Global-warming-caused changes of temperature and oxygen alter the proteomic profile of sea cucumber Apostichopus japonicus

Sea cucumber physiological response to abiotic stress: Emergent contaminants and climate change

The ocean is facing a multitude of abiotic stresses due to factors such as climate change and pollution. Understanding how organisms in the ocean respond to these global changes is vital to better predicting consequences. Sea cucumbers are popular echinoderms with multiple ecological, nutritional, and pharmaceutical benefits. Here, we reviewed the effects of environmental change on an ecologically important echinoderm of the ocean, aiming to understand their response better, which could facilitate healthy culture programs under environmental changes and draw attention to knowledge gaps. After screening articles from the databases, 142 studies were included on the influence of emergent contaminants and climate variation on the early developmental stages and adults of sea cucumbers. We outlined the potential mechanism underlying the physiological response of sea cucumbers to emerging contaminants and climate change. It can be concluded that the physiological response of sea cucumbers to emergent contaminants differs from their response to climate change. Sea cucumbers could accumulate pollutants in their organs but are aestivated when exposed to extreme climate change. Research showed that the physiological response of sea cucumbers to pollutants indicates that these pollutants impair critical physiological processes, particularly during the more susceptible early phases of development compared to adults, and the accumulation of these pollutants in adults is often observed. For climate change, sea cucumbers showed gradual adaptation to the slight variation. However, sea cucumbers undergo aestivation under extreme conditions. Based on this review, critical suggestions for future research are presented, and we call for more efforts focusing on the co-occurrence of different stressors to extend the knowledge regarding the effects of environmental changes on these economically and ecologically important species.

Dietary steroids promote body weight growth and induce gametogenesis by increasing the expressions of genes related to cell proliferation of sea cucumber (Apostichopus japonicus)

Steroids play a vital role in animal survival, promoting growth and development when administered appropriate concentration exogenously. However, it remains unclear whether steroids can induce gonadal development and the underlying mechanism. This study assessed sea cucumber weights post-culturing, employing paraffin sections and RNA sequencing (RNA-seq) to explore gonadal changes and gene expression in response to exogenous steroid addition. Testosterone and cholesterol, dissolved in absolute ethanol, were incorporated into sea cucumber diets. After 30 days, testosterone and cholesterol significantly increased sea cucumber weights, with the total weight of experimental groups surpassing the control. The testosterone-fed group exhibited significantly higher eviscerated weight than the control group. In addition, dietary steroids influenced gonad morphology and upregulated genes related to cell proliferation，such as RPL35, PC, eLF-1, MPC2, ADCY10 and CYP2C18. Thees upregulated differentially expressed genes were significantly enriched in the organic system, metabolism, genetic information and environmental information categories. These findings imply that steroids may contribute to the growth and the process of genetic information translation and protein synthesis essential for gonadal development and gametogenesis.

Alterations in mitochondrial structure and function in response to environmental temperature changes in Apostichopus japonicus

Global temperatures have risen as a result of climate change, and the resulting warmer seawater will exert physiological stresses on many aquatic animals, including Apostichopus japonicus. It has been suggested that the sensitivity of aquatic poikilothermal animals to climate change is closely related to mitochondrial function. Therefore, understanding the interaction between elevated temperature and mitochondrial functioning is key to characterizing organisms' responses to heat stress. However, little is known about the mitochondrial response to heat stress in A. japonicus. In this work, we investigated the morphological and functional changes of A. japonicus mitochondria under three representative temperatures, control temperature (18 °C), aestivation temperature (25 °C) and heat stress temperature (32 °C) temperatures using transmission electron microscopy (TEM) observation of mitochondrial morphology combined with proteomics and metabolomics techniques. The results showed that the mitochondrial morphology of A. japonicus was altered, with decreases in the number of mitochondrial cristae at 25 °C and mitochondrial lysis, fracture, and vacuolization at 32 °C. Proteomic and metabolomic analyses revealed 103 differentially expressed proteins and 161 differential metabolites at 25 °C. At 32 °C, the levels of 214 proteins and 172 metabolites were significantly altered. These proteins and metabolites were involved in the tricarboxylic acid (TCA) cycle, substance transport, membrane potential homeostasis, anti-stress processes, mitochondrial autophagy, and apoptosis. Furthermore, a hypothetical network of proteins and metabolites in A. japonicus mitochondria in response to temperature changes was constructed based on proteomic and metabolomic data. These results suggest that the dynamic regulation of mitochondrial energy metabolism, resistance to oxidative stress, autophagy, apoptosis, and mitochondrial morphology in A. japonicus may play important roles in the response to elevated temperatures. In summary, this study describes the response of A. japonicus mitochondria to temperature changes from the perspectives of morphology, proteins, and metabolites, which provided a better understanding the mechanisms of mitochondrial regulation under environment stress in marine echinoderms.

