The idea is a good? to identify the dominant nitrifying bacteria by NGS/QIIME2 procedure

Dear all,
The ammonia nitrogen of wastewater is removed by nitrifying bacteria. We plan to adjust the part wastewater treatment equipment, the wastewater discharge replace to wastewater reuse, the  wastewater volume remain deal by the remain existing equipment, the loading will be higher, and that could affect the nitrification efficiency. 
We evaluate the cases by Lab pilot test, collect the sludge sample, and analysis the change of  dominant nitrifying bacteria by NGS/QIIME2 procedure, to decide the wastewater future to reuse or discharge. Is the idea good? and what is the risk?