-accelerated consolidation of oil sands tailings. Pathway I: changes in porewater chemistry. Front Microbiol 5: 106.
40. Soh, J., Dong, X.L., Caffrey, S.M., Voordouw, G., and Sensen, C.W. (2013) Phoenix 2: a locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface. J Biotechnol 167: 393-403.
41. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
42. Tan, B., Dong, X.L., Sensen, C.W., and Foght, J. (2013) Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members. Genome 56: 599-611.
43. Tan, B., Charchuk, R., Li, C., Nesbø, C., Abu Laban, N., and Foght, J. (2014a) Draft genome sequence of uncultivated Firmicutes (Peptococcaceae 'SCADC') single cells sorted from methanogenic alkane-degrading cultures. Genome Announc 2: e00909-14.
44. Tan, B., Nesbø, C., and Foght, J. (2014b) Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions. ISME J, in press. doi:10.1038/ismej.2014.87.
45. Ulrich, A.C., and Edwards, E.A. (2003) Physiological and molecular characterization of anaerobic benzene-degrading mixed cultures. Environ Microbiol 5: 92-102.
46. Wang, Z.D., Fingas, M., Blenkinsopp, S., Sergy, G., Landriault, M., Sigouin, L., etal. (1998) Comparison of oil composition changes due to biodegradation and physical weathering in different oils. J Chromatogr A 809: 89-107.
47. Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697-703.
48. Widdel, F., and Bak, F. (1992) Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes. Balows, A., Trüper, H.G., Dworkin, M., Harder, W., and Schleifer, K.H. (eds). New York, USA: Springer-Verlag, pp. 3352-3378.
49. Winderl, C., Schaefer, S., and Lueders, T. (2007) Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker. Environ Microbiol 9: 1035-1046.
50. van der Zaan, B.M., Saia, F.T., Stams, A.J.M., Plugge, C.M., de Vos, W.M., Smidt, H., etal. (2012) Anaerobic benzene degradation under denitrifying conditions: Peptococcaceae as dominant benzene degraders and evidence for a syntrophic process. Environ Microbiol 14: 1171-1181.
51. Zengler, K., Richnow, H.H., Rossello-Mora, R., Michaelis, W., and Widdel, F. (1999) Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401: 266-269.