Integrated transcriptomic and metabolomic analysis reveals the response of pearl oyster (Pinctada fucata martensii) to long-term hypoxia

The frequency at which organisms are exposed to hypoxic conditions in aquatic environments is increasing due to coastal eutrophication and global warming. To reveal the effects of long-term hypoxic stress on metabolic changes of pearl oyster, commonly known as Pinctada (Pinctada fucata martensii), the present study performed the integrated analysis of transcriptomics and metabolomics to investigate the global changes of genes and metabolites following 25 days hypoxia challenge. Transcriptome analysis detected 1108 differentially expressed genes (DEGs) between the control group and the hypoxia group. The gene ontology (GO) analysis of DEGs revealed that they are significantly enriched in functions such as "microtubule-based process", "histone (H3-K4, H3-K27, and H4-K20) trimethylation", "histone H4 acetylation", "kinesin complex", and "ATPase activity", and KEGG pathway functions, such as "DNA replication", "Apoptosis", and "MAPK signaling pathways". Metabolome analysis identified 68 significantly different metabolites from all identified metabolites, and associated with 25 metabolic pathways between the control and hypoxia groups. These pathways included aminoacyl-tRNA biosynthesis, arginine and proline metabolism, and phenylalanine metabolism. Our integrated analysis suggested that pearl oysters were subject to oxidative stress, apoptosis, immune inhibition, and neuronal excitability reduction under long-term hypoxic conditions. We also found a remarkable depression in a variety of biological functions under long-term hypoxia, including metabolic rates, biomineralization activities, and the repression of reorganization of the cytoskeleton and cell metabolism. These findings provide a basis for elucidating the mechanisms used by marine bivalves to cope with long-term hypoxic stress.

Comparative proteomic and phosphoproteomic analysis reveals differential heat response mechanism in two congeneric oyster species

High-temperature stress caused by global climate change poses a significant threat to marine ectotherms. This study investigated the role of protein phosphorylation modifications in the molecular regulation network under heat stress in oysters, which are representative intertidal organisms that experience considerable temperature changes. Firstly, the study compared the extent of thermal damage between two congeneric oyster species, the relative heat-tolerant Crassostrea angulata (C. angulata) and heat-sensitive Crassostrea gigas (C. gigas), under sublethal temperature (37 °C) for 12 h, using various physiological and biochemical methods. Subsequently, the comparative proteomic and phosphoproteomic analyses revealed that high-temperature considerably regulated signal transduction, energy metabolism, protein synthesis, cell survival and apoptosis, and cytoskeleton remodeling through phosphorylation modifications of related receptors and kinases. Furthermore, the protein kinase A, mitogen-activated protein kinase 1, tyrosine-protein kinase Src, and serine/threonine kinase AKT, exhibiting differential phosphorylation modification patterns, were identified as hub regulators that may enhance glycolysis and TCA cycle to increase the energy supply, distribute protein synthesis, inhibit Caspase-dependent apoptosis activated by endogenous mitochondrial cytochrome release and maintain cytoskeletal stability, ultimately shaping the higher thermal resistance of C. angulata. This study represents the first investigation of protein phosphorylation dynamics in marine invertebrates under heat stress, reveals the molecular mechanisms underlying the differential thermal responses between two Crassostrea oysters at the phosphorylation level, and provides new insights into understanding phosphorylation-mediated molecular responses in marine organisms during environmental changes and predicting the adaptive potential in the context of global warming.

