From antioxidant defense to genotoxicity: Deciphering the tissue-specific impact of AgNPs on marine clam Ruditapes philippinarum

The escalating use of silver nanoparticles (AgNPs) across various sectors for their broad-spectrum antimicrobial capabilities, has raised concern over their potential ecotoxicological effects on aquatic life. This study explores the impact of AgNPs (50 μg/L) on the marine clam Ruditapes philippinarum, with a particular focus on its gills and digestive glands. We adopted an integrated approach that combined in vivo exposure, biochemical assays, and transcriptomic analysis to evaluate the toxicity of AgNPs. The results revealed substantial accumulation of AgNPs in the gills and digestive glands of R. philippinarum, resulting in oxidative stress and DNA damage, with the gills showing more severe oxidative damage. Transcriptomic analysis further highlights an adaptive up-regulation of peroxisome-related genes in the gills responding to AgNP-induxed oxidative stress. Additionally, there was a noteworthy enrichment of differentially expressed genes (DEGs) in key biological processes, including ion binding, NF-kappa B signaling and cytochrome P450-mediated metabolism of xenobiotics. These insights elucidate the toxicological mechanisms of AgNPs to R. philippinarum, emphasizing the gill as a potential sensitive organ for monitoring emerging nanopollutants. Overall, this study significantly advances our understanding of the mechanisms driving nanoparticle-induced stress responses in bivalves and lays the groundwork for future investigations into preventing and treating such pollutants in aquaculture.

Transcriptome analysis provides new insights into the immune response of Ruditapes philippinarum infected with Vibrio alginolyticus

Manila clam (Ruditapes philippinarum) is a bivalve species with commercial value, but it is easily infected by pathogenic microorganisms in aquaculture, which restricts the shellfish industry. Notably, the impact of Vibrio alginolyticus on clam culture is obvious. In this study, RNA-seq was performed to analyze clam hepatopancreas tissue in 48 h (challenge group, G48h) and 96 h (challenge group, G96h) after infection with V. alginolyticus and 0 h after injection of PBS (control group, C). The results showed that a total of 1670 differentially expressed genes were detected in the G48h vs C group, and 1427 differentially expressed genes were detected in the G96h vs C group. In addition, KEGG analysis showed that DEGs were significantly enriched in pathways such as Lysosome and Mitophagy. Moreover, 15 immune related DEGs were selected for qRT-PCR analysis to verify the accuracy of RNA-seq, and the results showed that the expression level of DEGs was consistent with that of RNA-seq. Therefore, the results obtained in this study provides a preliminary understanding of the immune defense of R. philippinarum and molecular insights for genetic breeding of V. alginolyticus resistance in Manila clam.

Exploring the mechanism of nonylphenol-induced ovarian developmental delay of manila clams, Ruditapes philippinarum: Applying RNAi to toxicological analysis

Nonylphenol (NP) contamination in the coastal environment of China poses ecological risks to aquatic organisms. However, the endocrine disruptive impacts of NP on bivalves, particularly on ovarian development, remain poorly understood. In this study, Manila clams Ruditapes philippinarum at the developing stage of gonad were exposed to 1.0 μg/L NP for 21 days. Utilizing RNA interference (RNAi) to suppress ER gene expression, we observed a delay in ovarian development as evidenced by histological observations under both NP and NPRi (NP with ER-RNAi) treatment, with Vtg elevation exclusive to the NP group. Comprehensive analyses encompassing transcriptomics, real-time quantitative PCR, and steroid hormone measurement revealed significant alterations in aldosterone synthesis, estrogen signaling, and thyroid hormone synthesis. These pathways showed similar perturbations in both NP and NPRi groups compared to controls. Notably, the NPRi group exhibited distinct enrichment in PPAR and insulin signaling pathways, may implicating these in ER function suppression. Steroid hormone biosynthesis was notably reduced in both treatments, pointing to a profound impact on hormone synthesis. The contrast between in vivo and in vitro findings suggests that NP's detrimental effects on ovarian development may primarily involve neuroendocrine regulation of steroidogenesis. This investigation highlights the complex dynamics of NP-induced endocrine disruption in bivalves, emphasizing the pivotal role of ER and associated pathways.

