Transcriptome and physiology analysis identify key metabolic changes in the liver of the large yellow croaker (Larimichthys crocea) in response to acute hypoxia

Gill and brain transcriptomic analysis of mandarin fish(Siniperca chuatsi)reveals hypoxia-induced mitochondrial dysfunction and modulation of metabolism

The oxygen content in the fish ponds is facing greater challenges than before in the aquaculture of mandarin fish (Siniperca chuatsi) due to the change of climate and eutrophication. Until now, little is known about the molecular mechanisms underlying the harmful effects of hypoxia on this species. In this work, we built transcriptomes for the mandarin fish that were exposed to decreased oxygen concentration at two times points (24 h and 96 h). The respiratory metabolism activities of pyruvate kinase (PK), hexokinase (HK), lactate dehydrogenase (LDH), succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) had different significantly changes during hypoxic treatment. Histological observation of the gill and brain also revealed some damages by hypoxia. A total of 196,355 transcripts were involved in the Gene Ontology analysis, and the numbers of differentially expressed genes (DEGs) in the brain and the gill between the control and experiment groups are 141 and 552 respectively involved in the different hypoxic stress time. The DEGs were then analyzed using KEGG enrichment analysis. The results showed significant differences in the expression of some genes involved in ribosome pathways,biosynthesis of amino acids, hippo signaling pathway, and pentose phosphate pathway,glycolysis/gluconeogenesis pathway and the TCA cycle. The huge number of transcriptome sequences collected in this study has enhanced the mandarin fish gene resources, and the identified DEGs and related pathway analysis give essential information for understanding biological responses to hypoxia.

Effects of different slaughtering methods on the energy metabolism, apoptosis process and quality of grouper (Epinephelus fuscoguttatus) during cold storage at 4 °C

BACKGROUND

The aquatic processing industry is increasingly aware of the need to ensure that slaughtering is carried out under high welfare standards, so there is a need to explore the impact of slaughter methods on fish fillets. This study aimed to investigate the effects of different slaughtering methods (M1, lethality by hammering; M2, gas mixture causing death; M3, lethality by clove oil anesthesia + ice slurry; M4, lethality by ice slurry; M5, lethality by gradient cooling) on the energy metabolism, apoptosis and flesh mass in grouper (Epinephelus fuscoguttatus).

RESULTS

Therefore, 120 fish (24 per treatment) were slaughtered by the five methods. The results showed that the succinate dehydrogenase (SDH) enzyme activity of M5 sample was higher. The serum glucose level of M2 samples and DAPI staining fluorescence of M2 samples were the highest, indicating that the stress response of M2 was strong. In addition, the texture, pH, total volatile basic nitrogen (TVB-N), thiobarbituric acid (TBA) and K value results showed M5 samples had better flesh quality.

CONCLUSION

Gradient cooling lethality had the least effect on oxidative damage and apoptosis in grouper during cold storage as the gradient cooling lethality had the least effect on antioxidant enzyme activities. © 2024 Society of Chemical Industry.

The weak association between hypoxia tolerance and thermal tolerance increases the susceptibility of abalone to climate change

The simultaneous occurrence of high temperatures and hypoxia events caused mass die-offs of aquatic animals. It is crucial to investigate the relationship between hypoxia tolerance and thermal tolerance of aquatic animals to predict the biological and ecological outcomes under global climate change scenarios. In this study, the hypoxia tolerance and thermal tolerance of Pacific abalone, Haliotis discus hannai, were measured by methods based on adhesion capacity (hypoxia adhesion duration and heat adhesion duration) and heart rate fluctuations (breakpoint of dissolved oxygen and Arrhenius breakpoint temperature). Weak correlations were found between hypoxia tolerance and thermal tolerance (Spearman correlation, r = -0.09, P = 0.2069; Pearson correlation, r = -0.04, P = 0.3313). Furthermore, a total of 21 significant SNPs and 19 candidate genes (such as cubn, lrp6, gria2, rft2, and casp8) were identified to be associated with hypoxia tolerance of Pacific abalone by conducting whole genome resequencing and genome-wide association study (GWAS). But there was no overlap between candidate genes associated with hypoxia tolerance and candidate genes associated with thermal tolerance, validating the weak correlation between hypoxia tolerance and thermal tolerance. This study highlights that individuals with greater hypoxia tolerance do not necessarily have greater thermal tolerance. Global warming and hypoxia may pose a greater threat to population size and genetic diversity of some aquatic animals than previously believed.

Effects of fishing stress on fatty acid and amino acid composition and glycolipid metabolism in triploid rainbow trout

Triploid Oncorhynchus mykiss is an important economic fish worldwide. Fishing stress can affect its growth and meat quality. This study first explored the effects of fishing stress on fatty acid and amino acid in triploid O. mykiss. Results showed fishing stress significantly reduced the content of docosadienoic acid, Gly, Arg, and DAA (P < 0.05). Targeted lipidomics analysis furthered suggested that some lipid molecules belonging to TG, DG, PC, Cer, ChE, and So were significantly up-regulated; while some lipid molecules belonging to Cer, LPE, LPC, PS, PC, and SM were significantly down-regulated, suggesting an accelerated glycolipid metabolism. Eventually, the glycolipid metabolism-related enzyme activity and gene expressions were examined, and the results indicated that O. mykiss was anti-oxidative stress by affecting relevant glycolipid metabolism signaling pathways and participating in cellular redox homeostasis. Findings of this study provide a theoretical foundation for further investigation into the mechanisms through which fishing stress affects O. mykiss.

Integrated miRNA-seq and functional analyses reveal the regulatory role of sha-miR-92a_L + 2R + 4 via targeting vegfaa in rainbow trout (Oncorhynchus mykiss) responding to acute hypoxia and reoxygenation stress

BACKGROUND

Hypoxia negatively affects the behavior, growth, reproduction and survival of fish, causing serious economic losses to aquaculture. Rainbow trout (Oncorhynchus mykiss), an important economic fish worldwide, belongs to a hypoxia-sensitive fish species, however, little is known about the regulatory mechanism of microRNAs (miRNAs) under hypoxia stress.

RESULTS

Rainbow trout were subjected to hypoxia stress for 3 h (H3h_L), 12 h (H12h_L), 24 h (H24h_L) and 3 h reoxygenation (R3h_L) to systemically evaluate the changes of miRNA expression profiles in liver, and functions of sha-miR-92a_L + 2R + 4 were investigated. We found 17, 144, 57 and 55 differentially expressed (DE) miRNAs in the H3h_L vs. control (N_L), H12h_L vs. N_L, H24h_L vs. N_L and R3h_L vs. N_L comparisons, respectively. Enrichment analysis revealed that the targets of DE miRNAs were significantly enriched in HIF signaling pathway, VEGF signaling pathway, FoxO signaling pathway and glycolysis/gluconeogenesis. Through miRNA-mRNA interaction and weighted gene co-expression network analysis (WGCNA), five key DE miRNAs (sha-miR-92a_L + 2R + 4, ssa-miR-128-3p, ssa-miR-101b-3p_R + 1, ola-miR-199a-5p_R + 2 and tni-miR-199_1ss18CG) were identified, which can target at least two hypoxia-responsive genes, such as vegfaa, ho, glut1a and junb. Functional analysis found that sha-miR-92a_L + 2R + 4 directly regulated vegfaa expression by targeting its 3'-UTR, overexpression of sha-miR-92a_L + 2R + 4 significantly decreased vegfaa expression in rainbow trout liver cells, while opposite results were obtained after transfection of sha-miR-92a_L + 2R + 4 inhibitor. Furthermore, overexpressed sha-miR-92a_L + 2R + 4 promoted rainbow trout liver cell proliferation and inhibited apoptosis.