Living in a hypoxic world: A review of the impacts of hypoxia on aquaculture

Hypoxia is a harmful result of anthropogenic climate change. With the expansion of global low-oxygen zones (LOZs), many organisms have faced unprecedented challenges affecting their survival and reproduction. Extensive research has indicated that oxygen limitation has drastic effects on aquatic animals, including on their development, morphology, behavior, reproduction, and physiological metabolism. In this review, the global distribution and formation of LOZs were analyzed, and the impacts of hypoxia on aquatic animals and the molecular responses of aquatic animals to hypoxia were then summarized. The commonalities and specificities of the response to hypoxia in aquatic animals in different LOZs were discussed lastly. In general, this review will deepen the knowledge of the impacts of hypoxia on aquaculture and provide more information and research directions for the development of fishery resource protection strategies.

The feces of sea urchins as food improves survival, growth, and resistance of small sea cucumbers Apostichopus japonicus in summer

Mass mortality and low growth highly decrease the production efficiency and sustainable aquaculture development of the sea cucumber Apostichopus japonicus in summer. Sea urchin feces was proposed to address the summer problems. A laboratory study was conducted for ~ 5 weeks to investigate survival, food consumption, growth and resistance ability of A. japonicus cultured with the feces of sea urchins fed kelp (KF feces, group KF), the feces of sea urchins fed prepared feed (FF feces, group FF), and the prepared sea cucumber feed (group S) at high temperature (25 °C). The sea cucumbers of group KF had better survival (100%) than those of the group FF (~ 84%), higher CT_max (35.9 °C) than those of the group S (34.5 °C), and the lowest skin ulceration proportion (0%) when  they were exposed to an infectious solution among the three groups. These results suggest that the feces of sea urchins fed kelp is a promising diet for improving the survival and enhancing the resistance in A. japonicus aquaculture in summer. Sea cucumbers fed significantly less FF feces after 24 h of ageing than the fresh FF feces, suggesting this kind of feces became unsuitable for A. japonicus in a short time (within 48 h). However, the 24 h of ageing at 25 °C for the high fiber feces of sea urchins fed kelp had no significant effects on the fecal consumption of sea cucumbers. In the present study, both fecal diets provide better individual growth to sea cucumbers than the prepared feed. Yet, the feces of sea urchins fed kelp provided the highest weight gain rate (WGR) to sea cucumbers. Therefore, the feces of sea urchins fed kelp is a promising food to reduce the mortality, to address the problems of summer, and to achieve higher efficiency in A. japonicus aquaculture in summer.

Integrated transcriptomic and metabolomic analysis sheds new light on adaptation of Pinctada fucata martensii to short-term hypoxic stress

Analyses of the transcriptome and metabolome were conducted to clarify alterations of key genes and metabolites in pearl oysters following exposure to short-term hypoxic treatment. We totally detected 209 DEGs between the control and hypoxia groups. Enrichment analysis indicated the enrichment of GO terms including "oxidation-reduction process", "ECM organization", "chaperone cofactor-dependent protein refolding", and "ECM-receptor interaction" KEGG pathway by the DEGs. In addition, between the two groups, a total of 28 SDMs were identified, which were implicated in 13 metabolic pathways, such as "phenylalanine metabolism", "D-amino acid metabolism", and "aminoacyl-tRNA biosynthesis". Results suggest that pearl oysters are exposed to oxidative stress and apoptosis under short-term hypoxia. Also, pearl oysters might adapt to short-term hypoxic treatment by increasing antioxidant activity, modulating immune and biomineralization activities, maintaining protein homeostasis, and reorganizing the cytoskeleton. The results of our study help unveil the mechanisms by which pearl oysters respond adaptively to short-term hypoxia.

