Site-specific bacterial and antimicrobial resistome profiles in seawater and sediments from Mediterranean marine aquaculture sites.

Aquaculture significantly contributes to meeting the growing global demand for food, primarily driven by the increase in the world population. Despite its importance, aquaculture has also been shown to impact aquatic ecosystems. From an anthropocentric perspective, it can cause disturbances in the affected ecosystems and contribute to the selection and spread of potential pathogens and antimicrobial resistance. With this focus, this study analysed three sites in the Mediterranean Sea: an active fish farm, a recently dismissed farm, and an unreplicated descriptive reference site. The bacterial community and antimicrobial resistome in water and sediment samples were characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Bacterial community composition differed strongly between water and sediments. Observed bacterial richness was lower at the recently dismissed farm than at the active farm in sediments, whereas no corresponding difference was detected in water. Sediments from both fish-farm sites also harboured several high-risk antimicrobial resistance genes. Overall, the study identified descriptive site- and matrix-specific patterns in bacterial richness, community composition and antimicrobial resistance gene distribution across marine aquaculture sites. These findings establish a valuable basis for future longitudinal studies aimed at resolving the ecological processes and temporal dynamics associated with changes in fish-farm operations.