Difference between revisions of "Methylibium petroleiphilum"

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A Microbial Biorealm page on the genus Methylibium petroleiphilum


Higher order taxa

A Microbial Biorealm page on the genus Methylibium petroleiphilum


Higher order taxa

Kingdom: Bacteria Phylum: Proteobacteria Class: Betaproteobacteria Order: Burkholderiales Family: Comamonadaceae Genus: Methylibium Species: petroleiphilum Strain: PM1 (extensively studied and all available data on) (1)


petroleiphilum Genus species

Methylibium petroliphilum

Description and significance

Methylibium petroleiphilum PM1 was first discovered in 1998 by Professor Kate Scow at UC Davis when purifying biofilters used for treating byproducts from oil refineries. The specific PM1 strain of the bacteria was isolated from a culture enriched with methyl tert-butyl ether (MTBE) from a biofilter from the Los Angeles County Joint Water Pollution Control Plant. (2)

The discovery of M. petroleiphilum PM1 was significant in that it was determined to be the first and currently only known species of bacteria capable of using MTBE as a sole source of carbon. The fact that MTBE is the sole carbon source is a key property of M. petroleiphilum PM1 which makes is a great candidate for bioremediation. (3) Starting in the last 15 years, oil refineries began using MTBE in oil and petroleum purification. MTBE however, is a carcinogen which on numerous occasions has entered water systems and caused massive contaminations. The detection of M. petroleiphilum PM1 in contaminated water supplies could be indicative that it plays a role in purifying the water supply. (4)

16S rRNA sequence analysis revealed that M. petroleiphilum PM1 was a novel genus with 93-96% similarities to the genera Leptothrix, Aquabacterium, Roseateles, Sphaerotilus, Idenella, and Rubrivivax. (5)

To date, M. petroleiphilum PM1 has been discovered in a vast number of MTBE contaminated water supplies such as the US, Mexico, and Europe, and it is assumed that M. petroleiphilum PM1 is abundantly found in any other MTBE tainted water supply in other parts of the world. (6)

M. petroleiphilum PM1is not known to be pathogenic. (6)

Genome structure

M. petroleiphilum PM1 has a 4,044,225 nucleotide (approximately 4Mb) circular chromosome and a 599,444 nucleotide (approximately 600kb) megaplasmid. The chromosome and megaplasmid contain 3,831 and 646 genes respectively. The G+C content of the chromosome and plasmid are 69.2% and 66% respectively; this suggests that the DNA has a relatively high melting temperature and is perhaps an adaptation to harsh environments that may cause irregular annealing. (5)

Genes of that encode enzymes that degrade and catabolize aromatic compounds and alkanes, pumps to uptake and expel metals (metal resistance), and methylotrophy are primarily found in the circular chromosome. (7)

The megaplasmid also encodes genes for alkane degradation and MTBE degradation and metabolism. Also, noted was that the plasmid contains some anomalies unlike plasmids in other bacteria such as t-RNA islands (some of which do not have a valid anti-codon sequence), irregular insertions, and an unusually large number of repeated elements and genes such as a 40 kb region identical to the chromosome as well as a smaller 29 kb region identical to the chromosome. Comparative genome hybridization experiments provide compelling evidence that M. petroleiphilum PM1 acquired its plasmid recently and also that the megaplasmid is what may contain the most critical genes involved in MTBE degradation and metabolism. Another interesting attribute of M. petroleiphilum PM1 is that varying isolates of the identical strain show approximately 99% conservation of the megaplasmid but chromosomal similarities were of a much lower order of magnitude. (7)

Cell structure and metabolism

M. petroleiphilum PM1 is a Gram-negative, motile bacteria with a rod shape and is non-pigmented, aerobic bacteria. The rod structure of the bacteria can range in size from 0.5-2.0 μM. The rods also do not contain any sheaths. Motility is achieved by the use of a polar flagellum. Reproduction occurs by generic binary fission. The fatty acids that make up the majority of the plasma membrane are composed of C16:1w7c and C16:0. (7)

An attribute that M. petroleiphilum PM1 shares with members of the Sphaerotilus-Leptothrix group is the presence of intracellular granules of poly-β-hydroxybutyrate. In addition, M. petroleiphilum PM1 has a cell morphology characteristic of the genus Aquabacterium with the exception of lacking a fibrillar matrix. (7)

M. petroleiphilum PM1is characterized as a methanotroph since it can use methane as a carbon source; however, M. petroleiphilum PM1 lacks all intracellular structures which normally characterize methanotrophs. (7)

Under optimal growth conditions, the bacteria can form cream color flat colonies with smooth features ranging from 2-3 mm in diameter. When grown under very basic conditions, the colonies maintain the same size and shape however tend to be white. Lack of pigmentation (such as orange or pink) is another unusual attribute of M. petroleiphilum PM1 that other methanotrophs poses. (7)