Exosomal microRNAs regulate the heat stress response in sea cucumber Apostichopus japonicus

Exosomes are small extracellular vesicles that contain nucleic acids such as microRNAs and may participate in important biological processes. We made the initial report of exosomes from sea cucumber Apostichopus japonicus, that were classically cup-shaped and had an average size of 74.65 nm, and identified specific exosome biomarkers (HSP70, TSG101, and CD9). We explored changes in the global expression of microRNAs in exosomes from the commercially important A. japonicus under normal conditions and heat-stressed conditions for 3 and 7 d. We found that heat stress increased exosome production and modified the expression profiles of the microRNAs that they contained. Novel_mir31, novel_mir132, novel_mir26, miR-92_1, and novel_mir27 were commonly found to be differentially expressed in three comparison groups, indicating their importance in the heat stress response. The microRNA expression levels were validated by qPCR. Function analysis of the target genes of these microRNAs indicated they were involved mainly in replication and repair in the initial response of A. japonicus to heat stress exposure. Conversely, during acclimation to the high temperature conditions, the target genes of the differentially expressed microRNAs were primarily involved in metabolism adjustments. Our results will contribute to a better understanding of the regulatory roles of exosomes in sea cucumber, and provide insights into the functions of sea cucumber exosome-shuttled microRNAs against environmental stresses exacerbated by global warming.

Characterization and Expression Analysis of Regeneration-Associated Protein (Aj-Orpin) during Intestinal Regeneration in the Sea Cucumber Apostichopus japonicus

Apostichopus japonicus achieves intestinal regeneration in a short period after evisceration, and multiple genes are involved in this process. The transcriptome of A. japonicus was screened for regeneration-associated protein (Aj-Orpin), a gene that is specifically upregulated during intestinal regeneration. The expression and function of Aj-Orpin were identified and investigated in this study. The 5′ and 3′ RACE polymerase chain reaction (PCR) was used to clone the full-length cDNA of Aj-Orpin. The open reading frame codes for a 164 amino-acid protein with an EF-hand_7 domain and overlapping signal peptides and transmembrane regions. Moreover, Aj-Orpin mRNA and protein expression during intestinal regeneration was investigated using real-time quantitative PCR and Western blot. The expression pattern of Aj-Orpin in the regenerating intestine was investigated using immunohistochemistry. The results showed that Aj-Orpin is an exocrine protein with two EF-hand-like calcium-binding domains. Expression levels were higher in the regenerating intestine than in the normal intestine, but protein expression changes lagged behind mRNA expression changes. Aj-Orpin was found to play a role in the formation of blastema and lumen. It was primarily expressed in the serosal layer and submucosa, suggesting that it might be involved in proliferation. These observations lay the foundation for understanding the role of Orpin-like in echinoderm intestinal regeneration.

Heat stress and evisceration caused lipid metabolism and neural transduction changes in sea cucumber: Evidence from metabolomics

When encountering adverse environmental conditions, some holothurians can eject their internal organs in a process called evisceration. As global warming intensified, eviscerated and intact sea cucumbers both experience heat stress, but how they performed was uncertain. We constructed 24 metabolomics profiles to reveal the metabolite changes of eviscerated and intact sea cucumbers under normal and high temperature conditions, respectively. Carboxylic acids and fatty acyls were the most abundant metabolic categories in evisceration and heat stress treatments, respectively. Neural transduction was involved in sea cucumber evisceration and stress response, and the commonly enriched pathway was "neuroactive ligand-receptor interaction". Lipid metabolism in eviscerated sea cucumbers differed from those of intact individuals and was more seriously affected by heat stress. Choline is a key metabolite for revealing the evisceration mechanism. Our results contribute to understanding the mechanisms of evisceration in sea cucumbers, and how sea cucumbers might respond to increasingly warming ocean conditions.

