Effects of hypoxia in the gills of the Manila clam Ruditapes philippinarum using NMR-based metabolomics

Comparative investigations on the metabolomic responses to cadmium in clams Ruditapes philippinarum from the Bohai Sea and South China Sea

Cadmium (Cd) is a typical heavy metal contaminant along China coasts. Clams Ruditapes philippinarum are widely distributed in multiple climatic zones. However, few research has been conducted on the different responses to Cd in clams from different climatic zones. In this study, the temperate zone Bohai Sea (BS) and tropical zone South China Sea (SCS) clams exhibited distinct background metabolome profiles, characterized by different strategies of osmotic regulation, energy metabolism, and anaerobiosis tendencies, suggesting different tolerance and enrichment capacities to Cd. After Cd treatments, the BS clams demonstrated quicker and higher accumulations of Cd than the SCS clams. Despite differences in their background metabolomes, both BS and SCS clams displayed similar metabolomic responses to Cd, such as anaerobiosis inhibition and increased energy demands. Overall, these findings suggested that the inconsistency of biological responses induced by geographic conditions should be considered in ecotoxicological studies. CAPSULE ABSTRACT: This study elucidated the biological differences in clams Ruditapes philippinarum from the Bohai Sea and South China Sea, and the metabolomic responses in these two clam populations after Cd (200 μg/L) treatments.

How water acidification influences the organism antioxidant capacity and gill structure of Mediterranean mussel (Mytilus galloprovincialis, Lamarck, 1819) at normoxia and hypoxia

The effect of water acidification in combination with normoxia or hypoxia on the antioxidant capacity and oxidative stress markers in gills and hemolymph of the Mediterranean mussel (Mytilus galloprovincialis), as well as on gill microstructure, has been evaluated through an in vivo experiment. Mussels were exposed to a low pH (7.3) under normal dissolved oxygen (DO) conditions (8 mg/L), and hypoxia (2 mg/L) for 8 days, and samples were collected on days 1, 3, 6, and 8 to evaluate dynamic changes of physiological responses. Cytoplasmic concentrations of reactive oxygen species (ROS) and levels of DNA damage were measured in hemocytes, while the activity of catalase (CAT) and superoxide dismutase (SOD) and histopathological changes were assessed in gills. The results revealed that while water acidification did not significantly affect the activity of SOD and CAT in gills under normoxic and hypoxic conditions, there was a trend towards suppression of CAT activity at the end of the experimental period (day 8). Similarly, we did not observe increased formation of ROS in hemocytes or changes in the levels of DNA damage during the experimental period. These results strongly suggest that the oxidative stress response system in mussels is relatively stable to experimental conditions of acidification and hypoxia. Experimental acidification under normoxia and hypoxia caused changes to the structure of the gills, leading to various histopathological alterations, including dilation, hemocyte infiltration into the hemal sinuses, intercellular edema, vacuolization of epithelial cells in gill filaments, lipofuscin accumulation, changes in the shape and adjacent gill filaments, hyperplasia, exfoliation of the epithelial layer, necrosis, swelling, and destruction of chitinous layers (chitinous rods). Most of these alterations were reversible, non-specific changes that represent a general inflammatory response and changes in the morphology of the gill filaments. The dynamics of histopathological alterations suggests an active adaptive response of gills to environmental stresses. Taken together, our data indicate that Mediterranean mussels have a relative tolerance to water acidification and hypoxia at tissue and cellular levels.

Transcriptomic profiling of the thermal tolerance in two subspecies of the bay scallop Argopecten irradians

The bay scallop is a eurythermal species with high economic value and now represents the most cultured bivalve species in China. Two subspecies of the bay scallop, the northern subspecies Argopecten irradians irradians Korean population (KK) and the southern subspecies Argopecten irradians concentricus (MM), exhibited distinct adaptations to heat stress. However, the molecular mechanism of heat resistance of the two subspecies remains unclear. In this study, we compared the transcriptomic responses of the two subspecies to heat stress and identified the involved differentially expressed genes (DEGs) and pathways. More DEGs were found in the KK than in the MM when exposed to high temperatures, indicating elevated sensitivity to thermal stress in the KK. Enrichment analysis suggests that KK scallops may respond to heat stress more swiftly by regulating GTPase activity. Meanwhile, MM scallops exhibited higher resistance to heat stress mainly by effective activation of their antioxidant system. Chaperone proteins may play different roles in responses to heat stress in the two subspecies. In both subspecies, the expression levels of antioxidants such as GST were significantly increased; the glycolysis process regulated by PC and PCK1 was greatly intensified; and both apoptotic and anti-apoptotic systems were significantly activated. The pathways related to protein translation and hydrolysis, oxidoreductase activity, organic acid metabolism, and cell apoptosis may also play pivotal roles in the responses to heat stress. The results of this study may provide a theoretical basis for marker-assisted breeding of heat-resistant strains.

