Seasonal Dynamics of Marine Bacterial Communities in Aquaculture Farms: The Case of the Northern Ionian Coastal Ecosystem (Mediterranean Sea)

Coastal aquaculture systems are complex environments with multiple microbial interactions that affect fish health and productivity. High-throughput amplicon sequencing is a valuable tool for identifying such bacterial communities and investigating the relationship between bacterial diversity and sustainability in these systems. In the present study, the seasonal dynamics of marine bacterial communities were assessed, in terms of diversity and composition, in three marine aquaculture farms in the northern Ionian Sea (western Greece) and a distant control site unaffected by aquaculture activities, using 16S rRNA amplicon metabarcoding. Results revealed that Proteobacteria, Bacteroidota, Cyanobacteria, and Verrucomicrobiota were the dominant phyla in the bacterial communities. Alpha diversity was significantly lower in the aquaculture farms compared to the control site. Season was the major factor driving bacterial community fluctuations. Comparative analysis between seasons revealed the presence of differentially abundant amplicon sequence variants (ASVs) in all pairwise comparisons, with the majority of them belonging to the phyla Bacteroidota (families Flavobacteriaceae, Cryomorphaceae) and Proteobacteria (family Rhodobacteraceae). Our study provides the first detailed description of bacterial communities present in Greek coastal aquaculture farms using amplicon metabarcoding analysis and expands our understanding of the impact of seasonality and environmental variables on marine bacterial community diversity and composition.