Aerobic nitrifying bacteria convert ammonia (NH3) into nitrate (NO3). Anaerobic denitrifying bacteria convert nitrate into nitrogen gas (N2). The key difference is that aerobic bacteria require oxygen while anaerobic bacteria must live in environments with little to no oxygen.
A 2-inch deep aquarium substrate will provide more area for roots to grow, will last longer and will be easier to secure plants in. Aquatic plants may not grow sufficiently if the substrate is too thin. However, certain plant species require little or no substrate at all.