Transcriptional and physiological profiles reveal the respiratory, antioxidant and metabolic adaption to intermittent hypoxia in the clam Tegillarca granosa

Tegillarca granosa can survive intermittent hypoxia for a long-term. We used the clam T. granosa as model to investigate the respiratory, antioxidant and metabolic responses to consecutive hypoxia-reoxygenation (H/R) stress at both physiological and transcriptional levels. The results showed that the clams were able to rapidly regulate oxygen consumption and ammonia excretion during H/R stress, and alleviate oxidative stress during the second-time challenge. The clams also efficiently balanced energy metabolism through the rapid conversion and decomposition of glycogen. According to the transcriptome profile, KEGG pathways of starch and sucrose metabolism, ECM-receptor interaction, and protein processing in endoplasmic reticulum were significantly enriched in H group (the second-time 24 h hypoxia exposure), while pathways associated with lipid metabolism were significantly enriched in h group (the first-time 24 h hypoxia exposure). DEGs including hspa5, birc2/3, and map3k5 might play important roles in alleviating endoplasmic reticulum stress, cpla2 and pla2g16 might mitigate oxidative stress by adjusting the composition of cellular membrane. In conclusions, our findings suggest that rapid adjustment of oxygen consumption, ammonia metabolism, glycogen metabolism, and the ability to adjust the composition of the membrane lipid may be critical for T. granosa in maintaining energy homeostasis and reducing oxidative damage during intermittent H/R exposure. This study preliminarily clarified the response of T. granosa to intermittent hypoxia stress on the physiological and molecular levels, offering insights into the hypoxia-tolerant mechanisms in this species and providing a reference for the following study on the other hypoxic-tolerant species.

Impact of anthropogenic global hypoxia on the physiological response of bivalves

Dissolved oxygen (DO) is an important parameter that affects the biology, physiology, and immunology of aquatic animals. In recent decades, DO levels in the global oceans have sharply decreased, partly due to an increase in atmospheric carbon dioxide, temperature, and anthropogenic nutrient loads. Although there have been many reports on the effects of hypoxia on the survival, growth, behavior, and immunity of bivalves, this information has not been well organized. Therefore, this article provides a comprehensive review of the effects of hypoxia on bivalves. In general, hypoxia negatively impacts the food consumption rate and assimilation efficiency, as well as increasing respiration rates in many bivalves. As a result, it reduces the energy allocation for bivalve growth, shell formation, and reproduction. In severe cases, prolonged exposure to hypoxia can result in mass mortality in bivalves. Moreover, hypoxia also has adverse effects on the immunity and response of bivalves to predators, including decreased burial depths, sensitivity to predators, impairment of byssus production, and negatively impacts on the integrity, strength, and composition of bivalve shells. The tolerance of bivalves to hypoxia largely depends on size and species, with larger bivalves being more susceptible to hypoxia and intertidal species being relatively more tolerant to hypoxia. The information in this article is very useful for elucidating the current research status of hypoxia on bivalves and determining future research directions.

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.

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 influence of temperature rise on the metabolic response of Ruditapes philippinarum clams to 17-α-ethinylestradiol

