Aquaculture has become one of the fastest-growing food-producing sectors since 1980s and accounted for almost half (49%) of global fish consumption in 2012 (FAO, 2014). In order to meet the growing human demands for aquatic products, aquaculture scale is bound to continue expand. However, aquaculture is a high-polluting industry. On average, only 25% of its nitrogen and phosphorus inputs could be recovered by target organisms (Crab et al., 2007), and the rest of nutrients are discharged into surrounding water. This is not only a waste of nutrients, but also causes serious pollution to the surrounding environment.

Aquaponics is considered to have potentials to solve the abovementioned problems. Aquaponics is the combination of conventional aquaculture and hydroponics, which could achieve co-culture of fish and plants at the same time. Fish, plants and microbes are three main components of aquaponics, and microbes play the bridge role of converting fish waste to plant nutrients (Somerville et al., 2014). Usually there are three common types of aquaponics designs, i.e., floating raft, nutrient film technology, and media-based bed, mainly classified according to hydroponics (Nelson and Pade, 2007). Of which, media-based bed could act as a filtration unit and provide surface area for microbial growth at the same time. This makes it popular in currently running aquaponics. A survey conducted by Love et al. (2014) discovered that 86% of their respondents adopted media-based aquaponics.

Nitrogen is a vital element for all living organisms. In aquaponics, fish feed that contains high content of protein is added into system and digested by fish. Most of the nitrogen is then excreted in the form of total ammonia (TAN), which is toxic to fish. Fortunately, nitrifying bacteria in aquaponics could first convert ammonia to nitrite (NO₂⁻) and then into nitrate (NO₃⁻) through nitrification. Nitrate would be reduced to N₂ through denitrification, but more importantly, it is an important fertilizer for plant growth. The establishment of cooperation among three components increases nitrogen utilization efficiency (NUE) and avoids nitrogen-rich wastewater discharge. To achieve higher productivity and better water quality in aquaponics, many kinds of regulation attempts have been conducted. Liang and Chien (2013) found that better fish growth, plant growth, and nutrients removal efficiency from water were obtained in aquaponics under 24-hour light than 12-hour light, and Endut et al. (2010) reported similar results at loading rate of 1.28 m/d. However, thorough study on nitrogen transformations in aquaponics is still lacking.

pH is one of the most important regulation factors for aquaponic systems, and it is needed to be balanced for fish, plants and microbes at the same time. Usually, recommended pH for plant cultivation was slightly acid (5.5–5.8) (Bugbee, 2003), while the optimal pH for nitrification was 7.5–8.0 (Kim et al., 2007). Fish can tolerate a wide pH range, and the optimal pH was different for different species (Arimoro, 2006, Lemarie et al., 2004). In aquaponics, providing the pH optima for every part is impossible, but knowing optimal pH range for the best overall performance is necessary. Tyson et al. (2008) had claimed that reconciling pH for aquaponics should be 7.5–8.0, but no difference in plant yields was detected in their research, which was unreasonable. Essential study is required to investigate the aquaponic performance under different pH conditions. In addition, to achieve the best sustainability, neither yield nor environment impacts could be ignored.

Since biological nitrogen transformations play the key role of bridge in aquaponics, it may cause environmental harms. Nitrous oxide (N₂O), the third biggest greenhouse gas with a global-warming potential 296 times higher than CO₂, is often generated from biological nitrification and denitrification processes. In nitrification, heterotrophic ammonia oxidation bacteria (AOB) could conduct nitrifier denitrification to produce N₂O, and the oxidation of hydroxylamine, intermediate during the oxidation of TAN to NO₂⁻, would also lead to N₂O production (Kampschreur et al., 2009). While in denitrification, N₂O which failed to be reduced in time might be emitted to the atmosphere. Previous study has shown that 1.5–1.9% of nitrogen input was lost in the form of N₂O in floating raft aquaponics, while 1.3% was found in conventional aquaculture (Hu et al., 2013, Hu et al., 2015). However, to date, no N₂O emission investigation has been conducted in media-based aquaponics.

In this study, media-based aquaponics was established to investigate the effects of pH on its nitrogen transformations, and special attention was paid to N₂O emission. ¹⁵N labeling experiment was used to determine the main source of N₂O emission, and quantitative polymerase chain reaction (Q-PCR) technology was applied to quantify the abundance of nitrifies and denitrifies to reveal the influence of pH on microbial community.