Stoichiometry of growth under variable scenarios of nutrient limitation: Differential homeostasis of body composition among growth phenotypes of the Manila clam

Fast- and slow-growing phenotypes from two separate breeding families of the Manila clam (Ruditapes philippinarum) were alternatively fed two monoalgal diets with high and low N content (C:N ratios of 4.9 and 13.5, respectively). After 35 days of food conditioning, clams were sacrificed, and the soft body was dissected out into five different tissue fractions to determine the corresponding ponderal ratios (tissue wt./body wt.) and a separate analysis of the elemental composition of these tissues. Previously reported C and N balances performed with the same conditioning diets were integrated and compared with tissue composition of the same phenotypes in order to assess the efficacy of mechanisms elicited to compensate for N deficit. Broad differences in dietary N content resulted in only minor changes in whole-body C:N composition which suggests a noticeable degree of homeostatic regulation of nutrient balances. This regulation was found to be stricter in fast-compared to slow-growing phenotypes and differed among the various body tissues. Using the threshold element ratio approach, physiological mechanisms were identified that partly compensate for large stoichiometric mismatches between low-N food and body tissues.

Metabolomics revealed more deleterious toxicity induced by the combined exposure of ammonia and nitrite on Ruditapes philippinarum compared to single exposure

NH3-N and NO2-N always co-exist in the aquatic environment, but there is not a clear opinion on their joint toxicities to the molluscs. Presently, clams Ruditapes philippinarum were challenged by environmental concentrations of NH3-N and NO2-N, singly or in combination, and analyzed by metabolomics approaches, enzyme assays and transmission electron microscope (TEM) observation. Results showed that some same KEGG pathways with different enriched-metabolites were detected in the three exposed groups within one day, and completely different profiles of metabolites were found in the rest of the exposure period. The combined exposure induced heavier and more lasting toxicities to the clams compared with their single exposure. ACP activity and the number of secondary lysosomes were significantly increased after the combined exposure. The present study shed light on the joint-toxicity mechanism of NH3-N and NO2-N, and provided fundamental data for the toxicity research on inorganic nitrogen.

Behavioral responses of intertidal clams to compound extreme weather and climate events

Rapidly increasing concentration of carbon dioxide (CO2) in the atmosphere not only results in global warming, but also drives increasing seawater acidification. Infaunal bivalves play critical roles in benthic-pelagic coupling, but little is known about their behavioral responses to compound climate events. Here, we tested how heatwaves and acidification affected the behavior of Manila clams (Ruditapes philippinarum). Under acidified conditions, the clams remained capable of burrowing into sediments. Yet, when heatwaves attacked, significant decreases in burrowing ability occurred. Following two consecutive events of heatwaves, the clams exhibited rapid behavioral acclimation. The present study showed that the behavior of R. philippinarum is more sensitive to heatwaves than acidification. Given that the behavior can act as an early and sensitive indicator of the fitness of intertidal bivalves, whether, and to what extent, behavioral acclimation can persist under scenarios of intensifying heatwaves in the context of ocean acidification deserve further investigations.

Effects of cadmium exposure on haemocyte immune function of clam Ruditapes philippinarum at different temperatures

Haemocytes are crucial for the immune defence of mollusks. It is important to explore the immune performance of haemocytes of mollusks under the stress of heavy metals with global warming. In order to study the effects of cadmium (Cd) exposure and temperature stress on the haemocyte immune function of clam Ruditapes philippinarum, clams were exposed to different Cd concentrations (0.05, 0.10 and 0.25 mg/L) at 20 °C, 25 °C and 30 °C respectively. Haemocyte mortality, reactive oxygen species (ROS) and superoxide dismutase (SOD) activity were measured at day 1, day 3, day 5 and day 7. The results showed that the changes of the three indexes were not obvious when exposed to 0.05 mg/L of Cd at 20 °C, while significant differences were observed with the increase of temperature, Cd concentration and exposure time. Under a condition of relative high temperature coupling with high concentration of Cd, the clams were significantly influenced, showing an obvious synergistic effect. Selected indexes reflect the clam's response to the combined stress of temperature and Cd. Moreover, R. philippinarum might be an ideal biological index species to the Cd pollution.

