Integrated multi-trophic aquaculture (IMTA) is an environmentally friendly and economically sustainable aquaculture mode. However long-term dynamics of the microbial community in different aquaculture types and their roles in the seasonal diseases of aquacultural organisms are largely unknown. Here, the spatio-temporal variation of surface bacterial communities for thirteen months in three different aquaculture types (shellfish mono-culture, algae mono-culture, and algae-shellfish co-culture) was investigated in Sanggou Bay, China. Although seasonality mainly influences the community structure, significant and subtle bacterial diversity and structure changes could be found among different aquaculture types. R-selected bacteria, most of which were potential (opportunistic) pathogen taxa and typified by Vibrio, increased and dominated in late summer and autumn. Network analysis showed a significant reduction in the number of nodes and connections in autumn, suggesting that elevated r-selected bacteria could reduce the complexity of microbial interactions. Then, six pathogenic bacterial isolates (including two new species) with intense multiple-antibiotic resistance, similar to the highly abundant Vibrio OTUs, were selected from a pathogenic database that was previously derived from the surrounding water of farmed shells in studied seawater. Subsequently, these isolates were selected for environmental challenge experiments and showed a significant reduction in feeding rates for four tested shellfish species, implying their cause of poor physiological activity and mortality in aquacultural shellfish. Moreover, we found abiotic factors (mainly transparency, seawater temperature, and dissolved oxygen) shaping bacterioplankton spatial distribution and closely related to the outbreaks of pathogenic bacteria. Nevertheless, bacterial interactions were dominated by different and specific mechanisms across seasons. Our results emphasize the necessity of monitoring bacterial communities and simple physicochemical parameters such as seawater temperature and dissolved oxygen, which may provide valuable information for preventing and controlling pathogenic bacteria.

Seawater bacterial community, monthly dynamics, bacterial pathogens, seasonal diseases, Vibrio, integrated multi-trophic aquaculture