Please don't be offended, but you've only got half the story right. Substrate doesn't carry enough beneficial bacteria to affect the cycle, except in under gravel filtration systems. It does, however, contain pieces of waste and food that can be disturbed and broken/dispersed. This increases the surface area of these nitrogen sources allowing them to be broken down faster, sometimes faster than the good bacteria can process the subsequent ammonia that results from this expedited decomposition.
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