In an MTBE-contaminated aquifer in North Hollywood California, an ex situ field-scale bioreactor self-colonized by native strains of the known MTBE-degrader Methylibium petrolphilum PM1 has been effectively treating the underlying MTBE plume for 2.5 years. As a followup to this study, a series of field column experiments were conducted to evaluate changes in the microbial community and in the densities of naturally-occurring MTBE-degrading bacteria in response to MTBE concentration. For 8 weeks, columns packed with granular activated carbon were continuously fed groundwater from the North Hollywood aquifer. Each triplicate set also received a feed of either 0.1, 1, 10, or 20 mg/L MTBE. Denaturing Gel Gradient Electrophoresis (DGGE) was performed for the GAC-associated bacterial communities in each column. A strong shift in the dominant microbial community was observed between columns with high and low MTBE loading rates. High MTBE columns were composed almost entirely of strain PM1 and of a Rubrivivax species—a very close relative to strain PM1. In addition, quantitative PCR measured densities of total bacteria and of strain PM1. Densities of PM1 were shown to be directly proportional to MTBE concentration for the four treatments. In addition, removal of MTBE across the length of each column was shown to be directly correlated to strain PM1 densities. These experiments provide compelling evidence of the importance of this organism as a qualitative and quantitative indicator of MTBE biodegradation potential.