Characterization, Microbial Community Structure, and Pathogen Occurrence in Two Typical Eel Farms

Pollutants and pathogens in aquaculture systems may cause economic losses and threaten public health. Yet, the risks associated with microbiological contaminants and their relationship with environmental factors remain largely unknown. In this study, two typical eel farms in southeast China were chosen for investigation of water quality and microbial community in the treatment processes. It was found that flocculant addition can only effectively reduce total phosphorus (TP) in both farms. However, excessive total nitrogen (TN) was found (6.16 mg/L and 6.74 mg/L, respectively). NH₄⁺ (3.98 mg/L) was the main nitrogen pollutant in QR farm, while NO₃^- (3.81 mg/L) and NO₂^- (1.22 mg/L) were the main nitrogen pollutants in ZJ farm. The treatment processes could not effectively remove nitrogen pollution, and the abundance of nitrogen functional bacteria was low. NO₂^- was positively correlated with Verrucomicrobiota (p < 0.05). NH₄⁺ and TN were significantly negatively correlated with Nitrospirota and unclassified_f_Anaerolineaceae, respectively (p < 0.05). Some typical pathogens associated with aquaculture (e.g., Lactococcus) and human beings (e.g., Escherichia-Shigella,) were found in the systems. This study proposes suggestions for aquaculture tailwater by analyzing the shortcomings of the existing treatment processes. Meanwhile, it offers certain support for the prevention of pathogen risks in aquaculture systems.