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Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain ([C.sub.5] to [C.sub.12]) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an ~4-Mb circular chromosome and an ~600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PMI's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (~99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.

The effects of environmental and pollutant variables on microbial communities in salt marshes along the California coastline are characterized by using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. The strong relationships observed between pollutant concentrations and some microbial indicators have shown the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes.

Ammonium oxidation by autotrophic ammonia oxidizing bacteria (AOB) is an important process in agricultural systems and nitrite. A real-time PCR assay was developed to estimate the AOB population size in soil and results were recorded.

Researchers were able to quantify a methyl tert-butyl ether (MTBE)-degrading bacterial strain called PM1 in culture, groundwater, and sediment using TaqMan PCR. The bacterium belongs to the Rubrivivax gelatinosus subgroup of the beta-Proteobacteria.

Toluene degradation has been linked with specific microbial populations in soil. Traditional culture-based approaches and phospholipid fatty acid (PLFA) and C-PLFA methods not affected by biases associated with laboratory cultivation were used to identify the indigenous populations responsible for disappearance of toluene in Yolo silt loam, a surface soil. PLFA analysis of a soil microbial community was coupled with (super.13)C isotope tracer analyses to measure the community's response to addition of 35 micrograms of (super.13)toluene/ml of soil solution. Results showed coupling the methods is effective for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil.

Research is conducted on the ability of the placed into groundwater isolated bacterial culture to use methyl tert-butyl ether (MTBE) as its energy and carbon source. Results indicate that strain PM1 can be used in the MTBE contaminated environment bioaugmentation.

A study was conducted on the influence of toluene and trichloroethylene on nitrogen cycling in soil. Results reveal that trichloroethylene concentrations do not affect arginine ammonification potential and denitrification enzyme activity. Results also show that such soil microbial populations as protozoa, bacteria and nematodes that promote nitrogen cycling have different sensitivities to toluene and trichloroethylene.

Flooding and a rise in soil carbon source do not influence the carbon and nitrogen fractions of the biomass of soil microbial community, whereas the active bacterial population and respiration rate increase. This response does not vary with soil type. But flooding and additional carbon input induce a change in the pattern of utilization of specific carbohydrates in the substrate. This results in a decreased metabolic diversity of the soil microbial community which is corroborated by Biolog microplate analysis.

Toluene functions as a cosubstrate to enhance microbial cometabolism and degradation of trichloroethylene (TCE) in soil. High initial toluene concentrations increase TCE population and the number of toluene degraders. High TCE concentrations decrease the number of TCE degraders and toluene degradation rate.

A study of three unsaturated soils revealed the biodegradation of trichloroethylene (TCE) and toluene, and measured the sorption and desorption of TCE and toluene. The soils contained various microbial organisms. It was observed that the introduction of phenol increased the rate of degradation of TCE in Rindge and Yolo silt soils whereas the degradation process was slower when methanol and ethylene were introduced in Rindge soil. The introduction of glucose did not affect the soils.

A molecular genetic system for Methylibium petroleiphilum PM1 is developed to demonstrate the involvement of enzyme MdpA in methyl tert-butyl ether (MTBE) removal. The results showed that MTBE-induced MdpA, constitutively expressed at low levels is involved in the regulation of tert-butyl alcohol (TBA) removal under certain conditions but is not directly responsible for TBA degradation.

The designing of pcrA gene based real-time quantitative PCR assay for detection of perchlorate-reducing bacteria in soil microbial communities is described. Partial sequencing of pcrA gene showed differences in the composition of perchlorate-reducing bacterial communities when exposed to various electron donors.

High-density whole-genome cDNA microarrays are used for examining substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. The analysis has predicted several unknown enzymes of the upper MTBE degradation pathway in Methylibium petroleiphilum PM1 and the regulation of metabolic processes that might occur in response to pollutant mixtures and perturbations in the environment.

Research has been conducted on methyl tert-butyl ether-contaminated groundwater. The authors report the discovery of bacterial strain discovered in this groundwater which is identical to the native strain PM1, degrading methyl tert-butyl ether, in its ribosomal 16S DNA sequence.