Study on epigenotoxicity, sex hormone synthesis, and DNA damage of benzo[a]pyrene in the testis of male Ruditapes philippinarum

Research on the mechanisms of reproductive toxicity caused by persistent organic pollutants (POPs) in marine animals has received significant attention. One group of typical POPs, called polycyclic aromatic hydrocarbons (PAHs), has been found to cause various reproductive toxicities in aquatic organisms, including epigenotoxicity, reproductive endocrine disruption, DNA damage effects and other reproductive toxicity, thereby affecting gonadal development. Interestingly, male aquatic animals are more susceptible to the disturbance and toxicity of environmental pollutants. However, current studies primarily focus on vertebrates, leaving a large gap in our understanding of the reproductive toxicity and mechanisms of PAHs interference in marine invertebrates. In this study, male Ruditapes philippinarum was used as an experimental subject to investigate reproduction-related indexes in clams under the stress of benzo[a]pyrene (B[a]P) at different concentrations (0, 0.8, 4 and 20 μg/L) during the proliferative, growth, maturity, and spawning period. We analyzed the molecular mechanisms of reproductive toxicity caused by PAHs in marine bivalves, specifically epigenotoxicity, reproductive endocrine disruption, and gonadal damage-apoptotic effect. The results suggest that DNA methylation plays a crucial role in mediating B[a]P-induced reproductive toxicity in male R. philippinarum. B[a]P may affect sex hormone levels, impede spermatogenesis and testis development in clams, by inhibiting the steroid hormone synthesis pathway and downregulating genes critical for cell proliferation, testis development, and spermatid expulsion. Moreover, the spermatids of male R. philippinarum were severely impaired under the B[a]P stress, leading to reduced reproductive performance in the clams. These findings contribute to a better understanding of the reproductive toxicity response of male marine invertebrates to POPs stress.

Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis

Single-nucleotide polymorphisms (SNPs) are the most commonly used DNA markers in population genetic studies. We used the Illumina HiSeq4000 platform to develop single-nucleotide polymorphism (SNP) markers for Manila clam Ruditapes philippinarum using restriction site-associated DNA sequencing (RAD-seq) genotyping. Eighty-eight SNP markers were successfully developed by using high-resolution melting (HRM) analysis, with a success rate of 44%. SNP markers were analyzed for genetic diversity in two clam populations. The observed heterozygosity per locus ranged from 0 to 0.9515, while the expected heterozygosity per locus ranged from 0.0629 to 0.4997. The value of FIS was estimated to be from -0.9643 to 1.0000. The global Fst value was 0.1248 (p < 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy-Weinberg equilibrium (p < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species.

Interference mechanism of benzo[a]pyrene exposure on the taste substance metabolisms in Ruditapes philippinarum

Aquatic animals are popular for their unique umami and high-quality protein. However, under the realistic background of increasing marine pollution, whether it affects the aquatic animal tastes, and what the interference mechanism is still remains unknown. Benzo[a]pyrene (B[a]P) is a typical Polycyclic aromatic hydrocarbons (PAHs) with high toxicity. In this study, we investigated the effects of B[a]P (0, 0.8, 4 and 20 μg/L) on the content and taste evaluation of Ruditapes philippinarum taste substances, and clarified the interference mechanism of B[a]P on taste substance metabolisms with transcriptome analysis. The results demonstrated that B[a]P significantly altered the contents and taste activity values (TAVs) of free amino acids (FAAs), 5'-nucleotides, organic acids, flavor peptides, organic bases, sugars and inorganic ions, as well as the gene expressions within their synthesis and decomposition, indicating that B[a]P affected these taste substance contents by interfering with their metabolisms, thereby changing the clam tastes (decreases of umami and sweetness, and increase of bitter taste). This study provided scientific basis for quality assurance of bivalve cultivation and control of marine pollution.

