Unless you are running an UGF (which almost no one does now) there will be effectively no nitrifying bacteria in and on the substrate. They live where conditions are best for them. In our aquariums this means they will be where there is the most food and oxygen. This means the filter. Effectively all of the nitrifying bacteria are in the filters, not randomly and evenly spread out on the decor and glass.
Substrate will affect your nitrate production when you have a course substrate that traps debris and you fail to remove that debris frequently enough. Other than that there should be no significant difference based on substrate.
Substrate will affect your nitrate production when you have a course substrate that traps debris and you fail to remove that debris frequently enough. Other than that there should be no significant difference based on substrate.
