Methylibium petroleiphilum PM1

Methylibium petroleiphilum strain PM1 is one of only a few pure culture isolates that can grow on and completely degrade the fuel additive MTBE (methyl tertiary butyl ether) [1,2]. MTBE is a commonly used fuel-oxygenate in the last two decades that is far more recalcitrant to biodegradation than other gasoline components and has contaminated numerous subsurface drinking water supplies [3]. Strain PM1 was isolated by Dr. Scow’s lab in 1998 from a sewage treatment plant biofilter that was used for treating discharge from oil refineries [1]. Strain PM1 is a methylotroph representing a new species within the Rubrivivax group (Comamonadaceae family) of the beta subclass of Proteobacteria [4].

Pilot and field studies have demonstrated the efficacy of aerobic bioremediation of MTBE by PM1 [5 - 9]. Furthermore, PM1-like bacteria (98-99% similar based on 16S rDNA sequences) have been shown to be naturally occurring in a number of MTBE-contaminated aquifers in California [10-12]. The presence of PM1-like bacteria has been correlated with MTBE degradation activity in numerous sites (S. Kane, K. Hristova, unpublished) using technologies such as real-time quantitative PCR [13]. In field studies, increases in PM1-like bacterial populations corresponded to MTBE removal. These results suggest that a PM1-like organism may play a major role in MTBE biodegradation under aerobic conditions in California aquifers.

To date, little to nothing is known concerning the biochemistry and genetics of aerobic MTBE metabolism, which involves a novel ether cleavage reaction described primarily for cometabolic MTBE-degrading organisms [14,15]. In addition to MTBE catabolism, PM1 has a broad range of metabolic capabilities such as the ability to aerobically degrade aromatic hydrocarbons including benzene, toluene, xylenes [16] and phenol. These unique metabolic capabilities point to a significant number of novel genes, providing fertile ground for genomics and proteomics studies. The genome sequence of PM1 provides a framework for characterizing the MTBE degradation pathway and other important metabolic pathways in this novel bacterium. Understanding PM1’s capacity to biodegrade petroleum constituents including relevant mixtures, and the genetic regulation of these catabolic processes will enhance our ability to protect and restore gasoline-impacted aquifers.

An in-depth analysis of the PM1 genome sequence was reported by Kane et al. [17], describing genes and operons on a ~4-Mb circular chromosome and a ~600-kb megaplasmid. The genes for MTBE degradation were shown to be coded on the megaplasmid using plasmid curing experiments and comparative genomic hybridization and resequencing analysis with PM1-like MTBE-degrading bacteria [17].

