Transgenerational regulation of cbln11 gene expression in the olfactory rosette of the European sea bass (Dicentrarchus labrax) exposed to ocean acidification

Integrated transcriptome and microRNA analysis reveals molecular responses to high-temperature stress in the liver of American shad (Alosa sapidissima)

BACKGROUND

Fish reproduction, development and growth are directly affected by temperature, investigating the regulatory mechanisms behind high temperature stress is helpful to construct a finer molecular network. In this study, we systematically analyzed the transcriptome and miRNA information of American shad (Alosa sapidissima) liver tissues at different cultivation temperatures of 24 ℃ (Low), 27 ℃ (Mid) and 30 ℃ (High) based on a high-throughput sequencing platform.

RESULTS

The results showed that there were 1594 differentially expressed genes (DEGs) and 660 differentially expressed miRNAs (DEMs) in the LowLi vs. MidLi comparison group, 473 DEGs and 84 DEMs in the MidLi vs. HighLi group, 914 DEGs and 442 DEMs in the LowLi vs. HighLi group. These included some important genes and miRNAs such as calr, hsp90b1, hsp70, ssa-miR-125a-3p, ssa-miR-92b-5p, dre-miR-15a-3p and novel-m1018-5p. The DEGs were mainly enriched in the protein folding, processing and export pathways of the endoplasmic reticulum; the target genes of the DEMs were mainly enriched in the focal adhesion pathway. Furthermore, the association analysis revealed that the key genes were mainly enriched in the metabolic pathway. Interestingly, we found a significant increase in the number of genes and miRNAs involved in the regulation of heat stress during the temperature change from 24 °C to 27 °C. In addition, we examined the tissue expression characteristics of some key genes and miRNAs by qPCR, and found that calr, hsp90b1 and dre-miR-125b-2-3p were significantly highly expressed in the liver at 27 ℃, while novel-m0481-5p, ssa-miR-125a-3p, ssa-miR-92b-5p, dre-miR-15a-3p and novel-m1018-5p had the highest expression in the heart at 30℃. Finally, the quantitative expression trends of 10 randomly selected DEGs and 10 DEMs were consistent with the sequencing data, indicating the reliability of the results.

CONCLUSIONS

In summary, this study provides some fundamental data for subsequent in-depth research into the molecular regulatory mechanisms of A. sapidissima response to heat stress, and for the selective breeding of high temperature tolerant varieties.

Ocean acidification alters the acute stress response of a marine fish

The absorption of anthropogenic carbon dioxide from the atmosphere by oceans generates rapid changes in seawater carbonate system and pH, a process termed ocean acidification. Exposure to acidified water can impact the allostatic load of marine organism as the acclimation to suboptimal environments requires physiological adaptive responses that are energetically costly. As a consequence, fish facing ocean acidification may experience alterations of their stress response and a compromised ability to cope with additional stress, which may impact individuals' life traits and ultimately their fitness. In this context, we carried out an integrative study investigating the impact of ocean acidification on the physiological and behavioral stress responses to an acute stress in juvenile European sea bass. Fish were long term (11 months) exposed to present day pH/CO₂ condition or acidified water as predicted by IPCC "business as usual" (RCP8.5) scenario for 2100 and subjected to netting stress (fish transfer and confinement test). Fish acclimated to acidified condition showed slower post stress return to plasma basal concentrations of cortisol and glucose. We found no clear indication of regulation in the central and interrenal tissues of the expression levels of gluco- and mineralocorticoid receptors and corticoid releasing factor. At 120 min post stress, sea bass acclimated to acidified water had divergent neurotransmitters concentrations pattern in the hypothalamus (higher serotonin levels and lower GABA and dopamine levels) and a reduction in motor activity. Our experimental data indicate that ocean acidification alters the physiological response to acute stress in European sea bass via the neuroendocrine regulation of the corticotropic axis, a response associated to an alteration of the motor behavioral profile. Overall, this study suggests that behavioral and physiological adaptive response to climate changes related constraints may impact fish resilience to further stressful events.

Transgenerational inheritance of wing development defects in Drosophila melanogaster induced by cadmium

The transgenerational inheritance of phenotype induced by environmental factors is a new focus in epigenetic research. In this study, Drosophila melanogaster (F₀) was cultured in the medium containing cadmium (Cd, 4.5 mg/kg) from eggs to adults, and offspring (F₁-F₄) were continuously kept in standard medium (without cadmium). The phenotype analysis showed that cadmium induced developmental defects on wings and apoptosis in the wing disc cells of Drosophila (F₀). The wing defects were transmitted for at least four generations even without Cd afterwards. And the effect on the mRNA expression of wing development related genes (shg, omb, F-actin, Mekk1) can be maintained for at least two or three generations. More importantly, under cadmium stress, the post-translational modification (PTM) on the histones H3K4me3 in the third instar larvae and ovaries or testes of adult flies increased significantly, while the levels of H3K9me3 and H3K27me3 decreased significantly. The expression of histone methylation related genes (dSet-1, ash1, Lsd1) increased significantly and these changes can be transmitted to offspring from one or two generations in ovaries or testes. These results suggest that the phenotypic defects of wings caused by cadmium can be inherited to the offspring, and this transgenerational inheritance effect may be related to the epigenetic regulation of histone methylation. Therefore, the adaptability of offspring should be considered when evaluating the toxicity and environmental risk of cadmium.

