Pond aquaculture undeniably offers the potential for food production worldwide. In China, 45.83% of aquatic production is currently from pond aquaculture. However, with the continuous expansion of this practice, environmental problems such as a high level of water consumption, aquaculture water deterioration, pollution from effluent and aquatic product quality decline seriously restrict the sustainable development of pond aquaculture. In this review, we summarise the (i) the impacts of pond aquaculture on the environment, (ii) research progress in pond aquaculture ecological engineering, (iii) existing technologies regarding pond aquaculture ecological engineering systems, (iv) effects of applying pond aquaculture ecological engineering and (v) summary and prospects. Moreover, we discuss the merits and drawbacks of each method and technology, and future research priorities are reviewed. With this, an understanding of the role played by ecological engineering in pond aquaculture is provided, as well as guidance for precisely managing aquaculture water and effluent, aquaculture practices, and technological developments. In summary, the pond aquaculture ecological engineering can be managed so as to improve animal welfare and the stability of water treatment systems, reducing the adverse effects on the environment and public health, and enabling the sustainable development of pond aquaculture.

Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5–39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster.

The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.