The integrated analyses of metabolomics and transcriptomics in gill of GIFT tilapia in response to long term salinity challenge

Effects of temperature and salinity on CO2 fluxes dynamics and respiration metabolism in the sea cucumber Apostichopus japonicus (Selenka)

Global warming has led to higher temperatures and extreme precipitation events, significantly affecting the physiological status of sea cucumbers and causing substantial economic losses in the aquaculture industry. This study explored the effects of high temperature (HT), low salinity (LS), and their combination (TS) on CO2 fluxes at the water-air interface, energy allocation, and the expression of respiratory metabolism-related genes in sea cucumbers. The results showed that HT and/or LS treatments reduced growth performance by 8.37-21.64 % and increased respiratory metabolic carbon content by 17.85-57.68 %. Respiratory metabolizable energy increased by 22.59 % (HT) and 25.87 % (TS). Enzyme activities and gene expression of pyruvate dehydrogenase (PDH), pyruvate kinase (PK), and hexokinase (HK) in respiratory tree were significantly higher than in body wall in response to high temperature stress. Conversely, activities and gene expression of α-ketoglutarate dehydrogenase (OGDH), lactate dehydrogenase (LDH), and malate dehydrogenase (MDH) were significantly higher in body wall in response to low salinity stress. These results indicate that the respiratory tree is more responsive to high temperature, while low salinity primarily affects the body wall. CO₂ fluxes positively correlated with respiratory metabolizable energy, respiratory metabolic carbon content, and LDH activities (R > 0.51, p < 0.05), but negatively correlated with OGDH activity and specific growth rate (R > 0.50, p < 0.05). The respiratory tree's specific functions resulted in higher CO2 fluxes in HT group compared to LS group. Furthermore, the combined stress resulted in highest CO2 fluxes, suggesting an additive effect on the physiological metabolism of sea cucumber. This study provides insights into the adaptation mechanisms of aquatic animals to environmental stresses.

Regulation of PGC-1α of the Mitochondrial Energy Metabolism Pathway in the Gills of Indian Medaka (Oryzias dancena) under Hypothermal Stress

Ectothermic fish exposure to hypothermal stress requires adjusting their metabolic molecular machinery, which was investigated using Indian medaka (Oryzias dancena; 10 weeks old, 2.5 ± 0.5 cm) cultured in fresh water (FW) and seawater (SW; 35‱) at room temperature (28 ± 1 °C). The fish were fed twice a day, once in the morning and once in the evening, and the photoperiod was 12 h:12 h light: dark. In this study, we applied two hypothermal treatments to reveal the mechanisms of energy metabolism via pgc-1α regulation in the gills of Indian medaka; cold-stress (18 °C) and cold-tolerance (extreme cold; 15 °C). The branchial ATP content was significantly higher in the cold-stress group, but not in the cold-tolerance group. In FW- and SW-acclimated medaka, the expression of genes related to mitochondrial energy metabolism, including pgc-1α, prc, Nrf2, tfam, and nd5, was analyzed to illustrate differential responses of mitochondrial energy metabolism to cold-stress and cold-tolerance environments. When exposed to cold-stress, the relative mRNA expression of pgc-1α, prc, and Nrf2 increased from 2 h, whereas that of tfam and nd5 increased significantly from 168 h. When exposed to a cold-tolerant environment, prc was significantly upregulated at 2 h post-cooling in the FW and SW groups, and pgc-1α was significantly upregulated at 2 and 12 h post-cooling in the FW group, while tfam and nd5 were downregulated in both FW and SW fish. Hierarchical clustering revealed gene interactions in the cold-stress group, which promoted diverse mitochondrial energy adaptations, causing an increase in ATP production. However, the cold-tolerant group demonstrated limitations in enhancing ATP levels through mitochondrial regulation via the PGC-1α energy metabolism pathway. These findings suggest that ectothermic fish may develop varying degrees of thermal tolerance over time in response to climate change. This study provides insights into the complex ways in which fish adjust their metabolism when exposed to cold stress, contributing to our knowledge of how they adapt.