Untargeted Nuclear Magnetic Resonance metabolomics was employed to study the effects of warming conditions (17-21 °C) and exposure to 17-α-ethinylestradiol (EE2) on the polar metabolome of Ruditapes philippinarum clams, to identify metabolic markers for monitoring/prediction of deviant environmental conditions. Warming alone triggered changes in alanine/aspartate/glutamate, aromatic amino acids, taurine/hypotaurine and homarine/trigonelline pathways, as well as in energy metabolism, suggesting osmoregulatory adaptations and glycolytic/tricarboxylic acid (TCA) cycle activation, possibly accompanied to some extent by gluconeogenesis to preserve glycogen reserves. At 17 °C, the lowest EE2 concentration (5 ng/L) specifically engaged branched-chain and aromatic amino acids to activate the glycolysis/TCA cycle. Notably, a partial metabolic recovery was observed at 25 ng/L, whereas higher EE2 concentrations (125 and 625 ng/L) again induced significant metabolic disturbances. These included enhanced glycogen biosynthesis and increased lipid reserves, sustained by low-level glutathione-based antioxidative mechanisms that seemed active. At 21 °C, response to EE2 was notably weak at low/intermediate concentrations, becoming particularly significant at the highest EE2 concentration (625 ng/L), suggesting higher protection capacity of Ruditapes philippinarum clams under warming conditions. At 625 ng/L, disturbances in alanine/aspartate/glutamate and taurine/hypotaurine metabolisms were observed, with no evidence of enhanced carbohydrate/protein catabolism. This low energy function profile was accompanied by marked antioxidative mechanisms and choline compounds modulation for cell membrane protection/repair. These results help monitor clams´ response to temperature rise and EE2 exposure, paving the way for future effective guidance and prediction of environmental damaging effects.

Physiological and molecular responses to hypoxia stress in Manila clam Ruditapes philippinarum

Hypoxia has become one of the major environmental problems in the aquaculture industry. As one of the most commercially important bivalves, Manila clam Ruditapes philippinarum may be suffering substantial mortality attributable to hypoxia. The physiological and molecular responses to hypoxia stress in Manila clam were evaluated at two levels of low dissolved oxygen: 0.5 mg/L (DO 0.5 mg/L) and 2.0 mg/L (DO 2.0 mg/L). With the prolongation of hypoxia stress, the mortality rate was 100% at 156 h under DO 0.5 mg/L. In contrast, 50% of clams survived after 240 h of stress at DO 2.0 mg/L. After the hypoxia stress, some severe structural damages were observed in gill, axe foot, hepatopancreas tissues, such as cell rupture and mitochondrial vacuolization. For the hypoxia-stressed clams, the significant rise and decline of enzyme activity (LDH and T-AOC) was observed in gills, in contrast to the reduction of glycogen content. Furthermore, the expression levels of genes related to energy metabolism (SDH, PK, Na⁺/K⁺-ATPase, NF-κB and HIF-1α) was significantly affected by the hypoxia stress. It is therefore suggested that the short-term survival of clams under hypoxia may be dependent on stress protection by antioxidants, energy allocation, and tissue energy reserves (such as glycogen stores). Despite this, the prolongation of hypoxia stress at DO 2.0 mg/L may cause the irreversible damages of cellular structures in clam tissues, eventually leading to the death of clams. We therefore support the hypothesis that the extent of hypoxia impacts on marine bivalves may be underestimated in the coastal areas.

Influence of Ecological Factors on the Metabolomic Composition of Fish Lenses

Multiple stressors related to changes in environmental conditions (such as water temperature, salinity, and natural and anthropogenic pollution) may cause biological responses of aquatic organisms that lead to significant variations in the biochemical reactions in their tissues and thereby change the concentrations of metabolites. We used a quantitative NMR-based metabolomic analysis of the fish lens for the evaluation of the influence of environmental factors on metabolic processes in aquatic animals. For this purpose, three species of freshwater fish-Perca fluviatilis, Rutilus rutilus lacustris, and Gymnocephalus cernua-were caught at approximately the same time at three locations in Siberia (Russia) that differed in levels of dissolved oxygen (LDO) and water purity, and the concentrations of 57 major metabolites in the fish lenses were determined. We found that the metabolomic profiles of the fish lenses strongly depended on the location. The obtained data demonstrated that two typical stressors for aquatic animals-a reduced LDO and anthropogenic water pollution-caused a largely similar metabolic response in the fish lenses that led to an increase in the concentrations of several amino acids and a decrease in sarcosine and phosphoethanolamine. At the same time, the composition of the major lens osmolytes depended mostly on the oxygen level, while variations in AMP (decrease) and NAD (increase) corresponded to the water pollution. We suggest that the eye lens is a very convenient tissue for studying the impact of ecological factors on the metabolic state of aquatic animals, fish in particular.