Genome-wide analysis of the hard clam mitogen-activated protein kinase kinase gene family and their transcriptional profiles under abiotic stress

Mitogen-activated protein kinase kinase (MAPKK) was the hub component of the Mitogen-activated protein kinase (MAPK) signaling pathway and played an important role in the cellular response to environmental stress. In this study, we identified five MmMAPKK genes in hard clam Mercenaria mercenaria and found that all MmMAPKK genes contain a conserved protein kinase domain. The MmMAPKK genes derived from dispersed duplication were unevenly distributed in three chromosomes. Although the genome size was highly variable among different bivalve mollusks, the number of MAPKK genes was relatively stable. Phylogenetic analysis showed that bivalve MAPKK was divided into five clades, and amino acid sequences of MAPKK from the same clade consisted of similar conserved motifs. The syntenic analysis demonstrated that MmMAPKKs had the highest number of homologous gene pairs with Cyclina sinensis. MmMAPKKs were ubiquitously expressed in all examined tissues, and all MmMAPKK genes were highly expressed in the ovary. MmMAPKK genes showed stress-specific expression under envirionmental stress. MmMAPKK7 showed an upregulated in heat and heat plus hypoxia stress while MmMAPKK1 showed an upregulated in hypoxic stress groups. Dynamic changes of MmMAPKK7, MmMAPKK6 and MmMAPKK1 in hemocytes were observed in response to air exposure. MmMAPKK4 significantly downregulated after air exposure for five days. MmMAPKK7 and MmMAPKK6 might participate in adaptation to low salinity stress. Our results provided useful information about MAPKK and laid a foundation for further studies on MAPKK evolution in the bivalve.

Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)

Some sea cucumbers are economically and ecologically important, but they are threatened by thermal and hypoxic stress in changing oceanographic conditions. We construct circRNAs profiles, reveal circRNAs characters, and illustrate the potential regulatory roles of circRNAs in one commercially important species of sea cucumber, Apostichopus japonicus. Reads are distributed in intergenic (44.14%), exonic (48.26%) and intronic (7.60%) regions of the genome. A total of 1684 circRNAs were identified, and the most common spliced length is 269 nt in the present study. In three treatments (HT [thermal stress], LO [hypoxic stress], and HL [combined thermal and hypoxic stress]), 24, 27 and 27 differentially expressed (DE) circRNAs were identified, respectively. Five novel DE-circRNAs commonly occur in these treatments (novel_circ_0003311, novel_circ_0000229, novel_circ_0003944, novel_circ_0001458 and novel_circ_0000707), and based on them, potential circRNA-miRNA binding pairs were predicted. Sanger sequencing, RNase R treatment experiment and qPCR validation identified the accuracy of the circRNAs. Key circRNAs identified in the present study were covalently closed and were more stable under RNase R treatment than linear RNAs. Based on function analysis, circRNAs could regulate metabolic process, signal transduction, and ion responses in A. japonicus when exposed to thermal and hypoxic stress, and 'regulation of response to stimulus' is a common gene ontology (GO) term that is significantly enriched in each treatment; GO terms for 'DNA' and 'stress' are commonly enriched in heat-related treatments (HT and HL); and GO terms for 'protein' are commonly enriched in hypoxia-related treatments (LO and HL). When environmentally stressed, 'metabolism,' 'transport and catabolism,' 'membrane transport,' and 'signal transduction' were significantly responded in sea cucumber based on KEGG analysis. We provide insights into circRNA functions in stress regulation and lay a foundation for invertebrate circRNA research.

Combined Effects of Elevated Temperature and Crude Oil Pollution on Oxidative Stress and Apoptosis in Sea Cucumber (Apostichopus japonicus, Selenka)

