Here is a picture http://imgur.com/a/TdW6B The thin dark line in the bottom picture is trapped gasses they are made by anaerobic bacteria about an inch below the bubbles. The gases are trapped because of the mica and the sort of clay i use to bind the dirt and manure too, and that is just below the red crushed potters clay.
You wont see much in the way of manure in the close up because all this went through a mosquito screen, only the tiniest partials are there and they are all bonded to clay.
I basically tried to recreate actual lake bed the kind when you step on it releases gases. The plants run there roots just above and a little bit through this layer and absorb all or almost all of the compounds that would normally cause huge spikes. The anaerobic bacteria don't produce the same kinds of spikes you would get if the soil had access to more oxygen.
When using this method i was told you need at least 4-6 inches of soil in the tank to create the layers needed to support all the kinds of bacteria needed to balance out the tank. I started with about 4 and a half but the expansion that happened over the coarse of months from trapped gases and bacteria increased that to about 5-6 in some places. Even under the rocks on the right hand side, bacteria are stronger then expected.
As for issues I do water changes about every never, But when i do it, it's cause i am cleaning out the filter and only 20 gallons, which is rare because the filter is about 10times the size needed for the tank so the water stays clean mechanically and the bacteria in the soil do most of the rest of the work.
I allow the top of the tank to remain open at all times and only refill for water evaporation about 5 gallons per 3 days. The filter is a (400gph at my tanks height) pump and a bunch of filter floss and activated carbon in a large 5 gallon pail,when the carbon is done is when i do the 20 gallon water change roughly every 2-3 months.
I check my nitrate and nitrite levels every 4 days to see if there has been any change. I haven't had one since i stopped adding fish. The plants and bacteria did there job so far. I gave up on checking ammonia levels recently cause last time i saw one was in the first 3 days of this tanks start up, for what ever reason ammonia compounds seam to be almost non existent in my tank i think bacteria get to them first.
Can you tell by my obnoxious and over the top reply, i put too much work into my substrate? XD