CONCLUSION

This study deepens our understanding of the crucial roles of miRNAs under hypoxia stress in rainbow trout. These results can contribute to devise strategies for improving rainbow trout survival rate and aquaculture production during hypoxia stress and help speeding up the selective breeding of hypoxia-tolerant rainbow trout.

Regulation mechanism of oxidative status, immunity and apoptosis induced by hypoxia and heat exposure via PI3K/Akt signaling pathway in Megalobrama amblycephala

Megalobrama amblycephala, a main herbivorous fish with notable economic benefits in China, often faces serious challenges to its survival and growth due to hypoxia and heat caused by factors such as global warming and intensive aquaculture. To evaluate the combined effects of these stressors, we performed a two-factor crossover test to assess the impacts of simultaneous exposure to hypoxia (2 mg/L) and heat (35 °C) on oxidative stress, immunity and apoptosis in M. amblycephala. These results showed that hypoxia and heat exposure significantly enhanced the expression of oxygen-sensing and heat shock protein (HSP) genes, hypoxia inducible factor 1α (Hif-1α), HIF-prolyl hydroxylase-2 (phd2) and factor inhibiting Hif-1 (fih-1), as well as hsp70 and hsp90α. Furthermore, M. amblycephala suffering from hypoxia and heat exposure exhibited several changes in liver tissues, with the most severe lesions and up-regulation of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) observed in those subjected to simultaneous exposure. Moreover, the combined hypoxia and heat exposure initially triggered an increase in the activities of total antioxidant capacity (T-AOC), superoxide dismutase (SOD) and catalase (CAT), and glutathione (GSH) contents, followed by a reduction, and the accumulation of malondialdehyde (MDA), which induced oxidative stress. This was accompanied by an increase and subsequent reduction in the contents of alkaline phosphatase (AKP), acid phosphatase (ACP), complement component 3 (C3) and C4, immunoglobulin M (IgM), and interferon-γ (IFN-γ) leading to immunosuppression. Additionally, hypoxia and heat exposure up-regulated the expression of antioxidant enzyme genes (nrf2, cu/zn-sod, mn-sod cat, ho-1, pi3k and gpx-1a), inflammatory genes (interleukin il-1β, il-8 and tnf-α), immunity effectors (igm and lyz), as well as apoptosis genes (casp3, casp8, casp9 and p53) and activated p-Akt/Akt, suggesting apoptosis may be linked with oxidative stress and inflammation and mediated through the PI3K/Akt signaling pathway. In short, the combined hypoxia and heat exposure disrupted homoeostasis in M. amblycephala, with a more pronounced detrimental effect than exposure to either stressor alone These results will contribute to understanding the mechanism of combined exposure to hypoxia and heat in fish and provide a fundamental base for fisheries management.

Curcumin attenuates ochratoxin A and hypoxia co-induced liver injury in grass carp (Ctenopharyngodon idella) by dual targeting endoplasmic reticulum stress and apoptosis via reducing ROS content

BACKGROUND

Ochratoxin A (OTA) is a toxin widely found in aquafeed ingredients, and hypoxia is a common problem in fish farming. In practice, aquatic animals tend to be more sensitive to hypoxia while feeds are contaminated with OTA, but no studies exist in this area. This research investigated the multiple biotoxicities of OTA and hypoxia combined on the liver of grass carp and explored the mitigating effect of curcumin (CUR).

METHODS

A total of 720 healthy juvenile grass carp (11.06 ± 0.05 g) were selected and assigned randomly to 4 experimental groups: control group (without OTA and CUR), 1.2 mg/kg OTA group, 400 mg/kg CUR group, and 1.2 mg/kg OTA + 400 mg/kg CUR group with three replicates each for 60 d. Subsequently, 32 fish were selected, divided into normoxia (18 fish) and hypoxia (18 fish) groups, and subjected to hypoxia stress for 96 h.

RESULTS

CUR can attenuate histopathological damage caused by coming to OTA and hypoxia by reducing vacuolation and nuclear excursion. The alleviation of this damage was associated with the attenuation of apoptosis in the mitochondrial pathway by decreasing the expression of the pro-apoptotic proteins Caspase 3, 8, 9, Bax, and Apaf1 while increasing the expression of the anti-apoptotic protein Bcl-2, and attenuation of endoplasmic reticulum stress (ERS) by reducing Grp78 expression and chop levels. This may be attributed to the fact that the addition of CUR increased the levels of catalase (CAT) and glutathione reductase (GSH), increased antioxidant capacity, and ensured the proper functioning of respiratory chain complexes I and II, which in turn reduced the high production of reactive oxygen species (ROS), thus alleviating apoptosis and ERS.

CONCLUSIONS

In conclusion, our data demonstrate the effectiveness of CUR in attenuating liver injury caused by the combination of OTA and hypoxia. This study confirms the feasibility and efficacy of adding natural products to mitigate toxic damage to aquatic animals.

Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander

Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.

Hypoxia-inducible factor-1α promotes macrophage functional activities in protecting hypoxia-tolerant large yellow croaker (Larimichthys crocea) against Aeromonas hydrophila infection

The immune system requires a high energy expenditure to resist pathogen invasion. Macrophages undergo metabolic reprogramming to meet these energy requirements and immunologic activity and polarize to M1-type macrophages. Understanding the metabolic pathway switching in large yellow croaker (Larimichthys crocea) macrophages in response to lipopolysaccharide (LPS) stimulation and whether this switching affects immunity is helpful in explaining the stronger immunity of hypoxia-tolerant L. crocea. In this study, transcript levels of glycolytic pathway genes (Glut1 and Pdk1), mRNA levels or enzyme activities of glycolytic enzymes [hexokinase (HK), phosphofructokinase (PFK), pyruvate kinase (PK), and lactate dehydrogenase A (LDHA)], aerobic respiratory enzymes [pyruvate dehydrogenase (PDH), isocitrate dehydrogenase (IDH), and succinate dehydrogenase (SDH)], metabolites [lactic acid (LA) and adenosine triphosphate (ATP)], levels of bactericidal products [reactive oxygen species (ROS) and nitric oxide (NO)], and transcripts and level changes of inflammatory factors [IL1β, TNFα, and interferon (IFN) γ] were detected in LPS-stimulated L. crocea head kidney macrophages. We showed that glycolysis was significantly induced, the tricarboxylic acid (TCA) cycle was inhibited, and metabolic reprogramming occurred, showing the Warburg effect when immune cells were activated. To determine the potential regulatory mechanism behind these changes, LcHIF-1α was detected and found to be significantly induced and transferred to the nucleus after LPS stimulation. LcHif-1α interference led to a significant reduction in glycolytic pathway gene transcript expression, enzyme activity, metabolites, bactericidal substances, and inflammatory factor levels; a significant increase in the aerobic respiration enzymes; and decreased migration, invasion, and phagocytosis. Further ultrastructural observation by electron microscopy showed that fewer microspheres contained phagocytes and that more cells were damaged after LcHif-1α interference. LcHif-1α overexpression L. crocea head kidney macrophages showed the opposite trend, and promoter activities of Ldha and Il1β were significantly enhanced after LcHif-1α overexpression in HEK293T cells. Our data showed that LcHIF-1α acted as a metabolic switch in L. crocea macrophages and was important in polarization. Hypoxia-tolerant L. crocea head kidney showed a stronger Warburg effect and inhibited the TCA cycle, higher metabolites, and bactericidal substance levels. These results collectively revealed that LcHif-1α may promote the functional activities of head kidney macrophages in protecting hypoxia-tolerant L. crocea from Aeromonas hydrophila infection.