Currently, global climate change and oil pollution are two main environmental concerns for sea cucumber (Apostichopus japonicus) aquaculture. However, no study has been conducted on the combined effects of elevated temperature and oil pollution on sea cucumber. Therefore, in the present study, we treated sea cucumber with elevated temperature (26 °C) alone, water-accommodated fractions (WAF) of Oman crude oil at an optimal temperature of 16 °C, and Oman crude oil WAF at an elevated temperature of 26 °C for 24 h. Results showed that reactive oxygen species (ROS) level and total antioxidant capacity in WAF at 26 °C treatment were higher than that in WAF at 16 °C treatment, as evidenced by 6.03- and 1.31-fold-higher values, respectively. Oxidative damage assessments manifested that WAF at 26 °C treatment caused much severer oxidative damage of the biomacromolecules (including DNA, proteins, and lipids) than 26 °C or WAF at 16 °C treatments did. Moreover, compared to 26 °C or WAF at 16 °C treatments, WAF at 26 °C treatment induced a significant increase in cellular apoptosis by detecting the caspase-3 activity. Our results revealed that co-exposure to elevated temperature and crude oil could simulate higher ROS levels and subsequently cause much severer oxidative damage and cellular apoptosis than crude oil alone on sea cucumber.

Molecular cloning, expression and functional analysis of NF-kB1 p105 from sea cucumber Holothuria leucospilota

The nuclear factor-κB (NF-κB) family is evolutionary conserved and plays key roles in the regulation of numerous basic cellular processes. In this study, a sea cucumber Holothuria leucospilota NF-κB1 p105 named HLp105 was first obtained. The full-length cDNA of HLp105 is 6564 bp long, with a 219 bp 5' untranslated region (UTR), a 2979 bp 3' UTR, and a 3366 bp open reading frame (ORF) encoding for 1121 amino acids with a deduced molecular weight of 123.92 kDa and an estimated pI of 5.31. HLp105 protein contains the conserved domain RHD, IPT, ANK and DEATH. HLp105 mRNA can be detected in all tissues examined, with the highest level in the intestine, followed by the transverse vessel, rete mirabile, coelomocytes, respiratory tree, bolishiti, cuvierian tubules, body wall, oesophagus and muscle. Challenged by LPS or poly (I:C), the transcription level of HLp105 was apparently up-regulated in the tissues examined. Besides, Over-expression of HLp105 in HEK293T cells, the apoptosis was inhibited, and the cytokines IL-1β and TNF-α were activated. The results are important for better understanding the function of NF-κB1 p105 in sea cucumber and reveal its involvement in immunoreaction.

Sea cucumbers in a high temperature and low dissolved oxygen world: Roles of miRNAs in the regulation of environmental stresses

The exacerbation of global warming has driven changes in environmental factors, including water temperature and oxygen concentration. The sea cucumber Apostichopus japonicus, an economically important aquatic animal, is constantly and directly challenged by heat and hypoxia. In this study, 12 small RNA libraries were constructed for this species, and a total of 21, 26 and 22 differentially expressed (DE) miRNAs were clarified in A. japonicus under thermal (26 °C), hypoxic (2 mg/L) and the combined stresses. Comparative miRNA sequencing analysis and real-time PCR were used to identify and validate the representative miRNAs, including Aja-miR-novel-299, Aja-let-7b-3p, Aja-miR-71b-5p, Aja-miR-novel-13218 and Aja-miR-2004 in response to high temperature, and Aja-miR-92b-3p, Aja-miR-210-5p and Aja-miR-novel-26331 in response to oxygen limitation. GO and KEGG pathway analysis revealed that the potential target genes of DE-miRNAs involved in biosynthesis, metabolism, immunity, cell growth and death, translation and signaling transduction. Key DE-miRNAs with potentially targeted genes associated with heat shock and hypoxia response were also determined. These results may help explaining the role of miRNA regulation in stress resistance, as well as the potential molecular regulation mechanism of the echinoderm A. japonicus in the context of global warming.