Metabolomics and biochemical assays reveal the metabolic responses to hypo-salinity stress and osmoregulatory role of cAMP-PKA pathway in Mercenaria mercenaria

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Metabolomics reveals the metabolic responses of hard clam to hypo-salinity stress.

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cAMP-PKA pathway and NKA play osmoregulatory roles in hard clams.

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Activated antioxidant responses and reorganized membrane lipids occurred at 5 d.

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Alaine and lactate accumulation suggest the onset of anaerobic metabolism at 1 d.

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Fatty acids β-oxidation is promoted to provide energy for osmoregulation.

Hypo-salinity events frequently occur in marine ecosystem due to persistent rainfall and freshwater inflow, reducing the cytosol osmolarity and triggering cellular stress responses in aquatic organisms. Euryhaline bivalves have developed sophisticated regulatory mechanisms to adapt to salinity fluctuations over a long period of evolution. In this study, we performed multiple biochemical assays, widely targeted metabolomics, and gene expression analysis to investigate the comprehensive metabolic responses to hypo-salinity stress and osmoregulation mechanisms in hard clam Mercenaria mercenaria, which is a euryhaline bivalve species widely cultured in China. During hypo-salinity stress, increased vacuoles appeared in gill filaments. The Na⁺ and Cl^- concentrations in gills significantly decreased because of the up-regulation of Na⁺/K⁺-ATPase (NKA) activity. The cAMP content dramatically decreased at 5 d post hypo-salinity stress. Meanwhile, the gene expression levels of adenylate cyclase, proteinkinase A, and sodium and calcium channel proteins were evidently down-regulated, suggesting that cAMP-PKA pathway was inhibited to prevent ambient inorganic ions from entering the gill cells. Antioxidant metabolites, such as serine and Tyr-containing dipeptides, were significantly up-regulated to resist oxidative stress. Glycerolipid metabolism was strengthened to stabilize membrane structure when hypo-salinity stress was prolonged to 5 days. At 1 d post hypo-salinity stress, an increase in alanine and lactate contents marked the initiation of anaerobic metabolism. Acylcarnitines accumulation indicated that fatty acids β-oxidation was promoted to provide energy for osmoregulation. The potential biomarkers of hypo-salinity stress were identified in hard clams. This study provides novel insights into the metabolic regulatory mechanisms to hypo-salinity stress in euryhaline bivalves.

Metabolomics on the study of marine organisms

BACKGROUND

Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms.

AIM OF REVIEW

This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.

Metabolic response of Mercenaria mercenaria under heat and hypoxia stress by widely targeted metabolomic approach

In the context of global climatic changes, marine organisms have been exposed to environmental stressors including heat and hypoxia. This calls for the design of multi-stressors to uncover the impact of oceanic factors on aquatic organisms. So far, little is known about the metabolic response of marine organisms, especially bivalves, to the combined effects of heat and hypoxia. In this study, we employed widely targeted metabolomic analysis to study the metabolic response of gills in hard clam, a heat- and hypoxia-tolerant bivalve. A total of 810 metabolites were identified. Results showed that the heat group (HT) and heat plus hypoxia group (HL) had a higher number of differential metabolites than the hypoxia group (LO). Glycolysis was affected by the heat and heat plus hypoxia stress. Moreover, anaerobic metabolic biomarkers were accumulated marking the onset of anaerobic metabolism. Environmental stresses may affect Tricarboxylic acid (TCA) cycle. Accumulation of carnitine and glycerophospholipid may promote fatty acid β oxidation and maintain cell membrane stability, respectively. The high content of oxidized lipids (i.e., Leukotriene) in HL and HT groups implied that the organisms were under ROS stress. The significantly differential metabolites of organic osmolytes and vitamins might relieve ROS stress. Moreover, accumulation of thermoprotective osmolytes (monosaccharide, Trimethylamine N-oxide (TMAO)) accumulation was helpful to maintain protein homeostasis. This investigation provided new insights into the adaptation mechanisms of hard clam to heat, hypoxia and combined stress at the metabolite level and highlighted the roles of molecules and protectants.

