Differences in Physiological Performance and Gut Microbiota between Deep-Sea and Coastal Aquaculture of Thachinotus Ovatus: A Metagenomic Approach

SIMPLE SUMMARY: In this manuscript, we determined the growth performance and physiological and biochemical indices of the aquaculture fish Trachinotus ovatus reared in deep-sea and coastal environments, and analyzed the species abundance and diversity of the fish’s intestinal microbes using high-throughput sequencing to screen for antibiotic resistance genes. We also analyzed environmental water samples to identify possible reasons for the observed differences between the two environments. The study found no significant difference in growth performance between deep-sea cultured fish and traditional coastal cultured fish during the feeding cycle. However, the physiological and biochemical indices and the number of antibiotic resistance genes in the gut microbial community of deep-sea cultured fish were superior to those of their coastal counterparts. Coastal cultured fish are particularly vulnerable to the impact of domestic water discharged from human activities on shore. This may be the cause of the observed phenomenon. These studies can offer additional data for comparing deep-sea aquaculture with traditional coastal aquaculture and provide a reference for the future development of fishery transformation and scientific standardization of deep-sea aquaculture. ABSTRACT: Aquaculture has become the fastest growing sector in global agriculture. The environmental degradation, diseases, and high density of mariculture has made for an inevitable shift in mariculture production from coastal to deep-sea areas. The influence that traditional coastal and emerging deep-sea farming environments exert on aquatic growth, immunity and gut microbial flora is unclear. To address this question, we compared the growth performance, physiological indicators and intestinal microbiological differences of deep-sea and coastal aquaculture in the Guangxi Beibu Gulf of China. The results showed that the growth performance and the complement of C3 and C4 (C3, C4), superoxide dismutase (SOD), and lysozyme (LYS), these physiological and biochemical indicators in the liver, kidney, and muscle of Trachinotus ovatus (T. ovatus), showed significant differences under different rearing conditions. Metagenome sequencing analysis showed Ascomycota, Pseudomonadota, and Bacillota were the three dominant phyla, accounting for 52.98/53.32 (coastal/deep sea), 24.30/22.13, and 10.39/11.82%, respectively. Aligned against the CARD database, a total of 23/2 (coastal/deep-sea) antibiotic resistance genes were screened and grouped into 4/2 genotypes. It indicated that compared with deep-sea fish, higher biological oxygen levels (3.10 times), inorganic nitrogen (110.00 times) and labile phosphate levels (29.00 times) in coastal waters might contributed to the existence of eutrophication with antibiotic resistance. The results of the study can provide complementary data on the study of the difference between deep-sea farming and traditional coastal farming, serving as a reference to future in-depth work on the transformation of fisheries development and scientific standardization of deep-sea farming.