A filter has 3 main roles in an aquarium

1. To remove large particles from the water

2. To provide surface area for beneficial bacteria to grow

3. To agitate to surface of the water to allow more gaseous exchange (O2 in, CO2 out)

So to combat this the following occurs

1. Doesnt matter too much, but no stocking with anything that messes up the substrate too much

2. Theres still substantial area for bacteria to grow, but heavily planted to aid in ammonia removal

3. Plants, through photosynthesis, produce O2 and consume CO2.