This study examined the effect of organic carbon (peptone vs. glucose) on two sequencing batch reactors performing simultaneous carbon oxidation and nitrification. Although each reactor had similar COD oxidation kinetics (0.029 and 0.036 mg COD mg VSS(-1) h(-1)), the Monod nitrification kinetics for the peptone-fed reactor (mu(m)=2.72 h(-1), K(s)=17.8 mg N L(-1)) were faster than for the glucose-fed reactor (mu(m)=0.868 h(-1), K(s)=26.5 mg L(-1)). The overall bacterial communities were profiled by 16S rRNA cloning and sequencing and revealed homology with a greater variety of bacteria from the peptone-fed reactor than the glucose-fed reactor. In addition, amoA cloning and sequencing, terminal restriction fragment length polymorphism, and fluorescent in situ hybridization experiments indicated greater AOB diversity and abundance in the peptone-fed reactor. This research provides evidence that the organic carbon source affects the make-up of the heterotroph community as well as AOB in mixed cultures.