A checklist for aerobic biological systems requiring ammonia & nitrite removal (nitrification)

Some additional notes:

• Ammonia oxidation by ammonia oxidizing bacteria (AOB) often called just Nitrosomonas. pH above 8.5 begins to create unionized ammonia toxicity - NH4+ conversion to NH3 gas. So their energy source can become toxic. At pH < 6.5 we start to see toxicity as ammonia species move out of AOB metabolic ranges. 
• Nitrite oxidizing bacteria (NOB) often called just Nitrobacter. Usually grow faster than AOB, and are not often the rate limiting step. However, we have seen nitrite buildup in industrial wastewater that causes bioassay problems this was due to NOB partial inhibition.
• If you suspect toxicity from sulfides, metals, or organics - test using Aster Bio's Tox-Bac & Tox-N bench tests which give toxicity to heterotrophic and AOB with 3 hours. 
• Adding nitrifier concentrates to systems with insufficient AOB/NOB activity - run toxicity tests! I also have best luck adding heterotrophic cultures along with or before adding the AOB/NOB. The heterotrophs can remove many inhibitory compounds and form biofilms that prevent nitrifier washout.