For proper metabolism, M. petroleiphilum PM1 does not require any vitamins or other organic nutrients and can derive all organic compounds from MTBE. The bacterium however does require the trace elements cobalt, copper, manganese, zinc, molybdenum, nickel, and iron. This strain also can metabolize and make use of other organic carbohydrates and amino acids as nutrient sources such as pyruvate, ethanol, L-aspargine, acetate, butanol, methanol, toluene, benzene, phenol, ethylbenzene, 3,4-dihydroxybenzoate, 2,5-dihydroxbenzoate, 3,5-dihydroxbenzoate, 2,6-dihydroxbenzoate and 2,3-dihydroxbenzoate. Unlike other methanotrophs, M. petroleiphilum PM1 has a wide variety of substrates to derive nutrients from. (7)

M. petroleiphilum PM1 grows optimally at pH 6.5 and around 30 degrees Celsius. (7)


M. petroleiphilum PM1 is found primarily in sites contaminated with MTBE as well as other aromatic hydrocarbon contaminated sites. The bacteria play a role in what appears to be a form of bioremediation by breaking down the hazardous compounds. (4). It is intuitive to think that both the environment and bacteria benefit since the bacteria have an abundant food supply of hydrocarbons such as MTBE and they clean the environment at the same time. Grows well in aerobic, warm, and close to neutral pH conditions. (7)


M. petroleiphilum PM1 is not known to be pathogenic. (7)

Application to Biotechnology

M. petroleiphilum PM1 is viewed as being a novel tool used in bioremediation for MTBE and other aromatic contaminated sites. Because of M. petroleiphilum PM1’s ability to degrade a wide variety of normally toxic organic compounds, it can grow fairly well without needing any extra nutrients. Superfund sites as well as contaminated aquifers in the United States are viewed as ideal candidates to see if perhaps M. petroleiphilum PM1 itself could be added directly into aquifers to reduce, if not completely eliminate, hazardous organic compounds. The largest concern of MTBE is that it readily enters aquifers and contaminates drinking water with a carcinogen. (8) Experiments with gas chromatography have revealed that the presence of M. petroleiphilum PM1 in culture with MTBE has shown drastic decreases in MTBE levels and increase carbon dioxide levels and water. (9)

In addition, understanding the novel genetic and metabolic pathways possessed by M. petroleiphilum PM1 could lead to possible ways for devising other strains of bacteria that could degrade a wider range of organic compounds that are carcinogen or toxic in other means to humans. The identification of the key enzymes in M. petroleiphilum PM1 used for degrading MTBE and other organic compounds could be used to further aid in the progression of the field of bioremediation but using the enzymes alone to degrade organic toxins in vitro prior to release into the environment. (8).

Current Research

Most current research is focused on understanding the magnitude of novel metabolic pathways involved in MTBE and aromatic substrate degradation. At the present time it is not clearly understood how the bacteria successfully breakdown MTBE and other aromatic substrates in a energetically favorable manner. (8).

In addition, isolating pure enzymes involved in these metabolic processes is another avenue of research. Pure enzymes could be used in industrial settings to prevent release of MTBE and other hydrocarbons that could be degraded by the appropriate enzymes. (8).

How to directly use the bacteria in bioremediation such as the contaminated Superfund sites and aquifers is where most active research takes place. UC Davis Department of Land, Air and Water Resources is the main research center for the studies of M. petroleiphilum PM1. Water filtration using the bacteria to purify and breakdown MTBE. (8).


(1). NCBI website (2). Hanson, J. R. et al. 1999. Biodegradation of methyl tert-butyl ether by a bacterial pure culture. Appl. Environ. Microbiol. 65:4788-4792. (3). Kane, S. R. et al. 2001. Aerobic biodegradation of methyl tert-butyl ether by aquifer bacteria from leaking underground storage tank sites. Appl. Environ. Microbiol. 67:5824-5829. (4). Kane, S. R. et al. 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. (5). Bruns et al. 2001. Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacteria in compost biofilter enrichments. Environ Microbiol. 3: 220-225. (6). Nakatsu, C. et al. 2006. Methylibium petroleiphilum gen. nov., sp. Nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. International Journal of Systematic and Evolutionary Microbiology. 56: 983-989. (7). Kane, S. R. et al. 2007. Whole-Genome Analysis of the Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Meythylibium petroleiphilum PM1. Journal of Bacteriology. 5: 1931-1945. (8). Hristova K. B. et al. 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. (9). Hristova, K. R. et al. 2001. Detection and quantification of MTBE-degrading strain PM1 by real-time TaqMan PCR. Appl. Environ. Microbiol. 67: 5154-5160.

Edited by KLB