Multi-site investigation of microbial community profiles in mariculture waters and sediments

Marine aquaculture is expanding globally, yet its ecological impacts on microbial communities across the seawater and sediment compartments remain poorly understood. The aim of this study was to assess how the aquatic microbial communities respond to contrasting levels of aquaculture impact, moving beyond the site-specific approach that characterized most previous research. We investigated five mariculture sites, collecting seawater and sediment samples from aquaculture areas (i.e., nearby fish cages) and non-aquaculture control areas. Microbial community profiles were analyzed through 16S rRNA gene amplicon sequencing to explore taxonomic composition and diversity, test for compartment and impact-related differences, and identify discriminant taxa across fish farms. Moreover, sediment organic matter quality was characterized through proteins, lipids, carbohydrates, and biopolymeric carbon (BPC) to evaluate the association between enrichment of aquaculture-driven organic matter and benthic microbial community profiles. Our results revealed that surface seawater assemblages were dominated by site-specific taxa and did not differ significantly between aquaculture and non-aquaculture areas. In contrast, aquaculture sediments exhibited reduced diversity and a community shift toward anaerobic and sulfate-reducing taxa, with positive correlations to enhanced protein and lipid deposition. Benthic microbial responses were associated not only with the quantity but also with the biochemical quality of sedimentary organic matter. By integrating multi-site analyses, this study shows that aquaculture-related organic enrichment is associated with consistent microbial community patterns across distinct environments, providing a basis for the development of sediment-focused monitoring approaches in aquaculture.