[1] Hanson, J.R., C.E. Ackerman, and K.M. Scow. 1999. Biodegradation of methyl tert-butyl ether by a bacterial pure culture. Appl. Environ. Microbiol. 65:4788-4792.
[2] Bruns, M.A., J.R. Hanson, J. Mefford, and K.M. Scow. 2001. Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacteria in compost biofilter enrichments. Environ. Microbiol. 3:220-225.
[3] Johnson, R., J. Pankow, D. Bender, C. Price, and J. Zogorski. 2000. MTBE: To what extent will past releases contaminate community water supply wells? Environ. Sci. Technol. 34:210A-217A.
[4] Nakatsu, C.H., K. Hristova,S. Hanada,X.-Y. Meng, J.R. Hanson, K.M. Scow, and Y. Kamagata. 2006. Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. Int. J. Sys. Evol. Microbiol. 56:983-989.
[5] Eweis, J.B., E.D. Schroeder, D.P. Chang, and K.M. Scow. 1998. Biodegradation of MTBE in a pilot-scale biofilter, p. 342-346. In: Wickramanayake, G.B., and R.E. Hinchee (Eds.). Natural attenuation. Chlorinated and recalcitrant compounds. Battelle Press, Columbus, Ohio.
[6] Wilson, R.D., D.M. Mackay, and K.M. Scow. 2001. In situ MTBE biodegradation supported by diffusive oxygen release. Environ. Sci. Technol. 36:190-199.
[7] Stavnes S.A., J. Fleischman, J. Goetz, K. Hristova, S. Hunt, M. Kemper, K. Knutson, W. Mahaffee, M. Roulier, K. Scow, D.J. Slomczynski, and W.J. Davis-Hoover. 2002. MTBE bioremediation with BioNets containing Isolite, PM1, SOS or air. 2B-66. In: A. R. Gavaskar and A.S.C. Chen (Eds.), Proceedings of the Third International Conference of Chlorinated and Recalcitrant Compounds. Battelle Press, Columbus, OH.
[8] Davis-Hoover , W.J., S.A. Stavnes, J.J. Fleischman, S. C. Hunt , J. Goetz, M. Kemper, M. Roulier ,K. Hristova, K. Scow, K. Knutson, W.R. Mahaffey, and D.J. Slomczynski. 2003. BTEX/MTBE bioremediation: Bionets containing Isolite, PM1, SOS or air. E-25. In: V.S. Magar and M.E. Kelley (Eds.) Proceedings of the Seventh International In Situ and On-site Bioremediation Symposium. Battelle Press, Columbus, OH.
[9] Smith, A., K. Hristova, I. Wood, D.M. Mackay, E. Lory, and K.M. Scow. 2004. Comparison of biostimulation versus bioaugmentation with bacterial strain PM1 for treatment of groundwater contaminated with methyl tertiary butyl ether (MTBE). Environ. Health Prospect. (in press).
[10] Kane, S.R., H.R. Beller, T.C. Legler, C.J. Koester, H.C. Pinkart, R.U. Halden, and A. M. Happel. 2001. Aerobic biodegradation of methyl tert-butyl ether by aquifer bacteria from leaking underground storage tank sites. Appl. Environ. Microbiol. 67:5824-5829.
[11] Kane, S.R., T.C. Legler, L.M. Balser, and K.T. O’Reilly. 2003. Aerobic biodegradation of MTBE by aquifer bacteria from LUFT sites. E-12. In: V.S. Magar and M.E. Kelley (Eds.) Proceedings of the Seventh International In Situ and On-site Bioremediation Symposium. Battelle Press, Columbus, OH.
[12] Hristova, K., B. Gebreyesus, D. Mackay, and K.M. Scow. 2003. Naturally occurring bacteria similar to the methyl tert-butyl ether (MTBE)-degrading strain PM1 are present in MTBE-contaminated groundwater. Appl. Environ. Microbiol. 69(5):2616-2623.
[13] Hristova, K.R., C.M. Lutenegger, and K.M. Scow. 2001. Detection and quantification of MTBE-degrading strain PM1 by real-time TaqMan PCR. Appl. Environ. Microbiol. 67: 5154-5160.
[14] Steffan, R.J., K. McClay, S. Vainberg, C. W. Condee, and D. Zhang. 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. 63:4216-4222.
[15] Smith, C.A., K.T. O’Reilly, and M.R. Hyman. 2003. Characterization of the initial reactions during the cometabolic oxidation of methyl tert-butyl ether by propane-grown Mycobacterium vaccae JOB5. Appl. Environ. Microbiol. 69:796-804.
[16] Deeb, R.A., H.-Y. Hu, J.R. Hanson, K.M. Scow, and L. Alvarez-Cohen. 2001. Substrate interactions in BTEX and MTBE mixtures by an MTBE-degrading isolate. Environ. Sci. Technol. 35(2):312-317.
[17] Kane, S.R., A.Y. Chakicherla, P.S.G. Chain, R. Schmidt, M.W. Shin, T.C. Legler, K.M. Scow, F.W. Larimer, S.M. Lucas, P.M. Richardson, and K.R. Hristova. 2007. Whole-genome analysis of methyl/ tert/-butyl ether-degrading beta-Proteobacterium Methylibium petroleiphilum PM1. J. Bacteriol. 189:1931-45.