Assessment of the effectiveness of a novel BioFilm-Membrane BioReactor oil-polluted wastewater treatment technology by applying biomarkers in the mussel Mytilus galloprovincialis

Petrochemical industries and oil refineries are sources of hazardous chemicals into the aquatic environments, and often a leading cause of reduced oxygen availability, thus resulting in adverse effects in biota. This study is an expansion of our previous work on the assessment of the BioFilm-Membrane Bioreactor (BF-MBR) to mitigate the impact of oil-polluted wastewater on marine environments. Specifically, this study evaluated the reduction of selected chemical constituents (hydrocarbons and trace metals) and toxicity related to hypoxia and DNA damage to mussels Mytilus galloprovincialis, before and after treatment of oil-polluted wastewater with the BF-MBR. The application of a multidisciplinary approach provided evidence of the efficiency of BF-MBR to significantly reducing the pollutants load from oily contaminated seawaters. As result, the health status of mussels was preserved by a hypoxic condition due to oily pollutants, as evidenced by the modulation in the gene expression of HIF-1α and PHD and changes in the level of hypotaurine and taurine. Moreover, ameliorative effects in the energy metabolism were also found in mussel gills showing increased levels of glycogen, glucose and ATP, as well as a mitigated genotoxicity was revealed by the Micronucleus and Comet assays. Overall, findings from this study support the use of the BF-MBR as a promising treatment biotechnology to avoid or limiting the compromise of marine environments from oil pollution.

Comparative Analysis of Metabolic Differences of Jersey Cattle in Different High-Altitude Areas

In high-altitude area, hypoxia is a serious stress for humans and other animals, disrupting oxygen homeostasis and thus affecting tissue metabolism. Up to now, there are few reports on the metabolic changes of dairy cows at different altitudes. In this experiment, metabonomics technology and blood biochemical indexes were used to study the metabolic changes of dairy cows in different altitudes. The results showed that the different metabolites were mainly enriched in amino acid metabolism and sphingolipid metabolism, and sphingolipid metabolism showed a negative correlation with increased altitude. The results of this study will enrich the hypoxia-adaptive mechanism of dairy cows in high-altitude areas and provide a theoretical basis for the nutritional regulation of performance and disease treatment of dairy cows in high-altitude areas.

Integrated transcriptome and metabolome analysis reveals molecular responses of the clams to acute hypoxia

Mudflat shellfish have evolved well-adapted strategies for coping with dynamic environmental fluxes and stressful conditions, including oxygen availability. The Manila clams Ruditapes philippinarum are worldwide cultured shellfish in marine intertidal zone, which usually encounter great risk of acute hypoxia exposure in coastal habitats. To reveal the effects of acute hypoxia on metabolic changes of the clams, we performed the integrated analysis of transcriptomics and metabolomics to investigate the global changes of genes and metabolites during acute hypoxia stress at the whole-organism level. The comparative transcriptome analysis reveals that the clams show the remarkable depression in a variety of biological performance, such as metabolic rates, neuronal activity, biomineralization activity, and cell proliferation and differentiation at the hypoxic condition. The metabolomic analysis reveals that amino acid metabolism plays a critical role in the metabolic changes of the clams in response to acute hypoxia. A variety of free amino acids may not only be served as the potential osmolytes for osmotic regulation, but also may contribute to energy production during the acute hypoxia exposure. The metabolite analysis also reveals several important biomarkers for metabolic changes, and provides new insights into how clams deal with acute hypoxia. These findings suggest that clams may get through acute hypoxia stress by the adaptive metabolic strategy to survive short-period of acute hypoxia which is likely to occur in their typical habitat. The present findings will not only shed lights on the molecular and metabolic mechanisms of adaptive strategies under stressful conditions, but also provide the signaling metabolites to assess the physiological states of clams in aquaculture.

Nanopore long-read RNAseq reveals regulatory mechanisms of thermally variable reef environments promoting heat tolerance of scleractinian coral Pocillopora damicornis

Some scleractinian corals exhibit high thermal adaptability to climate changes, although the mechanism of their adaptation is unclear. This study investigated the adaptability of scleractinian coral Pocillopora damicornis to thermally variable reef environments by applying a nanopore-based RNA sequencing method to characterize different transcription responses that promote heat tolerance of P. damicornis. We identified 1414 novel genes and optimized 6256 mis-annotated loci. Based on full-length transcriptome data, we identified complex alternative polyadenylation and alternative splicing events, which can improve our understanding of the genome annotation and gene structures of P. damicornis. Furthermore, we constructed differentially expressed lncRNA-mRNA co-expression networks, which may play a crucial role in the P. damicornis thermal adaptive response. KEGG function enrichment analysis revealed that P. damicornis from the high-temperature pool had a lower metabolic rate than that from the low-temperature pool. We hypothesize that metabolic readjustment, in the form of a lower metabolic rate, positively correlated with increased heat tolerance in P. damicornis in thermally variable reef environments. Our study provides novel insights into lncRNAs that promote thermally tolerance of scleractinian corals in the thermally variable reef environment, suggesting potential mechanisms for their adaptation to global warming in the future.

