TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preferred Method: The effector gene is gox, nahAc, pox, ditA1, merP, merT, amoA or mntA, preferably gox. Adjusting control processes comprises adjusting the mean cell retention time (MCRT), hydraulic retention time (HRT), mixed liquor volatile suspended solids (MLVSS), microorganism community structure, temperature, pH, dissolved oxygen concentration, salt concentration, macronutrient levels, micronutrient levels, and organic compound influent rate. The qPCR or qRT-PCR is competitive, noncompetitive, kinetic, or their combinations. EXAMPLE - Activated sludge, 3-4.5 ml samples were obtained, which contained 150-200 mg of sludge solids. Nucleic acids (DNA or RNA) were extracted. Using either the GA1/GA2 (AAGACCAAACAAGGTGAAGGAG/TCATCGCCTAGCGAATTAGC) primer set or the GA4/GA2 (GCTCGTGACCCTCTTGTTTC/GA2) primer set, gox polymerase chain reaction (PCR) products of either 504 bp or 192 bp in length were generated. A competitor template was also generated using PCR and contained a 50 bp deletion near the 3' prime end of both the 504 bp and 192 bp gox PCR product. Deletion of 50 bp from the 504 bp gox PCR product to generate the cgox PCR product was facilitated using primer GA3 (TCATCGCCTAGCGAATTAGCGAACGCCGTT) which targeted the 3' prime end of the gox gene and a region 50 bp upstream of this binding site. Primer binding resulted in 50 bp of gox DNA being looped away from the primer site and excluded from PCR extension. This yielded a 454 bp DNA sequence, specifically, the 50 bp sequence defined by the thymine residue at position 435 to the thymine residue at position 484 of the 504 bp gox PCR product were deleted.    This competitor gox (i.e., cgox) DNA fragment was ligated into a PCR II-TOPO plasmid vector containing two promoter sites allowing directional transcription which generated either sense or antisense RNA strands. cgox mRNA for competitive RT-PCR was prepared. 0.1-5 micro-g of DNA-free RNA template was combined with 25.2 pmoles of antisense primer (GA2s:TCATCG or GA2) and 0.01-25 pg cgox mRNA. To this primer/template mixture was added 5.5 micro-l of master mix containing 200 units MMLV reverse transcriptase/reaction, 1X MMLV reverse transcriptase reaction buffer. Reverse transcription was allowed to proceed. Quantification of PCR products was performed by agarose gel electrophoresis. Results from gox competitive quantitative reverse transcriptase-PCR (qRT-PCR) experiments demonstrated linear amplification for cgox mRNA, as determined by quantification of cgox and gox product following electrophoretic separation in 2% agarose gels. Negative control lanes (i.e. RNA samples prepared without a reverse transcription step) were without bands after such electrophoresis.