Wastewater is usually very high in ammonia, a component of urea, which occurs naturally in urine. Ammonia is generally removed from the wastewater in the tertiary, or third, step of the sewage treatment process. (The primary stage removes the sludge, or solid matter, and the secondary stage uses mechanical and biological processes to break that sludge down.)
Tertiary treatment for nitrogen usually occurs in two steps - first the ammonia is nitrified, or converted into nitrates. This is an aerobic process which uses Nitrosomonas bacteria to convert ammonia, NH3, into nitrite, NO2, and then that into nitrate, NO3. Then denitrification is done under anaerobic conditions where other bacteria (there are many species used) convert the nitrates into atmospheric nitrogen gas, N2.
There are many case studies available, because no two treatment plants do it exactly the same way. What I've given you is an overview of the process. An important thing to keep in mind when thinking about wastewater treatment is that most of the work is done by living organisms; a treatment plant is really a model ecosystem. The first link below provides more technical information about the process, and the other two links will lead you to actual case studies.