AbstractFinfish aquaculture is one of the fastest-growing primary industries globally and is increasingly common in coastal ecosystems demanding effective impact monitoring tools. Bacterioplankton is ubiquitous in marine environment and its rapid response to environmental change makes them a potential bioindicator for environmental impacts. This study aims to verify the use of the taxonomic and functional profiles of bacterioplankton using high-throughput amplicon sequencing. Water was sampled

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... long a distance gradient in three different depths from two lease areas and three control sites in a low-oxygen, highly stratified marine embayment. Our results revealed a vertical variation in bacterioplankton community strongly associated to NOx, conductivity, salinity, temperature and PO4. The overall shift in the taxonomic profile (ASVs) were more noticeable than in the functional profile. Despite depth stratification, ASVs and functional annotations were detected as potential bioindicators for aquaculture activity. Differentially abundant bacteria found in lease areas were associated with nutrient enrichment (e.g., Desulfovibrionaceae, Psychromonadaceae, and Fusibacter) or are known as potential pathogens (e.g., Pseudomonas, Vibrio and Aliivibrio) and members of the fish gut microbiome (e.g., Leptotrichiaceae, Enterobacterales and Pseudomonadales). Differences in the predicted functional profile were strongest in the bottom waters near leases, where pathways assigned to organic compounds and vitamin degradation, fermentation, methanogenesis and antibiotic resistance were detected. Overall, our findings indicated that the use of 16S rRNA sequencing of bacterioplankton communities are a promising and alternative method for detecting variations along an aquaculture gradient in the water column.