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Aquaponics combines the hydroponic production of plants and the aquaculture production of fish into a sustainable agriculture system that uses natural biological cycles to supply nitrogen and minimizes the use of nonrenewable resources, thus providing economic benefits that can increase over time. Several production systems and media exist for producing hydroponic crops (bench bed, nutrient film technique, floating raft, rockwool, perlite, and pine bark). Critical management requirements (water quality maintenance and biofilter nitrification) for aquaculture need to be integrated with the hydroponics to successfully manage intensive aquaponic systems. These systems will be discussed with emphasis on improving sustainability through management and integration of the living components [plants and nitrifying bacteria (Nitrosomonas spp. and Nitrobacter spp.)] and the biofilter system. Sustainable opportunities include biological nitrogen production rates of 80 to 90 g·m⁻³ per day nitrate nitrogen from trickling biofilters and plant uptake of aquaculture wastewater. This uptake results in improved water and nutrient use efficiency and conservation. Challenges to sustainability center around balancing the aquaponic system environment for the optimum growth of three organisms, maximizing production outputs and minimizing effluent discharges to the environment.

Integrating hydroponic and aquaculture systems (aquaponics) requires balanced pH for plants, fish, and nitrifying bacteria. Nitrification prevents accumulation of fish waste ammonia by converting it to NO₃ ^–-N. The difference in optimum pH for hydroponic cucumber (Cucumis sativa) (5.5 to 6.0) and nitrification (7.5 to 9.0) requires reconciliation to improve systems integration and sustainability. The purpose of this investigation was to: 1) determine the ammonia biofiltration rate of a perlite trickling biofilter/root growth medium in an aquaponic system, 2) predict the relative contribution of nitrifiers and plants to ammonia biofiltration, and 3) establish the reconciling pH for ammonia biofiltration and cucumber yield in recirculating aquaponics. The biofiltration rate of total ammonia nitrogen (TAN) removal was 19, 31, and 80 g·m⁻³·d⁻¹ for aquaponic systems [cucumber, tilapia (Oreochromis niloticus), and nitrifying bacteria (Nitrosomonas sp. + Nitrobacter sp.)] with operating pH at 6.0, 7.0, and 8.0, respectively. With the existing aquaponic design (four plants/20 L perlite biofilter/100 L tank water), the aquaponic biofilter (with plants and nitrifiers) was three times more effective at removing TAN compared with plant uptake alone at pH 6.0. Most probable number of Nitrosomonas sp. bacteria cells sampled from biofilter cores indicated that the aquaculture control (pH 7.0) had a significantly higher (0.01% level) bacteria cell number compared with treatments containing plants in the biofilter (pH 6.0, 7.0, or 8.0). However, the highest TAN removal was with aquaponic production at pH 8.0. Thus, operating pH was more important than nitrifying bacteria population in determining the rate of ammonia biofiltration. Early marketable cucumber fruit yield decreased linearly from 1.5 to 0.7 kg/plant as pH increased from 6.0 to 8.0, but total marketable yield was not different. The reconciling pH for this system was pH 8.0, except during production for early-season cucumber market windows in which pH 7.0 would be recommended.