Advertisement

Biodegradation

, Volume 22, Issue 5, pp 961–972 | Cite as

Identification of tertiary butyl alcohol (TBA)-utilizing organisms in BioGAC reactors using 13C-DNA stable isotope probing

  • Denise Aslett
  • Joseph Haas
  • Michael HymanEmail author
Original Paper

Abstract

Biodegradation of the gasoline oxygenates methyl tertiary-butyl ether (MTBE) and ethyl tertiary-butyl ether (ETBE) can cause tertiary butyl alcohol (TBA) to accumulate in gasoline-impacted environments. One remediation option for TBA-contaminated groundwater involves oxygenated granulated activated carbon (GAC) reactors that have been self-inoculated by indigenous TBA-degrading microorganisms in ground water extracted from contaminated aquifers. Identification of these organisms is important for understanding the range of TBA-metabolizing organisms in nature and for determining whether self-inoculation of similar reactors is likely to occur at other sites. In this study 13C-DNA-stable isotope probing (SIP) was used to identify TBA-utilizing organisms in samples of self-inoculated BioGAC reactors operated at sites in New York and California. Based on 16S rRNA nucleotide sequences, all TBA-utilizing organisms identified were members of the Burkholderiales order of the β-proteobacteria. Organisms similar to Cupriavidus and Methylibium were observed in both reactor samples while organisms similar to Polaromonas and Rhodoferax were unique to the reactor sample from New York. Organisms similar to Hydrogenophaga and Paucibacter strains were only detected in the reactor sample from California. We also analyzed our samples for the presence of several genes previously implicated in TBA oxidation by pure cultures of bacteria. Genes Mpe_B0532, B0541, B0555, and B0561 were all detected in 13C-metagenomic DNA from both reactors and deduced amino acid sequences suggested these genes all encode highly conserved enzymes. One gene (Mpe_B0555) encodes a putative phthalate dioxygenase-like enzyme that may be particularly appropriate for determining the potential for TBA oxidation in contaminated environmental samples.

Keywords

Tertiary butyl alcohol Stable isotope probing Polaromonas Methylibium 

Notes

Acknowledgments

We thank Xiaomin Yang (Atlantic Richfield Company) for providing BioGAC samples from California. This research was supported by funding to MRH from the National Science Foundation (Grant CBET-0348392) and the American Petroleum Institute. DA was supported by a DoEd Graduate Assistantship in Areas of National Need fellowship.

