The people who deny bacteria in the substrate have probably not studied nor researched microbiology. The people who do this sort of research know better. If you look at the research into tank bacteria you will see they inevitably collect samples form filter media, substrate and even the water. While there are not many free floating nitrifiers in the water, there are a minute number. Plus it also provides support that most are in one's substrate and filter and insures all the potential types have been identified.
Research on planted vs non-planted shows that, in the latter, there are no aerobic bacteria once you get about 1/2 inch deep. In planted tanks there are multiple layers of bacteria even at greater depths. This is because the plants actively transport oxygen down to and out of their roots to help support them, Those bacteria in turn make things the plants use. If you want some research on this, read here
http
/m.m.aslo.info/lo/toc/vol_42/issue_3/0529.pdf
Finally, a tank will cycle whether or not one has a good functioning filter or not as long as all the other things they need are present. They will simply multiply elsewhere in the tank. Think about the sloppy fish keeper who almost never cleans their media to the point of it clogging and causing flow in the filter to slow. This causes the bacteria to suffer and even to die back. But the tank remains cycled because the bacteria elsewhere will use the ammonia etc. and they will multiply.
Moreover, the bacteria will always do best where the best supply of what they need is delivered.
A lot of the stinky stuff mentioned above may not be the aerobic nitrifiers, they are other anaerobix/anoxic bacteria. At the glass depth one must have plant roots or there is no oxygen. Even the facultative aerobes which can switch what they use from free oxygen to the the bound oxygen in nitrate will switch to using sulfates and then create hydrogen sulfide, the nasty rotten egg smelling gas. There is a difference between the brown muck in filter media and what is at the bottom of the substrate in an unplanted tank. But even the brown muck in ones filter can have the areobic bacateria die back when the flow rate is slowed. The bacteria need everything delivered to them via the curculation of water theought the biofilm in which they live. this means a filter needs flow though. When the much builds up to the point where it slows flow, it is also allowing the bacteria in the media to die.
When it comes to seeding nitrifying bacteria the following methods will all work to differing degrees:
-Adding viable bottled bacteria. One should turn off tank lights for 24 hours right before adding the bacteria.
-Adding cycled bio-media, substrate or decor from one or more of one's other tanks.
-Squeezing out sponges and/or relatively new floss into the water of the new tank with the filters running. One should turn off tank lights for 24 hours right before squeezing.
Adding live plants. These take up NH4, reducing the need for nitrifying bacteria. Live plants also have bacteria on them and their roots and will also help to seed a tank.
Of course you can use the above in combination and/ or sufficient quantity to achieve an instantly cycled tank.
Accumulating a complete spectrum of microorganisms and tiny critters takes months. However, the most important ones for the safety of our fish are the nitrifiers and they must colonize right away (i.e during cycling) while the rest will become well established later.
One suggestion here on seeding a tank. It is usually difficult to tell how much bacteria we might be adding with any of the methods above (except for bottled bacteria). But there is one easy way to know. Add some ammonia and test in 24 hours. How much of that ammonia is processed and whether any nitrite appears will tell you what level of cycling is in place. You can add the appropriate amount of ammonia for the fish load you expect to add and as long as you can test 0/0 in 24 hours, the tank is good to go. Processing 3 ppm will support a full load right away, 2 ppm will support a moderate load, .50 - 1 ppm a lighter load with gradual stocking to get to a full load.
