Bioremediation relies on the stability of enzymatic activities, particularly when bioavailable contaminant concentrations do not permit much renewal of microbial biomass. Starving Delftia acidovorans MC1 were found to lose specific degradation activity, while accumulating variants of the alpha-ketoglutarate-dependent dioxygenase RdpA, the enzyme initiating the degradation of (RS)-2-(2,4-dichlorophenoxy)propionate. These variants differed in their pI and originated from post-translational modification, since there is only one rdpA gene in the genome. It was tested if RdpA modification resulted from carbonylation by reactive oxygen species, known side products of dioxygenase reactions. Carbonylated amino acids in proteins of starved cells were specifically derivatized with 2,4-dinitrophenylhydrazine. Subsequent immunolabeling of the resulting hydrazones and mass spectrometry of tryptic digests confirmed different levels of carbonylation of RdpA.