Comprehensive analysis of differentially expressed mRNA, lncRNA and miRNA, and their ceRNA networks in the regulation of shell color in the Manila clam (Ruditapes philippinarum)

The regulatory mechanism of ceRNA network plays an important role in molecular function and biological processes, however, the molecular mechanism in the shell color of Ruditapes philippinarum has not yet been reported. In this study, we performed transcriptome sequencing on the mantle of R. philippinarum with different shell colors, and screened for mRNA, miRNA, and lncRNA. A total of 61 mRNAs, 3725 lncRNAs and 90 miRNAs were obtained from all the shell color comparison groups (all mRNAs, lncRNAs and miRNAs P < 0.05), and 7 mRNAs, 8 lncRNAs, and 4 miRNAs of the porphyrin pathway and melanin pathway were screened for competitive endogenous RNA (ceRNA) network construction. The results indicate that the ceRNA network composed of mRNA and lncRNA, centered around efu-miR-101, mle-bantam-3p, egr-miR-9-5p, and sma-miR-75p, may play a crucial regulatory role in shell color formation. This study reveals for the first time the mechanism of ceRNA regulatory networks in the shell color of R. philippinarum and providing important reference data for molecular breeding of shell color in R. philippinarum.

Metabolic adaptation of the clam Ruditapes philippinarum during air exposure and the positive effects of sodium nitroprusside pretreatment

The Manila clam (Ruditapes philippinarum), as one of the shellfish living in the intertidal zone, is known for its strong ability to withstand air exposure. Sodium nitroprusside (SNP), a donor of nitric oxide (NO), has been shown to be useful for antioxidant and immune regulation in aquatic animals. In this study, an untargeted metabolomics (LC-MS/MS) technique was employed for the first time in Manila clam to analyze the metabolic and histological impacts after air exposure and the positive effects of SNP pretreatment. During air exposure, a significant increase in taurine, L-glutamate, and several polyunsaturated fatty acids in clams was detected, which indicates that clams may experience inflammatory reactions, oxidative stress, and an increase in blood ammonia content. When clams were exposed to SNP for 6 h, arginine, spermine, L-glutamic acid, and glutathione content were all upregulated, indicating that the SNP exposure induced NO production and improved antioxidant capacity in clams. When the clams were exposed to air after SNP pretreatment, there were no significant differences in the levels of taurine, L-glutamate, or aliphatic acids between the experimental and control groups. Gill tissue was more severely damaged in clams directly exposed to air than in those that experienced air exposure after SNP pretreatment, especially in clams exposed to air for a long time (72 h). Both metabolomics and tissue section structure indicated that SNP pretreatment decreased the stress responses caused by air exposure in R. philippinarum. These findings provided fresh insights and a theoretical foundation for understanding the tolerance to air exposure and physiological functions of SNP (or NO) in R. philippinarum.

Enhancing Sediment Bioaccumulation Predictions: Isotopically Modified Bioassay and Biodynamic Modeling for Nickel Assessment

Quantifying metal bioaccumulation in a sedimentary environment is a valuable line of evidence when evaluating the ecological risks associated with metal-contaminated sediments. However, the precision of bioaccumulation predictions has been hindered by the challenges in accurately modeling metal influx processes. This study focuses on nickel bioaccumulation from sediment and introduces an innovative approach using the isotopically modified bioassay to directly measure nickel assimilation rates in sediment. Tested in sediments spiked with two distinct nickel concentrations, the measured Ni assimilation rates ranged from 35 to 78 ng g-1 h-1 in the Low-Ni treatment and from 96 to 320 ng g-1 h-1 in the High-Ni treatment. Integrating these rates into a biodynamic model yielded predictions of nickel bioaccumulation closely matching the measured results, demonstrating high accuracy with predictions within a factor of 3 for the Low-Ni treatment and within a factor of 1 for the High-Ni treatment. By eliminating the need to model metal uptake from various sources, this streamlined approach provides a reliable method for predicting nickel bioaccumulation in contaminated sediments. This advancement holds promise for linking bioaccumulation with metal toxicity risks in sedimentary environments, enhancing our understanding of metal-contaminated sediment risks and providing valuable insights to support informed decision-making in ecological risk assessment and management.