Expression of genes related to gonadal development and construction of gonadal DNA methylation maps of Trachinotus blochii under hypoxia

Chronic hypoxia can affect the growth and metabolism of fish and potentially impact gonadal development through epigenetic regulation. Trachinotus blochii (Golden pompano) is widely cultured near the coast and is sensitive to low oxygen conditions. We found that hypoxia and reoxygenation processes acted on multiple targets on the HPG axis, leading to endocrine disorders. Changes in the expression of key genes in the brain (gnrh), pituitary (fsh and lh), ovaries (cyp19a1a, foxl2, and er), and testes (dmrt1, ar, sox9, and gsdf) were associated with significant decreases in estrogen and testosterone levels. Hypoxia and reoxygenation lead to changes in DNA methylation levels in the gonads. Hypoxia upregulated the expression of dnmt1, dnmt3a, dnmt3b, tet1, and tet2 in females and dnmt3a and dnmt3b in males, while reoxygenation down-regulated the expression of dnmt1, dnmt3a, dnmt3b, tet1, and tet2 in males. Whole genome methylation sequencing showed that the number of differentially methylated regions was highest on chromosome 10 (5192) and lowest on chromosome 24 (275). Differentially methylated genes in females and males, as well as between males and females, were enriched in the oxytocin signaling pathway, fatty acid metabolism pathway, and HIF-1a pathway. In summary, hypoxia and reoxygenation can induce endocrine disorders, affect the expression of HPG axis genes, change the methylation pattern and modification pattern of gonad DNA, and then have potential effects on gonad development.

Integration of physiological, miRNA-mRNA interaction and functional analysis reveals the molecular mechanism underlying hypoxia stress tolerance in crucian carp (Carassius auratus)

Hypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. Compared with the control, increased T-SOD, CAT, GSH-Px, T-AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress. Based on RNA-seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif-1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre-miR-125c-3p/novel_173, dre-miR-181b-5p, and dre-miR-338-5p/dre-miR-17a-3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, and glycolysis/gluconeogenesis. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. Furthermore, research found that hk2 is a target of dre-miR-17a-3p, overexpression of dre-miR-17a-3p significantly decreased the expression level of hk2, while the opposite results were obtained after dre-miR-17a-3p silencing. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp.

Comparative transcriptomics combined with physiological and functional analysis reveals the regulatory mechanism of rainbow trout (Oncorhynchus mykiss) under acute hypoxia stress

Hypoxia, largely triggered by global warming and water contamination, has become an environmental issue of great concern, posing a great threat to aquatic ecosystem. As one of the world's most economically important fish, rainbow trout (Oncorhynchus mykiss) is extremely intolerant of hypoxic environments, however, little is known about the roles of non-coding RNAs (ncRNAs) in the response of rainbow trout to hypoxia stress. Herein, effects of moderate (Tm12L) and severe hypoxia for 12 h (Ts12L) and 12 h reoxygenation on histology, biochemical parameters (antioxidant, metabolism and immunity) and transcriptome (lncRNA, miRNA and mRNA) in rainbow trout liver were investigated. We further validated the regulatory relationships between LOC110519952, novel-m0023-5p and glut1a via dual‑luciferase reporter, overexpression and silencing assays. Compared with Tm12L, the liver in Ts12L showed more severe oxidative damage. Anaerobic, lipid and protein metabolism was enhanced under hypoxia stress, especially in Ts12L. We also found that Tm12L could strengthen innate immune response, which was inhibited in Ts12L. Besides, several hypoxia-related genes (glut1a, vegfaa, hmox, epoa, foxo1a and igfbp1) and ceRNA networks were identified from 1824, 427 and 545 differentially expressed mRNAs, miRNAs and lncRNAs, including LOC118965299-novel-m0179-3p-epoa, LOC110519952-novel-m0023-5p-glut1a, MSTRG.7382.2-miR-184-y-hmox and LOC110520012-miR-206-y-vegfaa. Through in vitro and in vivo functional analysis, we demonstrated that glut1a is a target of novel-m0023-5p, and LOC110519952 can positively regulate glut1a by targeting novel-m0023-5p. Introduction of LOC110519952 could attenuate the promoting effects of novel-m0023-5p on rainbow trout liver cell viability and proliferation. This study highlights the differences in the regulatory mechanism of rainbow trout under different concentrations of hypoxia stress and provides valuable data for further research on the molecular mechanisms of fish adaptation to hypoxic environments.

Unveiling the hidden effects of hypoxia: Pituitary damage and hormonal imbalance in fat greenling (Hexagrammos otakii)

BACKGROUND

In fisheries, hypoxia stress is one of the most common environmental stresses that often lead to the death of large numbers of fish and cause significant economic losses. The pituitary, an important endocrine gland, lies below the hypothalamus region of the brain. It plays a crucial part in controlling vital physiological functions in fish, such as growth, reproduction, and responses to stress. However, the detailed mechanisms of how hypoxia affects these physiological processes via the pituitary remain largely unknown.

METHODS

Fat greenlings (Hexagrammous otakii) were exposed to different dissolved oxygen (DO = 7. 6 mg/L and DO = 2 mg/L) for 24 h. miRNA-mRNA association analysis of H. otakii pituitary after hypoxia stress. Detecting apoptosis in H. otakii pituitary using Tunel and qPCR. Subsequent detection of hormones in H. otakii liver, gonads and serum by ELISA.

RESULTS

In this study, hypoxia causes immune system disorders and inflammatory responses through the combined analysis of miRNAs and mRNAs. Subsequent verification indicated a significant accumulation of reactive oxygen species (ROS) subsequent to hypoxia treatment. The overproduction of ROS cause oxidative stress and apoptosis in the pituitary, ultimately causing pituitary damage and reduced growth hormone and luteinising hormone release.

CONCLUSIONS

According to the association study of miRNA-mRNA, apoptosis problems caused by hypoxia stress result in H. otakii pituitary damage. In the meantime, this work clarifies the possible impact of hypoxia-stress on the pituitary cells, as well as on the gonadal development and growth of H. otakii.

Multi-omics analysis identifies sex-specific hepatic protein-metabolite networks in yellow catfish (Pelteobagrus fulvidraco) exposed to chronic hypoxia

Hypoxia disrupts the endocrine system of teleosts. The liver plays important roles in the endocrine system, energy storage, and metabolic processes. The aim of this study was to investigate the sex-specific hepatic response of yellow catfish under chronic hypoxia at the multi-omics level. Common hepatic responses in both sexes included the HIF-1 signaling pathway, glycolysis/gluconeogenesis, and steroid biosynthesis. Hypoxia dysregulated primary bile acid biosynthesis, lipid metabolism, and vitellogenin levels in female fish. Endoplasmic reticulum function in females also tended to be disrupted by hypoxia, as evidenced by significantly enriched pathways, including ribosome, protein processing in the endoplasmic reticulum, and RNA degradation. Other pathways, including the TCA cycle, oxidative phosphorylation, and Parkinson's and Huntington's disease, were highly enriched by hypoxia in male fish, suggesting that mitochondrial function was dysregulated. In both sexes of yellow catfish, the cell cycle was arrested and apoptosis was inhibited under chronic hypoxia. Multi-omics suggested that SLC2A5, CD209, LGMN, and NEDD8 served as sex-specific markers in these fish under chronic hypoxia. Our results provide insights into hepatic adaptation to chronic hypoxia and facilitate our understanding of sex-specific responses in fish.

