Culturable bacterial diversity in a recirculating aquaculture system for sole fish farming: analysis of potential pathogens and putative bioremediation, probiotic and antimicrobial significance

This study is the first to characterize the culturable bacterial diversity within a Recirculating Aquaculture System (RAS) for sole farming (Solea senegalensis) in Portugal, providing a comprehensive insight into its complex bacterial dynamics. Phylogenetic analysis revealed that Pseudomonadota (76.4%) was the most abundant phylum, followed by Actinomycetota (10.7%) and Bacteroidota (9.8%). At the class level, Gammaproteobacteria (65.7%) and Actinomycetes (10.7%) dominated, with Alteromonadales (33.9%) and Vibrionales (13.7%) as the prevalent orders. A comparison with previous metagenomic studies of similar RAS systems demonstrated overlap in dominant phyla but also identified unique genera, particularly Actinomycetota and Vibrionales. A total of 48 bacterial genera were identified, with 34 exclusives to the RAS and 8 exclusives to its water supply. Our findings highlight the presence of bacteria with biotechnological potential, including groups previously identified as probiotics, those with antimicrobial properties, and others involved in bioremediation. Although human pathogenic bacterial were also identified, their pathogenicity was not confirmed. The high bacterial diversity with possible biotechnological applications found in the RAS underscores the promise of these artificial environments as source of sustainable solutions for both human and aquaculture health.