Temperature adaptations of the thermophilic snail Echinolittorina malaccana: insights from metabolomic analysis

The periwinkle snail Echinolittorina malaccana, for which the upper lethal temperature is near 55°C, is one of the most heat-tolerant eukaryotes known. We conducted a multi-level investigation - including cardiac physiology, enzyme activity, and targeted and untargeted metabolomic analyses - that elucidated a spectrum of adaptations to extreme heat in this organism. All systems examined showed heat intensity-dependent responses. Under moderate heat stress (37-45°C), the snail depressed cardiac activity and entered a state of metabolic depression. The global metabolomic and enzymatic analyses revealed production of metabolites characteristic of oxygen-independent pathways of ATP generation (lactate and succinate) in the depressed metabolic state, which suggests that anaerobic metabolism was the main energy supply pathway under heat stress (37-52°C). The metabolomic analyses also revealed alterations in glycerophospholipid metabolism under extreme heat stress (52°C), which likely reflected adaptive changes to maintain membrane structure. Small-molecular-mass organic osmolytes (glycine betaine, choline and carnitine) showed complex changes in concentration that were consistent with a role of these protein-stabilizing solutes in protection of the proteome under heat stress. This thermophilic species can thus deploy a wide array of adaptive strategies to acclimatize to extremely high temperatures.

Comparative metabolome analysis provides new insights into increased larval mortality under seawater acidification in the sea urchin Strongylocentrotus intermedius

Mortality and metabolic responses of four-armed larvae of Strongylocentrotus intermedius under CO₂-induced seawater acidification were investigated. Gametes of S. intermedius were fertilized and developed to the four-armed larval stage in either current natural seawater pH levels (as Control; pH = 7.99 ± 0.01) or laboratory-controlled acidified conditions (OA₁: ΔpH = -0.3 units; OA₂: ΔpH = -0.4 units; OA₃: ΔpH = -0.5 units) according to the predictions of the Intergovernmental Panel on Climate Change (IPCC). The degrees of spicule exposure and asymmetry and mortality of four-armed larvae of S. intermedius were observed; each had a significant linearly increasing trend as the seawater pH level decreased. Comparative metabolome analysis identified a total of 87 significantly differentially expressed metabolites (SDMs, UP: 57, DOWN: 30) in OA-treated groups compared with the control group. Twenty-three SDMs, including carnitine, lysophosphatidylcholine (LPC) 18:3, lysophosphatidyl ethanolamine (LPE) 16:1, glutathione (GSH) and L-ascorbate, exhibited a linear increasing trend with decreasing seawater pH. Nine SDMs exhibited a linear decreasing trend as the seawater pH declined, including hypoxanthine, guanine and thymidine. Among all SDMs, we further mined 48 potential metabolite biomarkers responding to seawater acidification in four-armed larvae of S. intermedius. These potential metabolite biomarkers were mainly enriched in five pathways: glycerophospholipid metabolism, glutathione metabolism, purine metabolism, pyrimidine metabolism and the tricarboxylic acid cycle (TCA cycle). Our results will enrich our knowledge of the molecular mechanisms employed by sea urchins in response to CO₂-induced seawater acidification.

High-Resolution Magic Angle Spinning (HR-MAS) NMR-Based Fingerprints Determination in the Medicinal Plant Berberis laurina

Berberis laurina (Berberidaceae) is a well-known medicinal plant used in traditional medicine since ancient times; however, it is scarcely studied to a large-scale fingerprint. This work presents a broad-range fingerprints determination through high-resolution magical angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy, a well-established flexible analytical method and one of most powerful "omics" platforms. It had been intended to describe a large range of chemical compositions in all plant parts. Beyond that, HR-MAS NMR allowed the direct investigation of botanical material (leaves, stems, and roots) in their natural, unaltered states, preventing molecular changes. The study revealed 17 metabolites, including caffeic acid, and berberine, a remarkable alkaloid from the genus Berberis L. The metabolic pattern changes of the leaves in the course of time were found to be seasonally dependent, probably due to the variability of seasonal and environmental trends. This metabolites overview is of great importance in understanding plant (bio)chemistry and mediating plant survival and is influenceable by interacting environmental means. Moreover, the study will be helpful in medicinal purposes, health sciences, crop evaluations, and genetic and biotechnological research.