The extensive transgenerational transcriptomic effects of ocean acidification on the olfactory epithelium of a marine fish are associated with a better viral resistance

Background

Progressive CO₂-induced ocean acidification (OA) impacts marine life in ways that are difficult to predict but are likely to become exacerbated over generations. Although marine fishes can balance acid–base homeostasis efficiently, indirect ionic regulation that alter neurosensory systems can result in behavioural abnormalities. In marine invertebrates, OA can also affect immune system function, but whether this is the case in marine fishes is not fully understood. Farmed fish are highly susceptible to disease outbreak, yet strategies for overcoming such threats in the wake of OA are wanting. Here, we exposed two generations of the European sea bass (Dicentrarchus labrax) to end-of-century predicted pH levels (IPCC RCP8.5), with parents (F1) being exposed for four years and their offspring (F2) for 18 months. Our design included a transcriptomic analysis of the olfactory rosette (collected from the F2) and a viral challenge (exposing F2 to betanodavirus) where we assessed survival rates.

Results

We discovered transcriptomic trade-offs in both sensory and immune systems after long-term transgenerational exposure to OA. Specifically, RNA-Seq analysis of the olfactory rosette, the peripheral olfactory organ, from 18-months-old F2 revealed extensive regulation in genes involved in ion transport and neuronal signalling, including GABAergic signalling. We also detected OA-induced up-regulation of genes associated with odour transduction, synaptic plasticity, neuron excitability and wiring and down-regulation of genes involved in energy metabolism. Furthermore, OA-exposure induced up-regulation of genes involved in innate antiviral immunity (pathogen recognition receptors and interferon-stimulated genes) in combination with down-regulation of the protein biosynthetic machinery. Consistently, OA-exposed F2 challenged with betanodavirus, which causes damage to the nervous system of marine fish, had acquired improved resistance.

Conclusion

F2 exposed to long-term transgenerational OA acclimation showed superior viral resistance, though as their metabolic and odour transduction programs were altered, odour-mediated behaviours might be consequently impacted. Although it is difficult to unveil how long-term OA impacts propagated between generations, our results reveal that, across generations, trade-offs in plastic responses is a core feature of the olfactory epithelium transcriptome in OA-exposed F2 offspring, and will have important consequences for how cultured and wild fish interacts with its environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08647-w.

Transcriptomic profiling of clobetasol propionate-induced immunosuppression in challenged zebrafish embryos

In the ecotoxicological hazard assessment of chemicals, the detection of immunotoxicity is currently neglected. This is mainly due to the complexity of the immune system and the consequent lack of standardized procedures and markers for the comprehensive assessment of immunotoxic modes of action. In this study, we present a new approach applying transcriptome profiling to an immune challenge with a mixture of pathogen-associated molecular patterns (PAMPs) in zebrafish embryos, analyzing differential gene expression during acute infection with and without prior exposure to the immunosuppressive drug clobetasol propionate (CP). While PAMP injection itself triggered biological processes associated with immune activation, some of these genes were more differentially expressed upon prior exposure to CP than by immune induction alone, whereas others showed weaker or no differential regulation in response to the PAMP stimulus. All of these genes responding differently to PAMP after prior CP exposure showed additivity of PAMP- and CP-induced effects, indicating independent regulatory mechanisms. The transcriptomic profiles suggest that CP impaired innate immune induction by attenuating the response of genes involved in antigen processing, TLR signaling, NF-КB signaling, and complement activation. We propose this approach as a powerful method for detecting gene biomarkers for immunosuppressive modes of action, as it was able to identify alternatively regulated processes and pathways in a sublethal, acute infection zebrafish embryo model. This allowed to define biomarker candidates for immune-mediated effects and to comprehensively characterize immunosuppression. Ultimately, this work contributes to the development of molecular biomarker-based environmental hazard assessment of chemicals in the future.

Effect of long-term intergenerational exposure to ocean acidification on ompa and ompb transcripts expression in European seabass (Dicentrarchus labrax)

Since sensory system allows organisms to perceive and interact with their external environment, any disruption in their functioning may have detrimental consequences on their survival. Ocean acidification has been shown to potentially impair olfactory system in fish and it is therefore essential to develop biological tools contributing to better characterize such effects. The olfactory marker protein (omp) gene is involved in the maturation and the activity of olfactory sensory neurons in vertebrates. In teleosts, two omp genes (ompa and ompb) originating from whole genome duplication have been identified. In this study, bioinformatic analysis allowed characterization of the ompa and ompb genes from the European seabass (Dicentrarchus labrax) genome. The European seabass ompa and ompb genes differ in deduced amino acid sequences and in their expression pattern throughout the tissues. While both ompa and ompb mRNA are strongly expressed in the olfactory epithelium, ompb expression was further observable in different brain areas while ompa expression was also detected in the eyes and in other peripheral tissues. Expression levels of ompa and ompb mRNA were investigated in adult seabass (4 years-old, F0) and in their offspring (F1) exposed to pH of 8 (control) or 7.6 (ocean acidification, OA). Under OA ompb mRNA was down-regulated while ompa mRNA was up-regulated in the olfactory epithelium of F0 adults, suggesting a long-term intragenerational OA-induced regulation of the olfactory sensory system. A shift in the expression profiles of both ompa and ompb mRNA was observed at early larval stages in F1 under OA, suggesting a disruption in the developmental process. Contrary to the F0, the expression of ompa and ompb mRNA was not anymore significantly regulated under OA in the olfactory epithelium of juvenile F1 fish. This work provides evidence for long-term impact of OA on sensorial system of European seabass as well as potential intergenerational acclimation of omp genes expression to OA in European seabass.