Distribution patterns and influential factors of pathogenic bacteria in freshwater aquaculture sediments

Pathogenic bacteria, the major causative agents of aquaculture diseases, are a serious impediment to the aquaculture industry. However, the bioinformatics of pathogenic bacteria and virulence factors (VFs) in sediments, an important component of freshwater aquaculture ecosystems, are not well characterized. In this study, 20 sediment samples were collected from fish pond sediments (FPS), shrimp field sediments (SFS), fish pond sediment control (FPSC), and shrimp field sediment control (SFSC). Molecular biological information was obtained on a total of 173 pathogenic bacteria, 1093 virulence factors (VFs), and 8475 mobile genetic elements (MGEs) from these samples. The results indicated that (1) aquaculture patterns and sediment characteristics can affect the distribution of pathogenic bacteria. According to the results of the Kruskal-Wallis H test, except for Mycobacterium gilvum, there were significant differences (P < 0.05) among the four sediment types in the average abundance of major pathogenic bacteria (top 30 in abundance), and the average abundance of major pathogenic bacteria in the four sediment types followed the following pattern: FPS > SFS > FPSC > SFSC. (2) Pathogenic bacteria are able to implement a variety of complex pathogenic mechanisms such as adhesion, invasion, immune evasion, and metabolic regulation in the host because they carry a variety of VFs such as type IV pili, HSI-I, Alginate, Colibactin, and Capsule. According to the primary classification of the Virulence Factor Database (VFDB), the abundance of VFs in all four types of sediments showed the following pattern: offensive VFs > non-specific VFs > defensive VFs > regulation of virulence-related genes. (3) Total organic carbon (TOC), total phosphorus (TP), available phosphorus (AP), nitrite, and nitrate were mostly only weakly positively correlated with the major pathogenic bacteria and could promote the growth of pathogenic bacteria to some extent, whereas ammonia was significantly positively correlated with most of the major pathogenic bacteria and could play an important role in promoting the growth and reproduction of pathogenic bacteria. (4) Meanwhile, there was also a significant positive correlation between CAZyme genes and major pathogenic bacteria (0.62 ≤ R ≤ 0.89, P < 0.05). This suggests that these pathogenic bacteria could be the main carriers of CAZyme genes and, to some extent, gained a higher level of metabolic activity by degrading organic matter in the sediments to maintain their competitive advantage. (5) Worryingly, the results of correlation analyses indicated that MGEs in aquaculture sediments could play an important role in the spread of VFs (R = 0.82, P < 0.01), and in particular, plasmids (R = 0.75, P < 0.01) and integrative and conjugative elements (ICEs, R = 0.65, P < 0.05) could be these major vectors of VFs. The results of this study contribute to a comprehensive understanding of the health of freshwater aquaculture sediments and provide a scientific basis for aquaculture management and conservation.