Integrated Transcriptomics and Metabolomics Reveal Changes in Cell Homeostasis and Energy Metabolism in Trachinotus ovatus in Response to Acute Hypoxic Stress

Trachinotus ovatus is an economically important mariculture fish, and hypoxia has become a critical threat to this hypoxia-sensitive species. However, the molecular adaptation mechanism of T. ovatus liver to hypoxia remains unclear. In this study, we investigated the effects of acute hypoxic stress (1.5 ± 0.1 mg·L-1 for 6 h) and re-oxygenation (5.8 ± 0.3 mg·L-1 for 12 h) in T. ovatus liver at both the transcriptomic and metabolic levels to elucidate hypoxia adaptation mechanism. Integrated transcriptomics and metabolomics analyses identified 36 genes and seven metabolites as key molecules that were highly related to signal transduction, cell growth and death, carbohydrate metabolism, amino acid metabolism, and lipid metabolism, and all played key roles in hypoxia adaptation. Of these, the hub genes FOS and JUN were pivotal hypoxia adaptation biomarkers for regulating cell growth and death. During hypoxia, up-regulation of GADD45B and CDKN1A genes induced cell cycle arrest. Enhancing intrinsic and extrinsic pathways in combination with glutathione metabolism triggered apoptosis; meanwhile, anti-apoptosis mechanism was activated after hypoxia. Expression of genes related to glycolysis, gluconeogenesis, amino acid metabolism, fat mobilization, and fatty acid biosynthesis were up-regulated after acute hypoxic stress, promoting energy supply. After re-oxygenation for 12 h, continuous apoptosis favored cellular function and tissue repair. Shifting from anaerobic metabolism (glycolysis) during hypoxia to aerobic metabolism (fatty acid β-oxidation and TCA cycle) after re-oxygenation was an important energy metabolism adaptation mechanism. Hypoxia 6 h was a critical period for metabolism alteration and cellular homeostasis, and re-oxygenation intervention should be implemented in a timely way. This study thoroughly examined the molecular response mechanism of T. ovatus under acute hypoxic stress, which contributes to the molecular breeding of hypoxia-tolerant cultivars.

Ultrastructural, Antioxidant, and Metabolic Responses of Male Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) to Acute Hypoxia Stress

Tilapia tolerate hypoxia; thus, they are an excellent model for the study of hypoxic adaptation. In this study, we determined the effect of acute hypoxia stress on the antioxidant capacity, metabolism, and gill/liver ultrastructure of male genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Fish were kept under control (dissolved oxygen (DO): 6.5 mg/L) or hypoxic (DO: 1.0 mg/L) conditions for 72 h. After 2 h of hypoxia stress, antioxidant enzyme activities in the heart and gills decreased, while the malondialdehyde (MDA) content increased. In contrast, in the liver, antioxidant enzyme activities increased, and the MDA content decreased. From 4 to 24 h of hypoxia stress, the antioxidant enzyme activity increased in the heart but not in the liver and gills. Cytochrome oxidase activity was increased in the heart after 4 to 8 h of hypoxia stress, while that in the gills decreased during the later stages of hypoxia stress. Hypoxia stress resulted in increased Na+-K+-ATP activity in the heart, as well as hepatic vacuolization and gill lamella elongation. Under hypoxic conditions, male GIFT exhibit dynamic and complementary regulation of antioxidant systems and metabolism in the liver, gills, and heart, with coordinated responses to mitigate hypoxia-induced damage.

Health Risk Assessment of Antibiotic Pollutants in Large Yellow Croakers from Zhejiang Aquaculture Sites

Intensive aquaculture combatting the decline of large yellow croaker populations can trigger bacterial outbreaks, resulting in extensive antibiotic use. In this study, we screened 5 aquaculture sites in the coastal areas of Zhejiang and identified 17 antibiotics in large yellow croakers using UPLC-MS/MS. The distribution and occurrence of antibiotic pollutants were different in the different tissues of large yellow croakers, being primarily dominated by quinolones. Relatively higher average residue levels of enrofloxacin and ciprofloxacin were detected in the inedible parts, specifically the gills (37.29 μg/kg). Meanwhile, relatively high average residue levels of enrofloxacin and ciprofloxacin were also found in the edible parts, particularly in the muscle (23.18 μg/kg). We observed that the residue levels detected in the swim bladder exceeded the prescribed limit for fish muscle, but there is currently no specific regulatory limit established for this particular tissue. Despite the HI values of enrofloxacin and ciprofloxacin being below 0.01, the health risks should not be disregarded. The findings of this research provide significant practical implications for assessing antibiotic contamination and enhancing the risk management of coastal regions.

Effects of Bacillus halophilus on growth, intestinal flora and metabolism of Larimichthys crocea

The incorporation of probiotics into the diet of large yellow croaker has been demonstrated by several studies to confer partial disease resistance. Bacillus halophilic isolated from the intestinal flora was used to study its effects on performance growth indicators, intestinal tissue structure, intestinal flora and the metabolism of Larimichthys crocea. A total of 180 fishes with an initial body weight of (164.00 ± 54.00) g were fed diets with three different concentrations of Bacillus halophilic: 0 cfu/mL (FC0, control group), 108 cfu/mL (FC8, treatment group), and 1012 cfu/mL (FC12, treatment group). The results showed that there were no significant differences in specific growth rate among all groups (P > 0.05). Compared to the FC0 group, the final body weight and Weight gain rate were significantly higher in FC8 and FC12 groups (P < 0.05). The Survival of the FC12 group significantly improved (P < 0.05). Compared to the FC0 group, crude protein content in muscle of the FC8 group significantly increased (P < 0.05), crude fat content significantly increased in the FC12 group (P < 0.05), crude protein content in whole fish experimental groups significantly increased (P < 0.05), and ash content significantly increased in the FC8 group (P < 0.05). In terms of antioxidant ability, the content of LZM in blood increased significantly in the FC8 group (P < 0.05), GSH content in liver of the FC12 group increased significantly (P < 0.05), while the content of MDA and AKP in blood and liver had no significant difference (P > 0.05). At the level of intestinal structure, there were no significant differences in villus height, crypt depth and goblet cell number between control group and treatment groups (P > 0.05). At the phylum level, Firmicutes was the dominant phylum, and the genus level, Lactobacillus and Bacteroides were the dominant bacteria in FC8 and FC12. A total of 1070 metabolites were identified, among which lipid metabolites accounted for 46.7%. Metabolites were involved in six main ways, mainly related to the metabolism of amino acids and lipids. The correlation analysis between microbes and metabolites showed that the intestinal flora of Larimichthys crocea could promote the synthesis of metabolites, among which Bacteroides and Megamonas could promote the synthesis of beneficial metabolites such as amino acids and vitamins. Through this study, we found that Bacillus halophilic can significantly improve growth, the antioxidant immunity ability and promote the expression of growth related metabolites, with the FC12 group being the better successful.

