Effects of the red alga Gracilaria fisheri on the microbiota of the culture water, phycosphere, and intestine of hybrid grouper in a recirculating aquaculture system

This 30-day experiment evaluated the multifaceted effects of integrating the red alga Gracilaria fisheri into the recirculating aquaculture of pearl gentian grouper (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂), focusing on the microbiota of the culture water, fish intestine, and phycosphere. 16S rRNA high-throughput sequencing demonstrated that G. fisheri significantly enhanced microbial diversity in all three communities, evidenced by respective Shannon index increases of 0.4, 1.3, and 0.5. Concurrently, the abundance of dominant phyla and genera shifted: within the aquatic microbiota, Bacteroidetes increased by 16.3% while Proteobacteria, Bacteroidetes, and Verrucomicrobia declined; in the gut microbiota, Firmicutes and Bacteroidetes rose by 7% and 17.3%, inversely proportional to reductions in Proteobacteria and Actinobacteria; the phycosphere microbiota exhibited a 13% Proteobacteria increase with decreases in Bacteroidetes and Desulfobacterota. Specific genus-level successions occurred: Edaphobaculum was succeeded by Nautella in water; Pseudomonas and Ralstonia were replaced by Photobacterium and Lachnospiraceae_NK4A136_group in the gut; Pelomonas and Ralstonia were supplanted by Ruegeria and Psychroserpens in the phycosphere. Functionally, ecological functional abundance decreased in the aquatic microbiome, whereas metabolic functions for terpenoids and polyketides and the abundance of genetic information and cellular processes increased in the phycosphere and intestinal microbiota, with other functions waning. Statistical analysis revealed the strongest correlation between the aquatic and phycosphere microbiota (p < 0.01), followed by the aquatic and intestinal microbiota (p < 0.01), while the intestinal and phycosphere microbiota exhibited a weaker positive correlation (p = 0.05). Overall, G. fisheri optimized the aquaculture water environment and regulated fish intestinal microbiota structure, providing insights to refine grouper aquaculture management, augment farming efficiency, and offer a scientific foundation for sustainable industry progression.