Transcriptome analysis reveals differential immune related genes expression in Ruditapes philippinarum under hypoxia stress: potential HIF and NF-κB crosstalk in immune responses in clam

Background

Hypoxia is an important environmental stressor in aquatic ecosystems, with increasingly impacts on global biodiversity. Benthic communities are the most sensitive parts of the coastal ecosystem to eutrophication and resulting hypoxia. As a filter-feeding organism living in the seafloor sediment, Ruditapes philippinarum represents an excellent “sentinel” species to assess the quality of marine environment. In order to gain insight into the molecular response and acclimatization mechanisms to hypoxia stress in marine invertebrates, we examined hypoxia-induced changes in immune-related gene expression and gene pathways involved in hypoxia regulation of R. philippinarum.

Results

We investigated the response of the Manila clam R. philippinarum to hypoxia under experimental conditions and focused on the analysis of the differential expression patterns of specific genes associated with hypoxia response by RNA-seq and time course qPCR analysis. A total of 75 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, chaperones/heat shock proteins, immune alteration, and cell proliferation/apoptosis. Fourteen hypoxia responsive genes were validated significantly up/down regulated at different time 0, 2, 5, and 8 d in gills of R. philippinarum in hypoxia challenged group. Functional enrichment analysis revealed the HIF signaling pathway and NF-κB signaling pathway play pivotal roles in hypoxia tolerance and resistance in R. philippinarum.

Conclusion

The HIF signaling pathway and NF-κB signaling pathway play a critical role in hypoxia tolerance and resistance in Manila clam. The immune and defense related genes and pathways obtained here gain a fundamental understanding of the hypoxia stress in marine bivalves and provide important insights into the physiological acclimation, immune response and defense activity under hypoxia challenge. The reduced metabolism is a consequence of counterbalancing investments in immune defense against other physiological processes.

Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics

Marine mollusks are commonly subjected to heat stress. To evaluate the effects of heat stress on the physiological metabolism of the ark shell Scapharca subcrenata, clams were exposed to different high temperatures (24, 28 and 32 °C) for 72 h. The oxygen consumption and ammonia excretion rates were measured at 2, 12, 24, 48 and 72 h. The results indicated that the metabolic rates of the ark shell significantly increased with increasing heat stress, accompanied by mortalities in response to prolonged exposure. A metabolomics approach based on gas chromatography coupled with mass spectrometry was further applied to assess the changes of metabolites in the mantle of the ark shell at 32 °C. Moreover, multivariate and pathway analyses were conducted for the different metabolites. The results showed that the heat stress caused changes in energy metabolism, amino acid metabolism, osmotic regulation, carbohydrate metabolism and lipid metabolism through different metabolic pathways. These results are consistent with the significant changes of oxygen consumption rate and ammonia excretion rate. The present study contributes to the understanding of the impacts of heat stress on intertidal bivalves and elucidates the relationship between individual-level responses and underlying molecular metabolic dynamics.

Effects of hypoxia on survival, behavior, metabolism and cellular damage of Manila clam (Ruditapes philippinarum)