The role of salinity on genome-wide DNA methylation dynamics in European sea bass gills

Epigenetic modifications, like DNA methylation, generate phenotypic diversity in fish and ultimately lead to adaptive evolutionary processes. Euryhaline marine species that migrate between salinity-contrasted habitats have received little attention regarding the role of salinity on whole-genome DNA methylation. Investigation of salinity-induced DNA methylation in fish will help to better understand the potential role of this process in salinity acclimation. Using whole-genome bisulfite sequencing, we compared DNA methylation patterns in European sea bass (Dicentrarchus labrax) juveniles in seawater and after freshwater transfer. We targeted the gill as a crucial organ involved in plastic responses to environmental changes. To investigate the function of DNA methylation in gills, we performed RNAseq and assessed DNA methylome-transcriptome correlations. We showed a negative correlation between gene expression levels and DNA methylation levels in promoters, first introns and first exons. A significant effect of salinity on DNA methylation dynamics with an overall DNA hypomethylation in freshwater-transferred fish compared to seawater controls was demonstrated. This suggests a role of DNA methylation changes in salinity acclimation. Genes involved in key functions as metabolism, ion transport and transepithelial permeability (junctional complexes) were differentially methylated and expressed between salinity conditions. Expression of genes involved in mitochondrial metabolism (tricarboxylic acid cycle) was increased, whereas the expression of DNA methyltransferases 3a was repressed. This study reveals novel links between DNA methylation, mainly in promoters and first exons/introns, and gene expression patterns following salinity change.

Application of multi-omics combined with bioinformatics techniques to assess salinity stress response and tolerance mechanisms of Pacific oyster (Crassostrea gigas) during depuration

Depuration is a vital stage to ensure the safety of oyster consumption, and salinity had a great impact on the environmental adaptability of oysters, but the underlying molecular mechanism was poorly understood during depuration stage. Here, Crassostrea gigas was depurated for 72 h at different salinity (26, 29, 32, 35, 38 g/L, corresponding to ±20%, ±10% salinity fluctuation away from oyster's production area) and then analyzed by using transcriptome, proteome, and metabolome combined with bioinformatics techniques. The transcriptome showed that the salinity stress led to 3185 differentially expressed genes and mainly enriched in amino acid metabolism, carbohydrate metabolism, lipid metabolism, etc. A total of 464 differentially expressed proteins were screened by the proteome, and the number of up-regulated expression proteins was less than the down-regulated, indicating that the salinity stress would affect the regulation of metabolism and immunity in oysters. 248 metabolites significantly changed in response to depuration salinity stress in oysters, including phosphate organic acids and their derivatives, lipids, etc. The results of integrated omics analysis indicated that the depuration salinity stress induced abnormal metabolism of the citrate cycle (TCA cycle), lipid metabolism, glycolysis, nucleotide metabolism, ribosome, ATP-binding cassette (ABC) transport pathway, etc. By contrast with Pro-depuration, more radical responses were observed in the S38 group. Based on the results, we suggested that the 10% salinity fluctuation was suitable for oyster depuration and the combination of multi-omics analysis could provide a new perspective for the analysis of the mechanism changes.

Renal metabolomic profiling of large yellow croaker Larimichthys crocea acclimated in low salinity waters

Cultivation of Larimichthys crocea in low salinity water has been regarded as an effective way to treat diseases induced by pathogens in seawater. The kidney of euryhaline teleost plays important roles in not only osmoregulation but also regulation of intermediary metabolism. However, the renal responses of metabolism and osmoregulation in L. crocea to low salinity waters are still rarely reported. In this work, renal metabolomic analysis based on MS technique was conducted on the L. crocea following cultivation in salinities of 24, 8, 6, 4, and 2 ppt for 40 days. A total of 485 metabolites covering organic acids and derivatives (34.17 %), lipids and lipid-like molecules (17.55 %), organoheterocyclic compounds (12.22 %), nucleosides, nucleotides, and analogues (11.91 %), and organic oxygen compounds (10.97 %), were identified in L. crocea kidney. Compared with control group (salinity 24), nearly all amino acids, nucleotides, and their derivatives were decreased in the kidney of L. crocea, whereas most of lipid-related metabolites including phospholipid, glycerophospholipids, and fatty acids were increased. The decrease in urea and inorganic ions as well as TMAO, betaine and taurine in L. crocea kidney suggested the less demand for maintaining osmotic homeostasis. Several intermediary metabolites covering amino acids, TCA cycle intermediates, and fatty acids were also significantly changed to match with the shift of energy allocation from osmoregulation to other biological processes. The reduced energy demand for osmoregulation might contribute to the promotion of L. crocea growth under low salinity environment. What is more, carbamoylphosphate and urea that showed linear salinity response curves and higher ED₅₀ values were potential biomarkers to adaptation to low salinity water. Overall, the characterization of metabolomes of L. crocea kidney under low salinity provided a better understanding of the adaptive mechanisms to low salinity water and potentially contributed to a reference for optimal culture salinity and feed formula of L. crocea culture in low salinity water.