References

  1. Beyers DL, Meyer CL, Sun PT, Salanitro JP (2001) Method and apparatus for biodegradation of alkyl ethers and tertiary butyl alcohol. US Patent # 6458276Google Scholar
  2. Bradley PM, Landmeyer JE, Chapelle FH (1999) Aerobic mineralization of MTBE and tert-butyl alcohol by stream-bed sediment microorganisms. Environ Sci Technol 33:1877–1879CrossRefGoogle Scholar
  3. Bradley PM, Landmeyer JE, Chapelle FH (2002) TBA biodegradation in surface-water sediments under aerobic and anaerobic conditions. Environ Sci Technol 36:4087–4090PubMedCrossRefGoogle Scholar
  4. Cirvello JD, Radovsky A, Heath JE, Farnell DR, Lindamood C (1995) Toxicity and carcinogenicity of t-butyl alcohol in rats and mice following chronic exposure in drinking water. Toxicol Ind Health 11:151–165PubMedGoogle Scholar
  5. Clark JJJ (2002) tert-butyl alcohol: chemical properties, production and use, fate and transport, toxicology, and detection in groundwater and regulatory standards. In: Diaz AF, Drogos DL (eds) Oxygenates in gasoline: environmental aspects, vol. chapter 7. American Chemical Society, Washington, pp 92–106Google Scholar
  6. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35Google Scholar
  7. Deeb RA, Chu K-H, Shih T, Linder S, Suffet I, Kavanaugh MC, Alvarez-Cohen L (2003) MTBE and other oxygenates: environmental sources, analysis, occurrence, and treatment. Environ Eng Sci 20:433–447CrossRefGoogle Scholar
  8. Fortin NY, Morales M, Nakagawa Y, Focht DD, Deshusses MA (2001) Methyl tert-butyl ether (MTBE) degradation by a microbial consortium. Environ Microbiol 3:407–416PubMedCrossRefGoogle Scholar
  9. François A, Mathis H, Godefroy D, Piveteau P, Fayolle F, Monot F (2002) Biodegradation of methyl tert-butyl ether and other fuel oxygenates by a new strain, Mycobacterium austroafricanum IFP 2012. Appl Environ Microbiol 68:2754–2762PubMedCrossRefGoogle Scholar
  10. Goodfellow M, Jones AL, Maldonado LA, Salanitro J (2004) Rhodococcus aetherivorans sp. nov. A new species that contains methyl t-butyl ether-degrading Actinomycetes. Syst Appl Microbiol 27:61–65PubMedCrossRefGoogle Scholar
  11. Hanson JR, Ackerman CE, Scow KM (1999) Biodegradation of methyl tert-butyl ether by a bacterial pure culture. Appl Environ Microbiol 65:4788–4792PubMedGoogle Scholar
  12. Hatzinger PB, McClay K, Vainberg S, Tugusheva M, Condee CW, Steffan RJ (2001) Biodegradation of methyl tert-butyl ether by a pure bacterial culture. Appl Environ Microbiol 67:5601–5607PubMedCrossRefGoogle Scholar
  13. Hristova KR, Schmidt R, Chakicherla AY, Legler TC, Wu J, Chain PS, Scow KM, Kane SR (2007) Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Appl Environ Microbiol 73:7347–7357PubMedCrossRefGoogle Scholar
  14. Kane SR, Beller HR, Legler TC, Koester CJ, Pinkart HC, Halden RU, Happel AM (2001) Aerobic biodegradation of methyl tert-butyl ether by aquifer bacteria from leaking underground storage tank sites. Appl Environ Microbiol 67:5824–5829PubMedCrossRefGoogle Scholar
  15. Kharoune M, Kharoune L, Lebeault JM, Pauss A (2001) Isolation and characterization of two aerobic bacterial strains that completely degrade ethyl tert-butyl ether (ETBE). Appl Microbiol Biotechnol 55:348–353PubMedCrossRefGoogle Scholar
  16. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Nat Acad Sci USA 82:6955–6959PubMedCrossRefGoogle Scholar
  17. Larkin MA, Blackshields G, Brown NP, McGettigan CR, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) ClustalW and ClustalX version 2. Bioinformatics 23:2947–2948PubMedCrossRefGoogle Scholar
  18. Lykidis A, Pérez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper DS, Lapidus A, Lucas S, González B, Kyrpides NC (2010) The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS ONE 5:e9729PubMedCrossRefGoogle Scholar
  19. Madsen EL (2006) The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr Opin Biotechnol 17:92–97PubMedCrossRefGoogle Scholar
  20. Magic-Knezev A, Wullings B, Kooij DVD (2009) Polaromonas and Hydrogenophaga species are the predominant bacteria cultured from granular activated carbon filters in water treatment. J Appl Microbiol 107:1457–1467PubMedCrossRefGoogle Scholar
  21. Mo K, Lora CO, Wanken AE, Javanmardian M, Yang X, Kulpa CF (1997) Biodegradation of methyl t-butyl ether by pure bacterial cultures. Appl Microbiol Biotechnol 47:69–72PubMedCrossRefGoogle Scholar