Transcriptomic Response of the Liver Tissue in Trachinotus ovatus to Acute Heat Stress

Trachinotus ovatus is a major economically important cultured marine fish in the South China Sea. However, extreme weather and increased culture density result in uncontrollable problems, such as increases in water temperature and a decline in dissolved oxygen (DO), hindering the high-quality development of aquaculture. In this study, liver transcriptional profiles of T. ovatus were investigated under acute high-temperature stress (31 °C and 34 °C) and normal water temperature (27 °C) using RNA sequencing (RNA-Seq) technology. Differential expression analysis and STEM analysis showed that 1347 differentially expressed genes (DEGs) and four significant profiles (profiles 0, 3, 4, and 7) were screened, respectively. Of these DEGs, some genes involved in heat shock protein (HSPs), hypoxic adaptation, and glycolysis were up-regulated, while some genes involved in the ubiquitin-proteasome system (UPS) and fatty acid metabolism were down-regulated. Our results suggest that protein dynamic balance and function, hypoxia adaptation, and energy metabolism transformation are crucial in response to acute high-temperature stress. Our findings contribute to understanding the molecular response mechanism of T. ovatus under acute heat stress, which may provide some reference for studying the molecular mechanisms of other fish in response to heat stress.

Transcriptomes of Testes at Different Developmental Stages in the Opsariichthys bidens Predict Key Genes for Testis Development and Spermatogenesis

Testis development is a complex process involving multiple genes, and the molecular mechanisms underlying testis development in Opsariichthys bidens remain unclear. We performed transcriptome sequencing analysis on a total of 12 samples of testes from stages II, III, IV, and V of O. bidens and obtained a total of 79.52 Gb clean data, as well as 288,573 transcripts and 116,215 unigenes. Differential expression analysis showed that 22,857 differentially expressed genes (DEGs) were screened in six comparison groups (III vs. II, IV vs. II, V vs. II, IV vs. III, V vs. III, and V vs. IV). Kyoto Encyclopedia of Genes and Genomes enrichment analysis of DEGs showed that six comparison groups were significantly enriched for a total of 20 significantly up- or down-regulated pathways, including six pathways related to signal transduction, three pathways related to energy metabolism, five pathways related to disease, and two pathways related to ribosomes. Furthermore, our investigation revealed that DEGs were enriched in several important functional pathways, such as Huntington's disease signaling pathway, TGF-β signaling pathway, and ribosome signaling pathway. Protein-protein interaction network analysis of DEGs identified 63 up-regulated hub genes, including 9 kinesin genes and 2 cytoplasmic dynein genes, and 39 down-regulated hub genes, including 13 ribosomal protein genes. This result contributes to the knowledge of spermatogenesis and testis development in O. bidens.

Comparative Transcriptome Analysis of Head Kidney of Aeromonas hydrophila-infected Hypoxia-tolerant and Normal Large Yellow Croaker

The large yellow croaker (Larimichthys crocea) is one of the most economically important marine fish on the southeast coast of China and much of its yield is usually lost by hypoxia. To address this problem and lay a foundation for culturing a new strain of large yellow croaker with hypoxia tolerance, our research group screened a hypoxia-tolerant population of L. crocea. Surprisingly, we also found that hypoxia-tolerant population exhibited higher survival when infected with pathogens compared to the normal population during the farming operation. In order to understand the mechanism underlying the higher survival rate of the hypoxia-tolerant population and enrich the head kidney immune mechanism of L. crocea infected with pathogens, we compared and analyzed the head kidney transcriptome of the hypoxia-tolerant and normal individuals under Aeromonas hydrophila infection. We obtained 159.68 GB high-quality reads, of which more than 87.61% were successfully localized to the reference genome of L. crocea. KEGG analysis revealed differentially expressed genes in the signaling pathways involving immunity, cell growth and death, transport and catabolism, and metabolism. Among these, the toll-like receptor signaling pathway, Nod-like receptor signaling pathway, cytokine-cytokine receptor interaction, phagosome, apoptosis, and OXPHOS pathways were enriched in both groups after infection compared to before, and were enriched in infected tolerant individuals compared to normal individuals. In addition, we found that the expression of hif1α and its downstream genes were higher in the hypoxia-sensitive group of fish than in the normal group. In conclusion, our results showed some signaling pathways and hub genes, which may participate in A. hydrophila defense in the head kidney of two populations, and may contribute to the higher survival rate in the hypoxia-tolerant population. Overall, these findings increase our understanding of the defense mechanism within the head kidney of L. crocea under A. hydrophila infection, and suggest a preliminary hypothesis for why hypoxia-tolerant individuals may exhibit a higher survival rates after infection. Our study provides scientific evidence for the breeding of a new hypoxia-tolerant strain of L. crocea for aquaculture.

Blood biomarkers as diagnostic tools: An overview of climate-driven stress responses in fish

Global climate change due to anthropogenic activities affects the dynamics of aquatic communities by altering the adaptive capacities of their inhabitants. Analysis of blood provides valuable insights in the form of a comprehensive representation of the physiological and functional status of fish under various environmental and treatment conditions. This review synthesizes currently available information about blood biomarkers used in climate change induced stress responses in fish. Alterations in informative blood-based indicators are used to monitor the physiological fitness of individual fishes or entire populations. Specific characteristics of fish blood, such as serum and plasma metabolites, cell composition, cellular abnormalities, cellular and antioxidant enzymes necessitate adapted protocols, as well as careful attention to experimental designs and meticulous interpretation of patterns of data. Moreover, the sampling technique, transportation, type of culture system, acclimation procedure, and water quality must all be considered for valid interpretation of hemato-biochemical parameters. Besides, blood collection, handling, and storage time of blood samples can all have significant impacts on the results of a hematological analysis, so it is optimal to perform hemato-biochemical evaluations immediately after blood collection because long-term storage can alter the results of the analyses, at least in part as a result of storage-related degenerative changes that may occur. However, the scarcity of high-throughput sophisticated approaches makes fish blood examination studies promising for climate-driven stress responses in fish.

PacBio Full-Length and Illumina Transcriptomes of the Gill Reveal the Molecular Response of Corbicula fluminea under Aerial Exposure

Air exposure is a common stress for Corbicula fluminea, an economically important freshwater shellfish consumed in China, during aquaculture and transportation. However, little is known about its molecular responses to air exposure. Therefore, this study used a combination of PacBio full-length and Illumina transcriptomes to investigate its molecular responses to air exposure. A total of 36,772 transcripts were obtained using PacBio sequencing. Structural analysis identified 32,069 coding sequences, 1906 transcription factors, 8873 simple sequence repeats, and 17,815 long non-coding RNAs. Subcellular localization analysis showed that most transcripts were located in the cytoplasm and nucleus. After 96-h of air exposure, 210 differentially expressed genes (DEGs) in the gill were obtained via Illumina sequencing. Among these DEGs, most of the genes related to glycolysis, tricarboxylic acid cycle, lipid metabolism, and amino acid metabolism were upregulated. Additionally, many DEGs associated with immunity, cytoskeleton reorganization, autophagy, and ferroptosis were identified. These findings indicated that metabolic strategy change, immune response, cytoskeleton reconstruction, autophagy, and ferroptosis might be the important mechanisms that C. fluminea use to cope with air exposure. This study will enrich the gene resources of C. fluminea and provide valuable data for studying the molecular mechanisms coping with air exposure in C. fluminea and other freshwater mollusks.