Genome-Wide Identification and Characterization of MITF Genes in Ruditapes philippinarum and Their Involvement in the Immune Response to Vibrio anguillarum Infection

Studies have shown that the shellfish have innate immune system, which is a very important immune form of shellfish, and they rely on the innate immune system to resist diseases. As a transcription factor, Microphthalmia-associated transcription factor (MITF) plays a regulatory role in immune response and the shell color is also an important index for the breeding of excellent varieties of R. philippinarum. The research on immune response mechanism of RPMITFs can provide important reference data for the breeding of excellent clam varieties. In the genome of R. philippinarum, the RPMITF genes family of shell color-related gene family was selected as the target gene of this experiment. There are 12 RpMITF genes named RpMITF1, RpMITF2, RpMITF3, RpMITF4, RpMITF5, RpMITF6, RpMITF7, RpMITF8, RpMITF9, RpMITF10, RpMITF11, and RpMITF12. The open reading frame length is 639, 1233, 996, 1239, 675, 624, 816, 1365, 612, 1614, 1122, and 486 bp, encoding 212, 410, 331, 412, 224, 207, 271, 454, 203, 537, 373, and 161 aa, respectively. The predicted molecular weight range of amino acids is 18.85-62.61 kda, and the isoelectric point range is 5.26-9.44. Real-time quantitative PCR was used to detect the gene expression of RpMITF gene family in hepatopancreas tissues of two populations of Manila clam at 6 time points (0, 3, 6, 12, 24, and 48 h) after Vibrio anguillarum stress. The results show that RpMITF gene family was significantly expressed in hepatopancreas of two clam populations after V. anguillarum stress (P < 0.05).

Sex-specific responses of Ruditapes philippinarum to ocean acidification following gonadal maturation

Ocean acidification (OA) can seriously affect marine bivalves at different levels of biological organization, generating widespread consequences on progeny recruitment and population maintenance. Yet, few effort has been devoted to elucidating whether female and male bivalves respond differentially to OA in their reproductive seasons. Here, we estimated differences in physiological responses of female and male Manila clams (Ruditapes philippinarum) to OA during gonadal maturation. In comparison to OA-stressed male clams, females significantly depressed activities in enzymes related to energy metabolism (NKA, T-ATP), antioxidant defence (SOD and MDA), and non-specific immune function (ACP), and downregulated expression of AMPK that plays a key role in cellular metabolism, indicating that sex did significantly affect responses of R. philippinarum to OA. Such sex-based differences can be likely couched in energetic terms, given the much more energetically expensive cost of egg production than that of sperms. These results indicate that sex-specific responses to OA during reproductive seasons do exist in marine bivalves, and therefore accounting for such sex specificity is of paramount importance when projecting population sustainability and formulating conservation strategies in an acidifying ocean.

Genetic and Haplotype Diversity of Manila Clam Ruditapes philippinarum in Different Regions of China Based on Three Molecular Markers

China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of R. philippinarum, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including COI, 16SrRNA and ITS. Based on the results of the COI and ITS genes, the 14 populations showed a moderate to high level of genetic diversity, with an average haplotype diversity of 0.9242 and nucleotide diversity of 0.05248. AMOVA showed that there was significant genetic differentiation among all populations (mean FST of the total population was 0.4534). Pairwise FST analysis showed that genetic differentiation reached significant levels between Laizhou and other populations. Two Laizhou populations showed great divergence from other populations, forming an independent branch in the phylogenetic tree. The shared haplotypes Hap_2 and Hap_4 of COI appeared most frequently in most clam populations. In contrast, 16SrRNA analysis of the clam populations revealed the dominated haplotype Hap_2, accounting for 70% of the total number of individuals. The haplotype diversity of the Laizhou population (Laizhou shell-wide (KK) and Laizhou dock (LZMT)) was relatively higher than other populations, showing multiple unique haplotypes (e.g., Hap_40, Hap_41 and Hap_42). These findings of genetic and haplotype diversity of clam populations provide guiding information for genetic resource conservation and genetic improvement of the commercially important R. philippinarum.