  22. Müller RH, Rohwerder T, Harms H (2008) Degradation of fuel oxygenates and their main intermediates by Aquincola tertiaricarbonis L108. Microbiology 154:1414–1421PubMedCrossRefGoogle Scholar
  23. Muyzer G, Waal ECD, Uitterlinden AG (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 59:695–700PubMedGoogle Scholar
  24. Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, Murrell JC (2007) DNA stable-isotope probing. Nat Protoc 2:860–866PubMedCrossRefGoogle Scholar
  25. Pérez-Pantoja D, Iglesia RDI, Pieper DH, González B (2008) Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134. FEMS Microbiol Rev 32:736–794PubMedCrossRefGoogle Scholar
  26. Piveteau P, Fayolle F, Vandecasteele JP, Monot F (2001) Biodegradation of tert-butyl alcohol and related xenobiotics by a methylotrophic bacterial isolate. Appl Microbiol Biotechnol 55:369–373PubMedCrossRefGoogle Scholar
  27. Reinauer K, Zhang Y, Yang X, Finneran K (2008) Aerobic biodegradation of tert-butyl alcohol (TBA) by psychro- and thermo-tolerant cultures derived from granular activated carbon (GAC). Biodegradation 19:259–268PubMedCrossRefGoogle Scholar
  28. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. Humana Press, Totowa, NJGoogle Scholar
  29. Sabat G, Rose P, Hickey WJ, Harkin JM (2000) Selective and sensitive method for PCR amplification of Escherichia coli 16S rRNA genes in soil. Appl Environ Microbiol 66:844–849PubMedCrossRefGoogle Scholar
  30. Salanitro JP, Diaz LA, Williams MP, Wisniewski HL (1994) Isolation of a bacterial culture that degrades methyl t-butyl ether. Appl Environ Microbiol 60:2593–2596PubMedGoogle Scholar
  31. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Press, Cold Spring Harbor, New YorkGoogle Scholar
  32. Schäfer F, Breuer U, Benndorf D, Bergen MV, Harms H, Müller RH (2007) Growth of Aquincola tertiaricarbonis L108 on tert-butyl alcohol leads to the induction of a phthalate dioxygenase-related protein and its associated oxidoreductase subunit. Eng Life Sci 7:512–519CrossRefGoogle Scholar
  33. Schmidt TC, Zwank L, Elsner M, Berg M, Meckenstock RU, Haderlein SB (2004) Compound-specific stable isotope analysis of organic contaminants in natural environments: a critical review of the state of the art, prospects, and future challenges. Anal Bioanal Chem 378:283–300PubMedCrossRefGoogle Scholar
  34. Singleton DR, Powell SN, Sangaiah R, Gold A, Ball LM, Aitken MD (2005) Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil. Appl Environ Microbiol 71:1202–1209PubMedCrossRefGoogle Scholar
  35. Smith CA, Hyman MR (2004) Oxidation of methyl tert-butyl ether by alkane hydroxylase in dicyclopropylketone-induced and n-octane-grown Pseudomonas putida GPo1. Appl Environ Microbiol 70:4544–4550PubMedCrossRefGoogle Scholar
  36. Smith CA, O’Reilly KT, Hyman MR (2003) Characterization of the initial reactions during the cometabolic oxidation of methyl tert-butyl ether by propane-grown Mycobacterium vaccae JOB5. Appl Environ Microbiol 69:796–804PubMedCrossRefGoogle Scholar
  37. Steffan RJ, McClay K, Vainberg S, Condee CW, Zhang D (1997) Biodegradation of the gasoline oxygenates methyl tert-butyl ether, ethyl tert-butyl ether, and tert-amyl methyl ether by propane-oxidizing bacteria. Appl Environ Microbiol 63:4216–4222PubMedGoogle Scholar
  38. Steffan RJ, Vainberg S, Condee CW, McClay K, Hatzinger P (2000) Biotreatment of MTBE with a new bacterial isolate. In: Wickramanayake GB, Gavaskar AR, Alleman BC, Magar VS (eds) Bioremediation and phytoremediation of chlorinated and recalcitrant compounds. Battelle Press, Columbus, OHGoogle Scholar
  39. Sun PT, Walsh D, Meyer C, Pickle D (2003) The treatment of MTBE-contaminated groundwater in bioaugmented granular activated carbon beds—a case history. Proc Water Environ Fed 14:450–463Google Scholar
  40. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267PubMedCrossRefGoogle Scholar
  41. Wilson JT, Adair C, Kaiser PM, Kolhatkar R (2005) Anaerobic biodegradation of MTBE at a gasoline spill site. Ground Water Monit Remed 25:103–115CrossRefGoogle Scholar
  42. Yeager CM, Bottomley PJ, Arp DJ, Hyman MR (1999) Inactivation of toluene 2-monooxygenase in Burkholderia cepacia G4 by alkynes. Appl Environ Microbiol 65:632–639PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Department of Microbiology4545 Thomas Hall, North Carolina State UniversityRaleighUSA
  2. 2.Office of the New York State Attorney General, Environmental Protection BureauNew YorkUSA

Personalised recommendations