Metabolic response provides insights into the mechanism of adaption to hypoxia in largemouth bass (Micropterus salmoides) under intermittent hypoxic conditions

In metabolism, molecular oxygen is a necessary substrate. Oxygen imbalances are linked to a variety of circumstances in the organism's homeostasis. Recently, the positive effects of hypoxia treatment in improving exercise ability and hypoxia tolerance have become a research focus. We explored the effects of intermittent hypoxia exposure (IHE, for one hour or three hours per day) on the hypoxia tolerance of largemouth bass in this study. The results showed that (1) IHE significantly reduced the LOEcrit (the critical O₂ tension for loss of equilibrium) value of largemouth bass, indicating that its hypoxia tolerance was enhanced. (2) The level of oxidative stress in the liver decreased in the HH3 group (exposed to a hypoxic condition for 3 h per day) compared to HH1 group (exposed to a hypoxic condition for 1 h per day). (3) IHE reduced the content of lactic acid and enhanced the process of gluconeogenesis in the liver. (4) Importantly, lipid mobilization and fatty acid oxidation in the liver of largemouth bass were significantly enhanced during IHE. In short, the results of this study indicate that IHE can improve hypoxia tolerance by regulating the energy metabolism of largemouth bass.

Histological, physiological, and transcriptomic responses of hepatopancreas to air exposure in asian freshwater clam Corbicula fluminea

Corbicula fluminea (C. fluminea) is an important freshwater economy shellfish in China, but it often suffers from air exposure during transportation. In this study, we investigated the histological, physiological (mainly including respiratory metabolism, antioxidant capacity, and immune function), and transcriptomic responses of hepatopancreas in C. fluminea to different times of air exposure. At histological level, air exposure caused vacuolation of digestive cells (24-96 h) and enlargement of digestive tubule lumen (6-96 h) in hepatopancreas. At physiological level, the activities of enzymes related to glycolysis (hexokinase and pyruvate kinase) and anaerobic respiration (lactate dehydrogenase) were increased first (6-24 h) of air exposure, then came back to normal level or even decreased. The activity of aerobic respiration-related enzyme (succinic dehydrogenase) began to reduce from 24 h of air exposure. The activities of antioxidant enzymes (superoxide dismutase and catalase) were enhanced during 6-48 h of air exposure and then returned to control level or even inhibited. The content of malondialdehyde (MDA) increased from 96 h of air exposure. The activities of immune-related enzymes (acid phosphatase and alkaline phosphatase) increased during 6-48 h, then returned to normal or began to decline. At transcriptome level, 44 differentially expressed genes (DEGs) in the hepatopancreas were identified after 96-h air exposure. Among these DEGs, 8 were associated with glycolysis, TCA cycle, immune, and antioxidant, and were downregulated after 96-h air exposure. Taken together, these findings illuminated the response of C. fluminea to air exposure at histological, physiological, and transcriptomic levels, which will be beneficial to the aquaculture and transportation of C. fluminea.

Effects of heat shock on energy metabolism and antioxidant defence in a tropical fish species Psalidodon bifasciatus

Predictions about global warming have raised interest in assessing whether ectothermic organisms will be able to adapt to these changes. Understanding the physiological mechanisms and metabolic adjustment capacity of fish subjected to heat stress can provide subsidies that may contribute to decision-making in relation to ecosystems and organisms subjected to global climate change. This study investigated the antioxidant defence system and energy metabolism of carbohydrate and protein responses in the gill, liver and kidney tissues of Psalidodon bifasciatus (Garavello & Sampaio 2010), a Brazilian freshwater fish used in aquaculture and in biological studies, following exposure to heat shock at 31°C for 2, 6, 12, 24 and 48 h. The fish presented signs of stress in all tissues tested, as evidenced by increased lipid peroxidation concentration at 2 h and phosphofructokinase, hexokinase and malate dehydrogenase activity at 48 h in the gills; increased glutathione-S-transferase activity at 12 h, citrate synthase activity at 24 h and concentration of reduced glutathione (GSH) concentration at 12 and 48 h in the liver; and through increased activity of superoxide dismutase at 48 h, glutathione reductase at 24 h, glucose-6-phosphate dehydrogenase at 48 h and concentration of GSH at 24 h in the kidney. In the kidneys, changes in the antioxidant system were more prominent, whereas in the gills, there were greater changes in the carbohydrate metabolism. These results indicated the importance of glycolysis and aerobic metabolism in the gills, aerobic metabolism in the liver and pentose-phosphate pathway in the kidneys during homeostasis. The biomarker response was tissue specific, with the greatest number of biomarkers altered in the gills, followed by those in the kidneys and liver.

Tandem Mass Tagging-Based Quantitative Proteomics Analysis Reveals Damage to the Liver and Brain of Hypophthalmichthys molitrix Exposed to Acute Hypoxia and Reoxygenation

Aquaculture environments frequently experience hypoxia and subsequent reoxygenation conditions, which have significant effects on hypoxia-sensitive fish populations. In this study, hepatic biochemical activity indices in serum and the content of major neurotransmitters in the brain were altered markedly after acute hypoxia and reoxygenation exposure in silver carp (Hypophthalmichthys molitrix). Proteomics analysis of the liver showed that a number of immune-related and cytoskeletal organization-related proteins were downregulated, the ferroptosis pathway was activated, and several antioxidant molecules and detoxifying enzymes were upregulated. Proteomics analysis of the brain showed that somatostatin-1A (SST1A) was upregulated, dopamine-degrading enzyme catechol O methyltransferase (COMT) and ferritin, heavy subunit (FerH) were downregulated, and the levels of proteins involved in the nervous system were changed in different ways. In conclusion, these findings highlight that hypoxia–reoxygenation has potential adverse effects on growth, locomotion, immunity, and reproduction of silver carp, and represents a serious threat to liver and brain function, possibly via ferroptosis, oxidative stress, and cytoskeleton destruction in the liver, and abnormal expression of susceptibility genes for neurodegenerative disorders in the brain. Our present findings provide clues to the mechanisms of hypoxia and reoxygenation damage in the brain and liver of hypoxia-sensitive fish. They could also be used to develop methods to reduce hypoxia or reoxygenation injury to fish.

Transcriptome profiling reveals differential expression of immune-related genes in gills of hybrid yellow catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂) under hypoxic stress: Potential NLR-mediated immune response

Fish gills are the primary organ that respond to sudden changes in the dissolved oxygen (DO) level in the aquatic environment. Hypoxic stress impairs the normal function of gill tissues. However, little is known about the mechanisms of the response of yellow catfish gills to hypoxic stress. In this study, we compared transcriptomic and physiological changes in gill tissues of hybrid yellow catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂) between a hypoxia-treated group (DO: 1.5 mg/L) and a control group (DO: 6.5 mg/L). In fish in the hypoxia-treated group, gill filaments underwent adaptive changes, and the number of vacuoles in gill tissues increased. Exposure to hypoxic conditions for 96 h resulted in increased anaerobic metabolism and decreased antioxidant and immune capacity in gill tissues. Transcriptome analyses revealed 1556 differentially expressed genes, including 316 up-regulated and 1240 down-regulated genes, between fish in the hypoxia-treated and control groups. Functional analyses indicated that the main pathway enriched with differentially expressed genes was immune response, followed by energy metabolism and signal transduction. Under hypoxic stress, the transcript levels of genes involved in the NOD-like receptor signaling pathway initially increased rapidly but then decreased over time, suggesting that the NOD-like receptor-mediated immune response plays an essential role in hypoxia tolerance and resistance in hybrid yellow catfish. Our results provide novel insights into which immune-related genes and pathways are activated under hypoxic stress, and reveal details of early adaptation of the immune response and defense mechanisms under hypoxic stress.

