RNA-seq and qRT-PCR analyses reveal the physiological response to acute hypoxia and reoxygenation in Epinephelus coioides.

Hypoxia is a critical problem in intensive Epinephelus coioides aquaculture systems. In the present study, the physiological responses of E. coioides muscle to acute hypoxic stress (DO = 0.6 ± 0.1 mg/L) and reoxygenation (DO = 6.0 ± 0.1 mg/L) were analyzed by transcriptome sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR). RNA-seq was conducted on the muscle tissues of E. coioides in the hypoxia-tolerant (EMS), hypoxia-sensitive (EMW), and normoxic (CM) groups. Among the three groups, a total of 277 differentially expressed genes (DEGs) were identified. KEGG analysis revealed that the pathways significantly enriched after hypoxic stress are involved in the immune response, glycolysis/gluconeogenesis, energy metabolism, vasodilation and proliferation, cell proliferation, and apoptosis. qRT‒PCR verified that the differentially expressed genes FIH-1, PHD-2, PPARα, BCL-XL, LDH-A, and Flt-1 were significantly upregulated after hypoxic stress and returned to normal levels after reoxygenation, suggesting that these DEGs play important roles in responding to hypoxia treatment. In addition, the HIF-1 signaling pathway was also activated under hypoxic stress, and qRT‒PCR confirmed that the expression level of HIF-1α was significantly elevated under acute hypoxic stress, indicating that the HIF-1 signaling pathway is the central pathway in the E. coioides hypoxic response mechanism and activates other related pathways to adapt to hypoxic stress. These pathways jointly regulate energy metabolism, substance synthesis, blood vessel proliferation, cell proliferation, and differentiation and prolong survival time. These results provide ideas for understanding physiological regulation after hypoxic stress and reoxygenation and provide basic insights for the future breeding of hypoxia-tolerant E. coioides.

Composition and distribution of bacterial communities and antibiotic resistance genes in fish of four mariculture systems.

Fish-related antibiotic resistance genes (ARGs) have attracted attention for their potentially harmful effects on food safety and human health through the food chain transfer. However, the potential factors affecting these ARGs have not been fully explored. In this study, ARGs and bacterial communities in the fish gut, mucosal skin, and gill filaments in fish were comprehensively evaluated in four different mariculture systems formed by hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), Gracilaria bailinae, and Litopenaeus vannamei using different combinations. The results showed that 9 ARGs were detected in the gut and mucosal skin and 6 ARGs in the gill filaments. The detection rate of aphA1 was the highest, and the abundance was 1.91 × 10-3 - 6.30 × 10-2 copies per 16 S rRNA gene. Transposase gene (tnpA-04) was detected in all samples with the abundance of 3.57 × 10-3 - 3.59 × 10-2 copies per 16 S rRNA gene, and was strongly correlated with multiple ARGs (e.g., aphA1, tet(34), mphA-02). Proteobacteria, Deinococcus-Thermus, Firmicutes, and Bacteroidetes were the dominant phyla in the four mariculture systems, accounting for 65.1%-96.2% of the total bacterial community. Notably, the high relative abundance of Stenotrophomonas, a potential human pathogen, was elevated by 20.5% in the hybrid grouper gut in the monoculture system. In addition, variation partitioning analysis (VPA) showed that the difference in bacterial communities between mariculture systems was the main driving factor of ARGs distribution differences in hybrid groupers. This study provides a new comprehensive understanding of the characterization of fish-related ARGs contamination in different mariculture systems and facilitates the assessment of potential risks of ARGs and pathogen taxa to human health.

Comparative transcriptome analysis reveals physiological responses in liver tissues of Epinephelus coioides under acute hypoxia stress.

Hypoxia is a common stressor for aquatic animals, including Epinephelus coioides, with a considerable impact on sustainable aquaculture. E. coioides is a widely consumed fish in China owing to its high nutritious value and taste. However, water hypoxia caused by high density culture process has become a great threat to E. coioides culture, and its response to hypoxia stress has not been discussed before. Therefore, the aim of this study was to examine the response of E. coioides to acute hypoxia using transcriptomic techniques. To this end, RNA sequencing was performed on the liver tissues of fish exposed to normoxic and hypoxic conditions for 1 h. The results presented 503 differentially expressed genes (DEGs) in the liver tissue of fish exposed to hypoxic condition compared with those in the normoxic group. Enrichment analysis using the Gene Ontology database showed that the DEGs were mainly enriched for functions related to cell apoptosis signaling pathways, insulin resistance, antioxidant enzymes, and glycolysis/gluconeogenesis signaling pathways. KEGG enrichment analysis showed that HIF-1, PI3K-AKT, IL-17, NF-kappa B, and MAPK signaling pathways were significantly enriched by the DEGs. The DEGs were mainly involved in immune response, inflammatory response, cell apoptosis regulation, energy metabolism, and substance metabolism. Additionally, the hypoxia response in E. coioides was mainly regulated via the PI3K-AKT-HIF-1 signaling axis. Overall, the findings of this study contribute to the understanding of hypoxia stress response in E. coioides, and provides target genes for breeding hypoxia-tolerant Epinephelus spp.