Differential Cell Metabolic Pathways in Gills and Liver of Fish (White Seabream Diplodus sargus) Coping with Dietary Methylmercury Exposure

Mercury (Hg) is a dangerous and persistent trace element. Its organic and highly toxic form, methylmercury (MeHg), easily crosses biological membranes and accumulates in biota. Nevertheless, understanding the mechanisms of dietary MeHg toxicity in fish remains a challenge. A time-course experiment was conducted with juvenile white seabreams, Diplodus sargus (Linnaeus, 1758), exposed to realistic levels of MeHg in feed (8.7 μg g^-1, dry weight), comprising exposure (E; 7 and 14 days) and post-exposure (PE; 28 days) periods. Total Hg levels increased with time in gills and liver during E and decreased significantly in PE (though levels of control fish were reached only for gills), with liver exhibiting higher levels (2.7 times) than gills. Nuclear magnetic resonance (NMR)-based metabolomics revealed multiple and often differential metabolic changes between fish organs. Gills exhibited protein catabolism, disturbances in cholinergic neurotransmission, and changes in osmoregulation and lipid and energy metabolism. However, dietary MeHg exposure provoked altered protein metabolism in the liver with decreased amino acids, likely for activation of defensive strategies. PE allowed for the partial recovery of both organs, even if with occurrence of oxidative stress and changes of energy metabolism. Overall, these findings support organ-specific responses according to their sensitivity to Hg exposure, pointing out that indications obtained in biomonitoring studies may depend also on the selected organ.

Effects of Saline-Alkaline Stress on Metabolome, Biochemical Parameters, and Histopathology in the Kidney of Crucian Carp (Carassius auratus)

The salinization of the water environment caused by human activities and global warming has increased which has brought great survival challenges to aquatic animals. Crucian carp (Carassius auratus) is an essential freshwater economic fish with superior adaptability to saline-alkali water. However, the physiological regulation mechanism of crucian carp adapting to saline-alkali stress remains still unclear. In this study, crucian carp were exposed to freshwater or 20, 40, and 60 mmol/L NaHCO₃ water environments for 30 days, the effects of saline-alkali stress on the kidney were evaluated by histopathology, biochemical assays and metabolomics analysis from renal function, antioxidant capacity and metabolites level. Our results showed different degrees of kidney damage at different exposure concentrations, which were characterized by glomerular atrophy and swelling, renal tubular degranulation, obstruction and degeneration, renal interstitial edema, renal cell proliferation and necrosis. Saline-alkali stress could change the levels of several physiological parameters with renal function and antioxidant capacity, including creatinine (CREA), urea nitrogen (BUN), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px) and malondialdehyde (MDA). In addition, metabolomics analysis showed that differential metabolites (DMs) were involved in various metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, aminoacyl-tRNA biosynthesis, purine metabolism, glycerophospholipid metabolism, sphingolipid metabolism, glycolysis/gluconeogenesis and the TCA cycle. In general, our study revealed that saline-alkaline stress could cause significant changes in renal function and metabolic profiles, and induce severe damage in the crucian carp kidney through destroying the anti-oxidant system and energy homeostasis, inhibiting protein and amino acid catabolism, as well as disordering purine metabolism and lipid metabolism. This study could contribute to a deeper understanding the adverse effects of saline-alkali stress on crucian carp kidney and the regulatory mechanism in the crucian carp of saline-alkali adaptation at the metabolic level.

Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line

Transcriptional regulation is a major mechanism by which organisms integrate gene x environment interactions. It can be achieved by coordinated interplay between cis-regulatory elements (CREs) and transcription factors (TFs). Euryhaline tilapia (Oreochromis mossambicus) tolerate a wide range of salinity and thus are an appropriate model to examine transcriptional regulatory mechanisms during salinity stress in fish. Quantitative proteomics in combination with the transcription inhibitor actinomycin D revealed 19 proteins that are transcriptionally upregulated by hyperosmolality in tilapia brain (OmB) cells. We searched the extended proximal promoter up to intron1 of each corresponding gene for common motifs using motif discovery tools. The top-ranked motif identified (STREME1) represents a binding site for the Forkhead box TF L1 (FoxL1). STREME1 function during hyperosmolality was experimentally validated by choosing two of the 19 genes, chloride intracellular channel 2 (clic2) and uridine phosphorylase 1 (upp1), that are enriched in STREME1 in their extended promoters. Transcriptional induction of these genes during hyperosmolality requires STREME1, as evidenced by motif mutagenesis. We conclude that STREME1 represents a new functional CRE that contributes to gene x environment interactions during salinity stress in tilapia. Moreover, our results indicate that FoxL1 family TFs are contribute to hyperosmotic induction of genes in euryhaline fish.