Genetics Responses to Hypoxia and Reoxygenation Stress in Larimichthys crocea Revealed via Transcriptome Analysis and Weighted Gene Co-Expression Network

Simple Summary

Hypoxia, which occurs frequently in aquaculture, can cause serious harm to all aspects of the growth, reproduction and metabolism of cultured fish. Due to the intolerance of Larimichthys crocea to hypoxia, Larimichthys crocea often floats head or even dies under hypoxic environment. However, the molecular mechanism of hypoxia tolerance in Larimichthys crocea has not been fully described. Therefore, the aim of this study was to explore the hub regulatory genes under hypoxic stress environment by transcriptome analysis of three key tissues (liver, blood and gill) in Larimichthys crocea. We identified a number of important genes that exercise different regulatory functions. Overall, this study will provide important clues to the molecular mechanisms of hypoxia tolerance in Larimichthys crocea.

Abstract

The large yellow croaker (Larimichthys crocea) is an important marine economic fish in China; however, its intolerance to hypoxia causes widespread mortality. To understand the molecular mechanisms underlying hypoxia tolerance in L. crocea, the transcriptome gene expression profiling of three different tissues (blood, gills, and liver) of L. crocea exposed to hypoxia and reoxygenation stress were performed. In parallel, the gene relationships were investigated based on weighted gene co-expression network analysis (WGCNA). Accordingly, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that several pathways (e.g., energy metabolism, signal transduction, oxygen transport, and osmotic regulation) may be involved in the response of L. crocea to hypoxia and reoxygenation stress. In addition, also, four key modules (darkorange, magenta, saddlebrown, and darkolivegreen) that were highly relevant to the samples were identified by WGCNA. Furthermore, some hub genes within the association module, including RPS16, EDRF1, KCNK5, SNAT2, PFKL, GSK-3β, and PIK3CD, were found. This is the first study to report the co-expression patterns of a gene network after hypoxia stress in marine fish. The results provide new clues for further research on the molecular mechanisms underlying hypoxia tolerance in L. crocea.

Comparative transcriptomic analysis of the brain in Takifugu rubripes shows its tolerance to acute hypoxia

Hypoxia in water that caused by reduced levels of oxygen occurred frequently, due to the complex aquatic environment. Hypoxia tolerance for fish depends on a complete set of coping mechanisms such as oxygen perception and gene-protein interaction regulation. The present study examined the short-term effects of hypoxia on the brain in Takifugu rubripes. We sequenced the transcriptomes of the brain in T. rubripes to study their response mechanism to acute hypoxia. A total of 167 genes were differentially expressed in the brain of T. rubripes after exposed to acute hypoxia. Gene ontology and KEGG enrichment analysis indicated that hypoxia could cause metabolic and neurological changes, showing the clues of their adaptation to acute hypoxia. As the most complex and important organ, the brain of T. rubripes might be able to create a self-protection mechanism to resist or reduce damage caused by acute hypoxia stress.

Transcriptome sequencing provides insights into the mechanism of hypoxia adaption in bighead carp (Hypophthalmichthys nobilis)

Hypoxia negatively affects the behavior, immunology, physiology, and growth of fish. Therefore, uncovering the genetic mechanisms underlying hypoxia adaptation and tolerance in fish prior to any genetic improvement is essential. Bighead carp is one of the most important freshwater fish species in aquaculture worldwide; however, this species does not have a strong ability to tolerate hypoxia. In this study, the dissolved oxygen level (0.6 mg/L) was maintained above the asphyxiation point of bighead carp for a long time to simulate hypoxia stress. The liver, gills, and heart were sampled before (0 h) and after (1 h, 2 h, 4 h) the hypoxia tests. Glutathione peroxidase (GPx) and catalase (CAT) activities and malondialdehyde (MDA) levels in the liver were significantly (p < 0.05) elevated at 1 h after hypoxic stress. By observing tissue morphology, the cell structure of the liver and gill tissues was found to change to varying degrees before and after hypoxia stress. Transcriptome sequencing was performed on 36 samples of gill, liver, and heart at four time points, and a total of 293.55G of data was obtained. In the early phase (0-1 h), differentially expressed genes (DEGs, 807 genes upregulated, 654 genes downregulated) were mainly enriched in signal transduction, such as cytokine-cytokine receptor interactions and ECM-receptor interactions. In the middle phase (0-2 h), DEGs (1201 genes upregulated and 2036 genes downregulated) were mainly enriched in regulation and adaptation, such as the MAPK and FoxO signaling pathways. Finally, in the later phase (0-4 h), DEGs (3975 genes upregulated and 4412 genes downregulated) were mainly enriched in tolerance and apoptosis, such as the VEGF signaling pathway and apoptosis. The genes with the most remarkable upregulation at different time points in the three tissues had some similarities. Genetic differences in these genes may be responsible for the differences in hypoxia tolerance among individuals. Altogether, our study provides new insights into the molecular mechanisms of hypoxia adaptation in fish. Further, the key regulatory genes identified provide genetic resources for breeding hypoxia-tolerant bighead carp species.

Histopathological, hematological, and biochemical changes in high-latitude fish Phoxinus lagowskii exposed to hypoxia

Hypoxia is one of the most significant threats to biodiversity in aquatic systems. The ability of high-latitude fish to tolerate hypoxia with histological and physiological responses is mostly unknown. We address this knowledge gap by investigating the effects of exposures to different oxygen levels using Phoxinus lagowskii (a high-latitude, cold-water fish) as a model. Fish were exposed to different oxygen levels (0.5 mg/L and 3 mg/L) for 24 h. The loss of equilibrium (LOE), an indicator of acute hypoxia tolerance, was 0.21 ± 0.01 mg/L, revealing the ability of fish to tolerate low-oxygen conditions. We sought to determine if, in P. lagowskii, the histology of gills and liver, blood indicators, enzyme activities of carbohydrate and lipid metabolism, and antioxidants changed to relieve stress in response to acute hypoxia. Notably, changes in vigorous jumping behavior under low oxygen revealed the exceptional hypoxia acclimation response compared with other low-latitude fish. A decrease in blood parameters, including RBC, WBC, and Hb, as well as an increase in MCV was observed compared to the controls. The increased total area in lamella and decreased ILCM volume in P. lagowskii gills were detected in the present study. Our results also showed the size of vacuoles in the livers of the hypoxic fish shrunk. Interestingly, an increase in the enzyme activity of lipid metabolism but not glucose metabolism was observed in the groups exposed to hypoxia at 6 h and 24 h. After combining histology and physiology results, our findings provide evidence that lipid metabolism plays a crucial role in enhancing hypoxia acclimation in P. lagowskii. Additionally, SOD activity significantly increased during hypoxia, suggesting the presence of an antioxidant response of P. lagowskii during hypoxia. High expression levels of lipogenesis and lipolysis-related genes were detected in the 6 h 3 mg/L and 24 h 3 mg/L hypoxia group. Enhanced expression of lipid-metabolism genes (ALS4, PGC-1, and FASN) was detected during hypoxia exposure. Together, these data suggest that P. lagowskii's ability to tolerate hypoxic events is likely mediated by a comprehensive strategy.

