NOVELTY - Determining the levels of abundance and expression of an indicator and effector gene combination within a biotreatment system (BS), comprises isolating DNA and mRNA from microorganisms from a stream of a BS, determining levels of indicator gene abundance by quantitative polymerase chain reaction (qPCR) analysis of DNA and levels of effector gene abundance by qRT-PCR analysis of mRNA.    USE - Useful for determining levels of abundance and expression of an indicator and effector gene combination within a biotreatment system, controlling a biotreatment system and for optimizing a waste treatment system. The treatment system is a continuous flow activated sludge system, sequencing batch reactor system, a packed bed reactor system, immobilized bacteria system, fluidized bed reactor system, trickling filter system, or a rotating biological contactor system.    ADVANTAGE - The monitoring method is more sensitive than conventional methods and is also more specific as live cells that actively contribute to the degradative potential are assayed. The PCR-based methods allow for accurate, quantitative measurement of both the amount of DNA present for a given indicator gene and levels of expression for the effector gene.    DETAILED DESCRIPTION - Determining the levels of abundance and expression of an indicator and effector gene combination within a biotreatment system (BS), comprises isolating DNA and mRNA from microorganisms from a microorganism-containing stream of a BS, determining levels of indicator gene abundance by quantitative polymerase chain reaction (qPCR) analysis of DNA and levels of effector gene abundance by qRT-PCR analysis of mRNA, where indicator and effector genes are same or different.    INDEPENDENT CLAIMS are also included for the following:    (1) optimizing a waste treatment system which comprises sampling wastewater from a waste treatment system, collecting solids from the sample, isolating DNA and RNA from the solids, performing qPCR or competitive qPCR on the DNA to determine indicator gene abundance, performing quantitative RT-PCR (qRT-PCR) on the RNA to determine effector gene expression, where the indicator gene abundance correlates with the active microbial content (AMC) of the sample and the effector gene expression correlates with the active bioremedial content (ABC) of the sample, and the system is perturbed and repeating the steps until the AMC and ABC are within an empirically determined optimal operating range; and    (2) controlling BS, by sampling a microorganism-containing stream of BS, collecting microorganisms from the sample, isolating DNA and RNA from the microorganisms, determining AMC and ABC value for the sample by qPCR analysis of the DNA or RNA, respectively, or determining a specific bioremedial content (SBC) value for the sample by qPCR analysis of the DNA and qRT-PCR analysis of the RNA, and setting a target AMC, ABC or SBC value for the sample, comparing the determined AMC, ABC or SBC value to the target AMC, ABC or SBC value, and adjusting control processes to make the determined AMC, ABC or SBC values closer to the target values when repeating the above steps.