Effect of bacterial LPS, poly I:C and temperature on the immune response of coelomocytes in short term cultures of red sea urchin (Loxechinus albus)

In echinoderms, the immune system plays a relevant role in defense against infection by pathogens. Particularly, in sea urchins, the immune system has been shown to be complex, especially in terms of the variety of immune genes and molecules described. A key component of the response to external pathogens are the Toll-like receptors (TLRs), which are a well-characterized class of pattern recognition receptors (PRRs) that participate in the recognition of pathogen-associated molecular patterns (PAMPs). Despite the fact that TLRs have been described in several sea urchin species, for the red sea urchin (Loxechinus albus), which is one of the most important sea urchins across the world in terms of fisheries, limited information on the TLR-mediated immune response exists. In the present study, for the first time, we evaluated the effect of thermal stress, LPS and poly I:C treatment on the coelomocyte immune response of Loxechinus albus to determine how these factors modulate TLR and strongylocin (antimicrobial peptides of echinoderms) responses. We show that the tlr3-like, tlr4-like, tlr6-like and tlr8-like transcripts are modulated by poly I:C, while LPS only modulates the tlr4-like response; there was no effect of temperature on TLR expression, as evaluated by RT-qPCR. Additionally, we showed that strongylocin-1 and strongylocin-2 are modulated in response to simulated viral infection with poly I:C, providing the first evidence of strongylocin expression in L. albus. Finally, we determined that temperature and LPS modify the viability of coelomocytes, while poly I:C treatment did not affect the viability of these cells. This study contributes to the knowledge of immune responses in sea urchins to improve the understanding of the role of TLRs and strongylocins in echinoderms.

Different maturities drive proteomic and metabolomic changes in Chinese black truffle

Chinese black truffle (Tuber indicum) is rich in nutrition. However, commercial interests lead to the aroma components and nutrients of T. indicum being greatly affected by overexploitation without consideration of their maturity. This study investigated the proteomic and metabolomic profiles of truffle fruiting bodies at different maturities using a meta-proteomic approach. Among the 3007 identified proteins, the most up-expressed protein in the mature ascocarps was involved in the peptidyl-diphthamide biosynthetic process, while thiamine metabolism was the most differentially expressed pathway. Furthermore, a total of 54 metabolites identified upon LC-MS differed significantly, with 30 being up-expressed in the mature ascocarps, including organic acids, carnitine substances and polysaccharides. Additionally, the ash, protein, fat, crude fiber and total sugar contents were all higher in the mature ascocarps. Overall, our findings reveal that mature truffles have a higher nutritional value, providing a basis for further exploring protein functionality of T. indicum at different maturities.

Antioxidant Response and Oxidative Stress in the Respiratory Tree of Sea Cucumber (Apostichopus japonicus) Following Exposure to Crude Oil and Chemical Dispersant

Sea cucumber (Apostichopus japonicus) is mainly cultured in the coastal zone, where it is easily threatened by accidental oil spills. Chemical dispersant is one of the efficient oil spill responses for mitigating the overall environmental damage of oil spills. However, the impact of crude oil and chemical dispersants on sea cucumber is less well known. Hence, the present study focused on exploring the antioxidant response and oxidative stress in the respiratory tree of sea cucumber following exposure to GM-2 chemical dispersant (DISP), water-accommodated fractions (WAF), and chemically enhanced WAF (CEWAF) of Oman crude oil for 24 h. Results manifested that WAF exposure caused a significant increase in the reactive oxygen species (ROS) level (5.29 ± 0.30 AU·mgprot−1), and the effect was much more obvious in CEWAF treatment (5.73 ± 0.16 AU·mgprot−1). Total antioxidant capacity (T-AOC), as an important biomarker of the antioxidant defense capacity, showed an increasing trend following WAF exposure (0.95 ± 0.12 U·mgprot−1) while a significant reduction in T-AOC was observed following CEWAF exposure (0.23 ± 0.13 U·mgprot−1). Moreover, we also evaluated the oxidative damage of the macromolecules (DNA, protein, and lipid), and our results revealed that the presence of chemical dispersant enhanced oxidative damage caused by crude oil to sea cucumber.

