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Biological filtration refers to the breakdown of ammonia (NH~3~ and NH~4~+) into nitrite (NO~2~) and then further into nitrate (NO~3~) by naturally occurring, nitrifying bacteria. These bacteria live on the surface area of media contained in a tank--- collectively called the biofilter. The process of converting ammonia to nitrate will be detailed in the section on water quality.
In RAS, the biofilter is designed to operate at low pressure. There is a dedicated tank filled with substrate like Kaldnes media, granular media, plastic balls, or other inert materials that have a large specific surface area or surface area of the media per unit volume. The higher the specific surface area, the more bacteria can grow on the media, translating to a higher ammonia removal capacity. Typical biofilter designs for RAS include trickle towers, submerged media, fluidized beds, sand filters, and static bed filter. In aquaponics, the biofilter can either be a separate unit or part of the system. In deep water culture (DWC), the plant trough walls, raft bottoms, and plant roots provide a significant surface area for nitrifying bacteria to colonize. Unlike RAS, the AP system itself typically provides ample surface area for bacteria to colonize, particularly for coupled systems that are appropriately sized. The nutrient film technique (NFT) system (see section below) is an exception, as only a thin layer of water is applied to the plants. If the biofilter is a separate unit, it should be located after the solids removal unit.
Source: Janelle Hager, Leigh Ann Bright, Josh Dusci, James Tidwell. 2021. Kentucky State University. Aquaponics Production Manual: A Practical Handbook for Growers.