Influence of aquaculture practices on microbiota composition and pathogen abundance in pond ecosystems in South China
Shuhui Niu, Chuanlong Li, Jun Xie, Zhifei Li, Kai Zhang, Guangjun Wang, Yun Xia, Jingjing Tian, Hongyan Li, Wenping Xie, Wangbao Gong
Abstract
• Aquaculture practices significantly impact pond microbiota composition. • NH 4 + -N concentration increases pathogenic bacteria in pond water. • Higher nitrogen levels enhance Mycobacterium abundance in pond water. • Culture patterns and species affect Vibrio, Tenacibaculum , and Francisella abundance. • Pathogenic bacteria are more abundant in sediment than in water. Pond microbiota play a crucial role in maintaining water quality and the health of aquaculture species. This study aimed to explore the relationship between pond water and sediment microbiota (especially potential pathogens) and physicochemical parameters under different aquaculture conditions. Samples of pond water and sediment were collected from 21 monitoring sites across eastern, western, and northern Guangdong, and the Pearl River Delta in November 2021, March 2022, and July 2022. Microbial structures were analyzed using high-throughput sequencing of the 16S rRNA gene. The results indicated that sediment microbiota distribution was more uniform than that of water microbiota. Additionally, sampling time significantly influenced the uniformity of water microbiota distribution more than that sediment microbiota. Factors such as aquaculture species, culture pattern, NH 4 + -N, longitude, latitude, total nitrogen (TN), NO 3 − -N, NO 2 − -N, and total phosphorus (TP) were significantly correlated with water microbiota structure, and TN, TP, and organic carbon were significantly correlated with sediment microbiota structure. Furthermore, an increase in the NH 4 + -N concentration in the pond water significantly increased the variety of pathogenic bacteria. Higher nitrogen levels also increased the relative abundance of Mycobacterium in pond water, whereas the culture pattern (freshwater, seawater, brackish, modern captive culture, freshwater factory container aquaculture, or seawater factory culture) and species significantly influenced the relative abundances of Vibrio, Tenacibaculum, Pseudoalteromonas , and Francisella . Additionally, the relative abundance of pathogenic bacteria in the sediment microbiota was significantly higher than that in the water microbiota. Our results suggest that the culture patterns, species, and nitrogen concentrations should be considered when preventing pathogenic bacteria growth in aquaculture waters.