The regulation mechanism of lncRNAs and mRNAs in sea cucumbers under global climate changes: Defense against thermal and hypoxic stresses

The aquatic environment can be greatly impacted by thermal and hypoxic stresses, particularly caused by intensified global warming. Hence, there is an urgency to understand the response mechanisms of marine organisms to adverse environment. Although long non-coding RNAs (lncRNAs) are involved in many biological processes, their roles in stress responses still remain unclear. Here, differentially expressed (DE) lncRNAs and mRNAs were identified as responses to environmental stresses in the economically important sea cucumber, Apostichopus japonicus, and their potential roles were explored. Based on a total of 159, 355 and 495 significantly upregulated genes and 230, 518 and 647 significantly downregulated genes identified in the thermal, hypoxic and combination thermal + hypoxic stress treatments, respectively, we constructed DE-lncRNA-mRNA coexpression networks. Among the networks, eight shared pairs were identified from the three treatments, and based on the connectivity degree, MSTRG.27265, MSTRG.19729 and MSTRG.95524 were shown to be crucial lncRNAs. Among all the significantly changed lncRNAs identified by RT-qPCR and sequencing data, binding sites were found in four other lncRNAs (MSTRG.34610, MSTRG.10941, MSTRG.81281 and MSTRG.93731) with Aja-miR-2013-3p, a key miRNA that responds to hypoxia in sea cucumbers. The hypoxia-inducible factor (HIF-1α) was also shown as the possible targeted mRNA of Aja-miR-2013-3p. As indicated by a dual-luciferase reporter assay system, "HIF-1α gene/Aja-miR-2013-3p/MSTRG.34610" network and the "HIF-1α gene/Aja-miR-2013-3p/MSTRG.10941" network may play important roles in sea cucumbers under environmental stresses. Moreover, environmental stress altered the expression of multiple lncRNAs and mRNAs, thus affecting various biological processes in A. japonicus, including immunity, energy metabolism and the cell cycle. At the molecular level, more comprehensive responses were elicited by the combined thermal/hypoxic stress treatment than by individual stresses alone in sea cucumbers. This study lays the groundwork for future research on molecular mechanisms of echinoderm responses to thermal and hypoxic stress in the context of global climate changes.

Time course analysis of immunity-related gene expression in the sea cucumber Apostichopus japonicus during exposure to thermal and hypoxic stress

Temperature and dissolved oxygen concentration are important abiotic factors that can limit the growth and survival of sea cucumbers by affecting their immune systems. As global warming intensifies, sea cucumbers are increasingly exposed to adverse environmental conditions, which can cause severe economic losses and limit the sustainable development of sea cucumber aquaculture. It is therefore important to better understand how sea cucumbers respond to environmental stress, especially with regard to its effects on immunity. In the present study, the time series of immunity-related gene expression in sea cucumbers under thermal and hypoxic stresses were analyzed separately. The expression trends of 17 genes related to the nuclear factor κB (NF-κB) pathway, the protease family, the complement system, heat shock proteins (HSPs) and the transferrin family during exposure to two stresses at eight time points were concluded. These genes have interconnected roles in stress defense. The expression levels of genes relating to the NF-κB pathways and HSPs were strongly affected in the sea cucumber thermal stress response, while melanotransferrin (Mtf), ferritin (Ft) and mannan-binding C-type lectin (MBCL) were affected by hypoxia. In contrast, complement factor B (Bf), myosin V (Mys) and serine protease inhibitor (SPI) were not that sensitive during the initial period of environmental stress. Similar expression patterns under both thermal and hypoxic stress for certain genes, including an increase in Hsp90 and decreases in lysozyme (Lys), major yolk protein (MYP) and cathepsin C (CTLC) were observed in sea cucumbers. Conversely, NF-κB and Hsp70 were differentially affected by the two stress treatments. Lysozyme-induced immune defense was inconstant in sea cucumbers coping with stress. A gene ontology (GO) analysis of the selected genes revealed that the most co-involved terms related to immunity and iron ion. Our analysis suggests that sea cucumbers demonstrate complex and varied immune responses to different types of stresses. This dynamic image of the immune responses and stress tolerance of sea cucumbers provides new insights into the adaptive strategies of holothurians in adverse environments.