Physiological and biochemical responses of clams to recurrent marine heatwaves

In the past decade, the frequency, intensity and duration of marine heatwaves (MHWs) in the South China Sea have been increasing strikingly, resulting in serious impacts on intertidal bivalves and their ecosystems. The Manila clam, Ruditapes philippinarum, is one of the most ecologically and economically important bivalve species in the South China Sea, yet very little is known about its fate under intensifying MHWs events. Here, we examined how R. philippinarum responded to two consecutive scenarios of MHWs, with each composed of 4 °C and 8 °C rises of seawater temperatures, respectively. Up to 87% of Manila clams survived recurrent MHWs events, and significant increases in standard metabolic rate occurred predominantly under extreme conditions (+8 °C), indicating that the clams could trigger compensatory mechanisms to mitigate MHWs-induced thermal stress. Following acute and repeated exposures to MHWs, Manila clams showed similar responses in enzymes underpinning energy metabolism (NKA, CMA, and T-ATP), antioxidant defence (SOD, CAT, and MDA), and biomineralization (AKP and ACP), most of which exhibited significantly increasing and then decreasing trends with the intensification of MHWs. Of eight genes associated with physiological tolerance and fitness, ATAD3A, PFK, SOD, and C3 were significantly down-regulated in response to recurrent MHWs events, demonstrating the certain resistance to MHWs. These findings provide a better understanding that marine bivalves hold the potential to acclimate simulated MHWs events from the physiological and molecular processes.

A food-web model as a tool for the ecosystem-level management of bivalves in an Atlantic coastal lagoon

The Ria de Aveiro is an important coastal lagoon for wildlife in Portugal, where the production of bivalves reaches approximately 2700 tons annually. However, the illegal overfishing of bivalves is frequent in this lagoon, which causes critical changes in the ecosystem. In this study, using a developed food-web model (Ecopath model), the ecological carrying capacity (ECC) and maximum sustained yield (MSY) of the Manila clam, Ruditapes philippinarum were estimated, and the effects of further increases in clam biomass on other species were investigated. The results showed that 1) the current biomass and legal catch of R. philippinarum do not yet exceed the ECC (172.40 tons km-2) or the MSY (86.20 tons km-2 year-1) in Ria de Aveiro; 2) the harvested Manila clams of the MSY represent removing from the ecosystem ∼ 581 tons carbon (C) and ∼83 tons nitrogen (N) annually, with substantial ecological and economic implications; and 3) a further increase in the biomass levels of this species may cause the ecotrophic efficiency of other groups to become unrealistic, potentially leading to decreases in ecosystem transfer efficiency, biodiversity and health. The results here are expected to guide the sustainable development and management of bivalve aquaculture in Ria de Aveiro and the protection of the local environment.

Immunotoxic effects of exposure to the antifouling copper(I) biocide on target and nontarget bivalve species: a comparative in vitro study between Mytilus galloprovincialis and Ruditapes philippinarum

Edible bivalves constitute an important bioresource from an economic point of view, and studies on their immune responses to environmental pollutants are crucial for both the preservation of biodiversity and economic reasons. The worldwide diffusion of copper(I)-based antifouling paints has increased copper leaching into coastal environments and its potential impact on both target and nontarget organisms. In this study, immunotoxicity assays were carried out with short-term (60 min) cultures of hemocytes from the bivalves Mytilus galloprovincialis-a mussel dominant in the macrofouling community-and Ruditapes philippinarum-a clam dominant in the soft-sediment community-exposed to CuCl to compare the toxic effects on their immune responses. The LC50 values were similar, 40 μM (3.94 mg L-1) for the mussel and 44 μM (4.33 mg L-1) for the clam. In both species, apoptosis occurred after exposure to 1 µM (98.9 μg L-1) CuCl, the concentration able to significantly increase the intracellular Ca2+ content. Biomarkers of cell morphology and motility revealed microfilament disruption, a significant decrease in yeast phagocytosis and lysosome hydrolase (β-glucuronidase) inhibition beginning from 0.5 µM (49.5 μg L-1) CuCl in both the mussel and clam. The same concentration of CuCl affected biomarkers of oxidative stress, as a significant decrease in reduced glutathione content in the cytoplasm and inhibition of mitochondrial cytochrome-c oxidase (COX) were detected in both species. Comparison of the biomarkers showed that clam is more sensitive than the mussel regarding alterations to the lysosomal membrane and reactive oxygen species (ROS) production, which supports the potential harmful effects of antifouling biocides on the survival of nontarget pivotal species in the coastal community.