Comparison of effects in sustained and diel-cycling hypoxia on hypoxia tolerance, histology, physiology and expression of clock genes in high latitude fish Phoxinus lagowskii

Phoxinus lagowskii is a popular fish in Chinese cuisine. Though it is found mainly in China's high-latitude regions, where diel-cycling hypoxia (DCH) is known to have unique impacts on aquatic organisms, there is little known about its response to hypoxia. Currently, nothing is known about the changes in blood parameters, gill and liver morphology, glucose and lipid metabolism, or expression of genes involved in clock and glucose metabolism in response to sustained hypoxia (SH) and diel-cycling hypoxia (DCH). To elucidate the influence of sustained and diel-cycling hypoxia on fish hypoxia tolerance, resting oxygen consumption (MO₂) analysis was performed after ten days of hypoxia. This analysis revealed that hypoxia tolerance profoundly improved after ten days of either sustained or diel-cycling hypoxia acclimation, with DCH groups showing greater improvements than SH groups. Additionally, an increase in RBCs was found in P. lagowskii, suggesting an increase in the O₂-carrying capacity of the blood to tolerate hypoxia. Hemoglobin (Hb) concentrations in P. lagowskii were increased at four days of diel-cycling hypoxia, confirming that physiological and metabolic adaptation to hypoxia is based on the duration of O₂ exposure. Increased Hb and hematocrit (Hct) were found in DCH-exposed fish, both of which have been directly linked to high-latitude hypoxia tolerance. In the gills, lamella surface area increased in SH-exposed fish more than DCH-exposed fish, and these increases were accompanied by a decrease in the volume of interlamellar cell mass (ILCM). Histology changes in the liver showed a higher frequency of cytoplasmic vacuolization in DCH-exposed fish. PK increases in SH-exposed fish suggest that fish can use more energy sources in persistent hypoxia. Meanwhile, DCH-exposed fish use TG as an energy source. In SH-exposed fish, self-regulation of Cry1a was observed, whereas Cry1b gene was up-regulated significantly. In DCH-exposed fish, three of eight clock genes studied had increased expression, including Per1a, Clocka, and Cry1b, suggesting that SH and DCH result in different hypoxic responses. This study presents a novel approach to the study of fish responses to hypoxia in high latitude and shows that sustained hypoxia and diel-cycling hypoxia induce large differences in fish physiology.

Multi-omics analysis reveals the glycolipid metabolism response mechanism in the liver of genetically improved farmed Tilapia (GIFT, Oreochromis niloticus) under hypoxia stress

BACKGROUND

Dissolved oxygen (DO) in the water is a vital abiotic factor in aquatic animal farming. A hypoxic environment affects the growth, metabolism, and immune system of fish. Glycolipid metabolism is a vital energy pathway under acute hypoxic stress, and it plays a significant role in the adaptation of fish to stressful environments. In this study, we used multi-omics integrative analyses to explore the mechanisms of hypoxia adaptation in Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus).

RESULTS

The 96 h median lethal hypoxia (96 h-LH50) for GIFT was determined by linear interpolation. We established control (DO: 5.00 mg/L) groups (CG) and hypoxic stress (96 h-LH50: 0.55 mg/L) groups (HG) and extracted liver tissues for high-throughput transcriptome and metabolome sequencing. A total of 581 differentially expressed (DE) genes and 93 DE metabolites were detected between the CG and the HG. Combined analyses of the transcriptome and metabolome revealed that glycolysis/gluconeogenesis and the insulin signaling pathway were down-regulated, the pentose phosphate pathway was activated, and the biosynthesis of unsaturated fatty acids and fatty acid metabolism were up-regulated in GIFT under hypoxia stress.

CONCLUSIONS

The results show that lipid metabolism became the primary pathway in GIFT under acute hypoxia stress. Our findings reveal the changes in metabolites and gene expression that occur under hypoxia stress, and shed light on the regulatory pathways that function under such conditions. Ultimately, this information will be useful to devise strategies to decrease the damage caused by hypoxia stress in farmed fish.

Transcriptome analysis of genes and pathways associated with metabolism in Scylla paramamosain under different light intensities during indoor overwintering

Background

Scylla paramamosain is one of the commercially crucial marine crustaceans belonging to the genus Scylla, which is commonly distributed along the coasts of China, Vietnam, and Japan. Genomic and transcriptomic data are scarce for the mud crab. Light intensity is one of the ecological factors that affect S. paramamosain during indoor overwintering. To understand the energy metabolism mechanism adapted to light intensity, we analyzed the transcriptome of S. paramamosain hepatopancreas in response to different light intensities (0, 1.43, 40.31 μmol·m^− 2·s^− 1).

Results

A total of 5052 differentially expressed genes were identified in low light group (LL group, 3104 genes were up-regulated and 1948 genes were down-regulated). A total of 7403 differentially expressed genes were identified in high light group (HL group, 5262 genes were up-regulated and 2141 genes were down-regulated). S. paramamosain adapts to different light intensity environments through the regulation of amino acids, fatty acids, carbon and energy metabolism. Different light intensities had a strong impact on the energy generation of S. paramamosain by influencing oxygen consumption rate, aerobic respiration, glycolysis/gluconeogenesis pathway, the citrate cycle (TCA cycle) and fatty acid degradation.

Conclusion

Low light is more conducive to the survival of S. paramamosain, which needs to produce and consume relatively less energy to sustain physiological activities. In contrast, S. paramamosain produced more energy to adapt to the pressure of high light intensities. The findings of the study add to the knowledge of regulatory mechanisms related to S. paramamosain metabolism under different light intensities.

Supplementary Information

Supplementary information accompanies this paper at 10.1186/s12864-020-07190-w.

Hepatopancreas Transcriptome Profiling Analysis Reveals Physiological Responses to Acute Hypoxia and Reoxygenation in Juvenile Qingtian Paddy Field Carp Cyprinus carpio var qingtianensis

The Qingtian paddy field carp (Cyprinus carpio var qingtianensis) is a local carp cultivated in the rice field of Qingtian county, Zhejiang province, China. Its high tolerance to hypoxia makes it an ideal organism for studying the molecular regulation mechanism during hypoxia process as well as reoxygenation following hypoxia in fish. In this study, we counted the differentially expressed genes (DEGs) altered during hypoxic exposure and reoxygenation process. The results indicated that 2236 genes (1506 up-regulated genes and 730 down-regulated genes) were differentially expressed between the control and hypoxic groups. The results from Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that 1152 of 2236 genes were enriched, and those genes participated in energy metabolism, reactive oxygen species (ROS) elimination, acceleration of cell apoptosis, inhibition of growth, and other processes. We found activation of the pentose phosphate pathway in hypoxia treatment, suggesting that carbohydrates not only provide energy for metabolism but also provide NADPH for protecting the body from oxidative damage and ribosomes for promoting RNA synthesis. During reoxygenation, 4509 genes (1865 up-regulated genes and 2644 down-regulated genes) were differentially expressed. The results of KEGG enrichment analysis indicated that 2392 of 4509 genes were enriched, and participated in pyruvate and lactic acid metabolism, synthesis of amino acids and lipids, inhibition of cell apoptosis, regulation of cell growth and differentiation, and other processes. These differentially expressed genes effectively alleviate the body acidosis and promote the normal growth and development of the body. Through the analysis of KEGG pathway enrichment, we observed that the physiological regulation of Qingtian paddy field carp during the processes of hypoxia and reoxygenation is not a simple and reversible process. This work first reported the adaptive mechanism of hypoxia and the recovery mechanism of reoxygenation after hypoxia in common carp, and also provided new insights for the physiological regulation of fish under hypoxia treatment.