A method and system of treating wastewater that can provide operating flexibility is disclosed. The system is operated with a sequencing batch reactor, which is typically cycling to any of fill, react, settle, decant, and idle stages, to treat the wastewater. The system can further utilize a membrane filtration system to further treat water from the sequencing batch reactor and produce suitable water. A solids-reducing system can be connected to the sequencing batch reactor and reduce an amount of biodegraded solids by converting the character or distribution of microorganisms population in the biomass.