CO2-Induced Ocean Acidification Alters the Burrowing Behavior of Manila Clam Ruditapes philippinarum by Reversing GABAA Receptor Function

Biological burrowing behavior is an important driver shaping ecosystems that is being threatened by CO₂-induced ocean acidification; however, the effects of ocean acidification on burrowing behavior and its neurological mechanism remain unclear. This study showed that elevated pCO₂ significantly affected the burrowing behaviors of the Manila clam Ruditapes philippinarum, such as increased foot contraction, burrowing time, and intrabottom movement and decreased burrowing depth. Delving deeper into the mechanism, exposure to elevated pCO₂ significantly decreased extracellular pH and increased [HCO₃^-]. Moreover, an indicator GABA_A receptor, a neuroinhibitor for movement, was found to be closely associated with behavioral changes. In situ hybridization confirmed that the GABA_A receptor was widely distributed in ganglia and foot muscles, and elevated pCO₂ significantly increased the mRNA level and GABA concentration. However, the increase in GABA_A receptor and its ligand did not suppress the foot movement, but rather sent "excitatory" signals for foot contraction. The destabilization of acid-base homeostasis was demonstrated to induce an increase in the reversal potential for GABA_A receptor and an alteration in GABA_A receptor function under elevated pCO₂. This study revealed that elevated pCO₂ affects the burrowing behavior of Manila clams by altering GABA_A receptor function from inhibitory to excitatory.

Changes in biochemical metabolites in manila clam after a temporary culture with high-quality microalgal feed mixed with the dinoflagellate species Karlodinium veneficum and K. zhouanum

Phytoplankton composition is an important factor affecting the growth and physiological biochemical characteristics of filter-feeding bivalves. With the increasing trend in dinoflagellate biomass and blooms in mariculture areas, how the physio-biochemical traits and seafood quality of the mariculture organism are affected by the dinoflagellates, especially those at nonfatal levels, is not well understood. Different densities of two Karlodinium species, namely K. veneficum (KV) and K. zhouanum (KZ), mixed with high quality microalgal food Isochrysis galbana was applied in feeding manila clam Ruditapes philippinarum in a 14-day temporary culture, to comparatively study how the critical biochemical metabolites such as glycogen, free amino acids (FAAs), fatty acids (FAs), volatile organic compounds (VOCs) in the clam were affected. The survival rate of the clam showed dinoflagellate density and species specificity. The high-density KV group inhibited survival to 32% lower than that of the pure I. galbana control, respectively, while KZ at low concentrations did not significantly affect the survival compared with the control. In the high-density KV group, the glycogen and FAA contents decreased (p < 0.05), indicating that energy and protein metabolism were significantly affected. Amount of carnosine (49.91 ± 14.64 to 84.74 ± 8.59 μg/g of muscle wet weight) was detected in all the dinoflagellate-mixed groups, while it was not present in the field samples or in the pure I. galbana control, showing that carnosine participated in the anti-stress activities when the clam was exposed to the dinoflagellates. The global composition of FAs did not significantly vary among the groups. However, contents of the endogenous C₁₈ PUFA precursors linoleic acid and α-linolenic acid significantly decreased in the high-density KV group compared to all the other groups, indicating that high density of KV affected the metabolisms of fatty acids. From the results of the changed VOC composition, oxidation of fatty acids and degradation of free amino acids might occur in the clams exposed to dinoflagellates. The increased VOCs, such as aldehydes, and decreased 1-octen-3-ol probably produced a more fishy taste and reduced food flavor quality when the clam was exposed to the dinoflagellates. This present study demonstrated that the biochemical metabolism and seafood qulity of the clam were affected. However, KZ with moderate density in the feed seemed to be beneficial in aquaculture for increasing the content of carnosine, a high-valued substance with multiple bioactivities.

Coupling habitat-specific temperature scenarios with tolerance landscape to predict the impacts of climate change on farmed bivalves

