AnnouncingFAO Manual on Aquaponics available now in resources!
FeaturesPricingSupportSign In

Bacteria in aquaponics

2 months ago

3 min read

Bacteria are a crucial and pivotal aspect of aquaponics, serving as the bridge that connects the fish waste to the plant fertilizer. This biological engine removes toxic wastes by transforming them into accessible plant nutrients. Chapter 2 discussed the nitrogen cycle, especially the critical role of nitrifying bacteria, and outlined the essential parameters for maintaining a healthy colony. Chapter 4 discussed the aspects of biofilter materials that host these same bacteria. This brief chapter serves as a review of the bacteria, including details of the important bacterial groups. Heterotrophic bacterial activity is more fully discussed in terms of its role in the mineralization of solid fish waste. Unwanted bacteria are discussed, including: denitrifying bacteria, sulphate-reducing bacteria and pathogens. Finally, the timeline of bacterial cycling is discussed in regard to the establishment of a new aquaponic system.

Nitrifying bacteria and the biofilter Heterotrophic bacteria and mineralization Unwanted bacteria System cycling and starting a biofilter colony


  • In aquaponics, ammonia must be oxidized into nitrate to prevent toxicity to fish.

  • The nitrification process is a two-step bacterial process where ammonia-oxidizing bacteria convert ammonia (NH3) into nitrite (NO2 -), and then nitrite-oxidizing bacteria convert nitrite into nitrate (NO3-).

  • The five most important factors for good nitrification are: high surface area media for bacteria to grow and colonize; pH (6-7); water temperature (17-34 °C); DO (4-8 mg/litre); cover from direct exposure to sunlight

  • System cycling is the initial process of building a nitrifying bacteria colony in a new aquaponic unit. This 3-5 week process involves adding an ammonia source into the system (fish feed, ammonia-based fertilizer, up to a concentration in water of 1-2 mg/litre) in order to stimulate nitrifying bacteria growth. This should be done slowly and consistently. Ammonia, nitrite and nitrate are monitored to determine the status of the biofilter: the peak and subsequent drop of ammonia is followed by a similar pattern of nitrite before nitrate starts to accumulate. Fish and plants are only added when ammonia and nitrite levels are low and the nitrate level begins to rise.

  • Ammonia and nitrite tests are used to monitor the function of the nitrifying bacteria and the performance of the biofilter. In a functioning system, ammonia and nitrite should be close to 0 mg/litre. High levels of either ammonia or nitrite require a water change and management action. Usually, poor nitrification is due to a change in water temperature, DO or pH levels.

  • Another class of micro-organisms naturally occurring in aquaponics is that of heterotrophic bacteria. They decompose the solid fish waste, releasing some of the nutrients into the water in a process called mineralization.

Source: Food and Agriculture Organization of the United Nations, 2014, Christopher Somerville, Moti Cohen, Edoardo Pantanella, Austin Stankus and Alessandro Lovatelli, Small-scale aquaponic food production, Reproduced with permission.

Food and Agriculture Organization of the United Nations