The Manila clam Ruditapes philippinarum has become a common and dominant macrobenthic species in coastal areas of the northwestern Pacific and temperate waters of Europe; it is also a major cultured shellfish, with annual worldwide production exceeding 3.3 million tonnes. This species faces greater risk of exposure to hypoxia as eutrophication worsens throughout its coastal habitats; however, its tolerance to hypoxia remains unclear, and the toxicological indicators including LC₅₀ and LT₅₀ have not yet been assessed. Previous studies on the effects of hypoxia on marine benthos have focused largely on functional responses, such as metabolism and gene expression, leaving potential structural damage to the mitochondria or the cells unknown. In this study we assessed the effects of hypoxia on Manila clam in terms of survival, behavior, metabolism and cellular damage, using a newly designed automated hypoxia simulation device that features exceptional accuracy and good stability. The clams exhibited strong tolerance to hypoxia as the 20-day LC₅₀ for dissolved oxygen (DO) was estimated to be 0.57 mg L^-1, and the LT₅₀ at 0.5 mg L^-1 DO was 422 hours. Adaptations included fewer buried clams and a depressed metabolism, while the unexpected rise in the activities of key enzymes involved in glycolysis may indicate a diverse strategy of shellfish under hypoxia. Cellular damage was observed as collapse of the mitochondrial cristae and both cellular and mitochondrial vacuolization. This multi-level study complements and updates our knowledge of the effects of hypoxia on marine benthos, by improving our understanding of the potential for marine ecological transformation under hypoxic conditions and providing useful information for Manila clam farming.

Based on the Metabolomic Approach the Energy Metabolism Responses of Oriental River Prawn Macrobrachium nipponense Hepatopancreas to Acute Hypoxia and Reoxygenation

Hypoxia represents a major physiological challenge for prawns and is a problem in aquaculture. Therefore, an understanding of the metabolic response mechanism of economically important prawn species to hypoxia and re-oxygenation is essential. However, little is known about the intrinsic mechanisms by which the oriental river prawn Macrobrachium nipponense copes with hypoxia at the metabolic level. In this study, we conducted gas chromatography-mass spectrometry-based metabolomics studies and assays of energy metabolism-related parameters to investigate the metabolic mechanisms in the hepatopancreas of M. nipponense in response to 2.0 O₂/L hypoxia for 6 and 24 h, and reoxygenation for 6 h following hypoxia for 24 h. Prawns under hypoxic stress displayed higher glycolysis-related enzyme activities and lower mRNA expression levels of aerobic respiratory enzymes than those in the normoxic control group, and those parameters returned to control levels in the reoxygenated group. Our results showed that hypoxia induced significant metabolomic alterations in the prawn hepatopancreas within 24 h. The main metabolic alterations were depletion of amino acids and 2-hydroxybutanoic acid and accumulation of lactate. Further, the findings indicated that hypoxia disturbed energy metabolism and induced antioxidant defense regulation in prawns. Surprisingly, recovery from hypoxia (i.e., reoxygenation) significantly affected 25 metabolites. Some amino acids (valine, leucine, isoleucine, lysine, glutamate, and methionine) were markedly decreased compared to the control group, suggesting that increased degradation of amino acids occurred to provide energy in prawns at reoxygenation conditions. This study describes the acute metabolomic alterations that occur in prawns in response to hypoxia and demonstrates the potential of the altered metabolites as biomarkers of hypoxia.

Differential Gene Expression Profiles and Alternative Isoform Regulations in Gill of Nile Tilapia in Response to Acute Hypoxia

Fish often encounters exposures to acute environmental hypoxia either spatially or temporally. Gill organ plays important roles in response to hypoxic stress in fish. Few studies focus on the molecular regulation mechanisms of gills under hypoxic stress. In this study, we investigated the transcriptomic response to 12-h acute hypoxia in gill of a hypoxia tolerant fish, Nile tilapia Oreochromis niloticus through RNA sequencing (RNA-Seq). We sequenced messenger RNA from three control samples and three hypoxia-treated samples. Bioinformatics analysis identified 239 differentially expressed genes (DEG) and 34 genes (DUES) that had significant differential alternative isoform regulation events in at least one exonic region in gill in response to acute hypoxia. The spatiotemporal expression analysis in five tissues (heart, liver, brain, gill, and spleen) sampled at three time points (6, 12, and 24 h) under hypoxia treatment confirmed the significant association of differential exon usages in two DUES genes (TLDC2 and SSX2IPA) with hypoxia conditions. Further functional analysis suggested several energy and immune response-related pathways, e.g., metabolic pathway and antigen processing and presentation, contained the most abundant DEG genes. We found that some GO biological processes for DEG genes were significantly enriched under hypoxic stress, such as glycolysis, metabolic process, generation of precursor metabolites and energy, and cholesterol metabolic process. Our findings suggest abundant differential gene expression changes and alternative isoform regulation events in genes involved in the hypoxia response in gill. Our results provide a basis for exploring the gene regulation mechanism under hypoxic stress in fish.