Disentangling the microbiome of recirculating aquaculture systems of Atlantic salmon through nanopore sequencing

The microbial community in a recirculating aquaculture system (RAS) is pivotal in fish health, contributing significantly to the productive performance during the growing-out phase. Classical and molecular methods using PCR-specific probes have traditionally conducted bacterial com-munity surveillance. Unfortunately, these approaches mask the real bacterial diversity and abundance, population dynamics, and prevalence of pathogenic bacteria. In this study, we ex-plored the use of Oxford Nanopore Technology to characterize the microbiota and functional metagenomics in a commercial freshwater RAS. Intestine samples from Atlantic salmon and water samples from the inlet/outlet water, settling tank, and biofilters were collected. The full-length 16S rRNA gene was sequenced to reconstruct the microbial community, and bioinformatic tools were applied to estimate the functional potential in the RAS and fish mi-crobiota. The analysis showed that bacteria of denitrification processes were also found in water samples, as well as those metabolic pathways related to hydrogen sulfide metabolism. Fish clas-sified as sick showed a decrease in microbial diversity compared to fish without clinical symp-tomatology. Predominance of Proteobacteria in the ill fish and pathogens of the genera Aeromonas, Aliivibrio, and Vibrio, among others, were found in all intestinal samples. Notably, the analysis detected Aliivibrio wodanis in fish showing abnormal clinical conditions. Healthy salmon had a more significant contribution in pathways related to amino acid metabolism and short-chain fatty acid fermentation, which indicates more favorable fish conditions. These findings demon-strate the utility of nanopore sequencing methods in assessing the microbial community in RAS for salmon aquaculture.