Humic substances and Eisenia bicyclis bioactive extract modulate water, biofilter, and seabass (Dicentrarchus labrax) skin mucus bacterial communities

In an experimental marine culture system, humic substances (HS), Eisenia bicyclis (EB) extract, and their combination (MIX) were used to modulate biofilter, water, and fish skin mucus bacteriomes. In addition to this, we assessed their impact on water quality and seabass ( Dicentrarchus labrax ) health. Our results revealed that the addition of EB significantly increased total ammonia nitrogen (TAN) levels. Nevertheless, there were no adverse effects of the natural organic substances tested on fish health or other physicochemical parameters. The bacteriome analyses showed that these substances induced significant shifts in structural diversity across various biotopes in the culture system. For example, HS selectively enriched bacterial taxa including Bacteroidota in water and skin mucus, and significantly enriched nitrifying bacteria belonging to Nitrosomonadaceae in biofilters. Conversely, EB adversely affected putative nitrifying bacteria but enriched potentially beneficial Rhodobacterales populations in skin mucus. The MIX treatment enhanced microbial evenness in fish skin mucus and enriched Verrucomicrobiales populations, particularly Rubritalea sp., a genus linked to fish health and bioactive compound production. Our findings further showed that all treatments modulated putative functions relevant to host health and pathogen antagonism within the culture system. This study highlights the potential of natural organic substances as water additives to modulate microbial communities across biofilter, water, and fish skin biotopes, offering a promising strategy for targeted microbiome modulation in the aquaculture sector. • HS, EB, and their mixture modulated water, biofilter, and fish skin mucus bacteriome • Detailed analysis revealed biotope-specific variability in bacterial responses to treatments • Modulators demonstrated synergistic impacts on bacterial communities • Natural organic substances offer promising strategies for targeted microbiome modulation