Humic substances modulate fish bacterial communities in a marine recirculating aquaculture system

The stressful conditions of intensive aquaculture systems, combined with excessive antibiotic use, may have dysbiotic effects on aquaculture microbiomes and promote the spread of opportunistic pathogens. Here, we hypothesized that humic substances (HS), when added to the rearing water of a marine recirculating aquaculture system (RAS), will act as a chemical modulator of fish-associated bacterial communities and suppress potential pathogens. To test this, a 28-day RAS trial for juvenile European sea bass (Dicentrarchus labrax) was conducted with and without HS modulation. High-throughput sequencing of the 16S rRNA gene was used to evaluate role of HS in modulating fish bacterial assemblages (gut and skin mucus). In addition to this, biometric, digestive and oxidative stress parameters were measured to assess the impact of HS on fish performance. HS modulation was associated with an increased bacterial diversity and a distinct bacterial community composition in the fish skin mucus. HS modulation significantly increased the relative abundance of amplicon sequence variants (ASVs) related to the potentially beneficial Roseobacter clade and lowered the abundances of ASVs related to potential fish pathogens (e.g., Acinetobacter jonhsonii and Vibrio harveyi). In line with compositional differences, there was an enrichment of predictive KEGG categories related to antagonism and significantly lower abundances of KEGG categories related to pathogenesis and invasibility. In the fish gut, HS modulation was associated with a lower abundance of the orders Enterobacteriales and Bacillales. HS modulation also was associated with significant reductions in fish oxidative stress parameters and a significant increase in the activity of the digestive enzyme chymotrypsin. For the first time, our results demonstrate the potential of dissolved HS as a modulator of fish microbial communities.