Due to climate change, heatwaves are likely to become more frequent, prolonged and characterized by higher peak values, compared with climatological averages. However, the thermal tolerance of organisms depends on the actual exposure, which can be modulated by environmental context and microhabitat characteristics. This study investigated the frequency of occurrence of mass mortality events in the next decades for two species of farmed bivalves, the mussel Mytilus galloprovincialis and the clam Ruditapes philippinarum, in a shallow coastal lagoon, characterised by marked diurnal oscillations of water temperature. The effect of heatwaves was estimated by means of tolerance landscape models, which predict the occurrence of 50% mortality based on the exposure intensity and duration. Scenarios of water temperature up to the year 2100 were modelled by combining two mechanistic components, namely: 1) monthly mean water temperatures, simulated using a hydrodynamic model including the heat budget; 2) daily oscillations, estimated from the harmonic analysis of a twenty year-long site-specific time series of water temperature. Scenarios of mean daily sediment temperature were estimated by means of a cross-correlation model, using as input the water temperature one: the model parameters were estimated based on a comprehensive set of site-specific water and sediment temperature observations. The results indicate that for both species the risk of mass mortality rapidly increases starting from the 2060s. Furthermore, the daily patterns of water temperature seemed to be relevant, as overnight it falls below the predicted mortality thresholds for a few hours. These findings suggest that further studies should address: 1) the improvement of tolerance landscape models, in order to take into account the integrated effect of repeated non-lethal stress events on mortality rate; 2) the prediction of environmental temperature in specific habitat, by means of both process-based and data driven models.

In vitro study of deltamethrin-induced extracellular traps in hemocytes of Ruditapes philippinarum

Deltamethrin (DLM), a broad-spectrum pesticide, has been proven to have toxic effects on aquatic organisms. Here, we detected the formation of extracellular traps (ETosis) formation in Manila clam (Ruditapes philippinarum) hemocytes stimulated by three concentrations of DLM (0.01, 0.1 and 1 μg/mL) in vitro, and explored the underlying mechanisms induced by this pesticide. Extracellular DNA structure observation and quantitative results indicated that DLM exposure could obviously induce hemocytes ETosis, especially under high concentration of DLM induction. Moreover, DLM increased the levels of myeloperoxidase (MPO) and reactive oxygen species (ROS) in a dose-dependent manner, and enhanced the mRNA expression of several ROS-related genes. DPI (NADPH oxidase inhibitor) and ABAH (MPO inhibitor) could substantially inhibit DLM-induced extracellular traps (ETs), suggesting that the induced ETs release was caused by the induction of the ROS burst and MPO production. In addition, three concentrations of DLM-induced ETs were also accompanied by mitochondrial dysfunction, such as increasing the production of mitochondrial ROS, leading to a decrease in mitochondrial membrane potential (MMP) and activation of mitochondrial permeability transition pore (MPTP). Taken together, these results will shed new light on the immunotoxicity of DLM in clams and perhaps lays the foundation for health assessment in bivalves.

Understanding the aggregation, consumption, distribution and accumulation of nanoparticles of polyvinyl chloride and polymethyl methacrylate in Ruditapes philippinarum

Plastic products have become an integral part of our life. A widespread usage, high stability, uncontrolled disposal and slow degradation of plastics in the environment led to the generation and accumulation of nanoparticles of polymers (NPs) in the marine environment. However, little is known about the aggregation, consumption and distribution of NPs from common polymers such as polyvinyl chloride (NP-PVC) and polymethyl methacrylate (NP-PMMA) inside marine animal physiologies. In the current study, two types of polymers (PVC and PMMA) × four exposure concentrations (1, 5, 15 and 25 mg/L) × four times (4, 8, 12 and 24 h) exposure studies were conducted to understand the consumption and distribution of luminescent NP-PVC (98.6 ± 17.6 nm) and NP-PMMA (111.9 ± 37.1 nm) in R. philippinarum. Under laboratory conditions, NP-PVC showed a higher aggregation rate than NP-PMMA in seawater within a period of 24 h. Aggregations of NPs increased with an increase in initial NP concentrations, leading to significant settling of nanoparticles within 24 h exposure. Such aggregation and settling of particles enhanced the consumption of NPs by benthic filter-feeding R. philippinarum at all exposure concentrations during 4 h exposure. More interestingly, NP-PVC and NP-PMMA were observed in large amounts in both liver and gills (22.6 % - 29.1 %) of the clams. Furthermore, NP-PVC was detected in most organs of R. philippinarum as compared to NP-PMMA. This study demonstrates that different polymers distribute and accumulate differently in the same biological model under laboratory exposure conditions based on their chemical nature.

Toxicological mechanism of cadmium in the clam Ruditapes philippinarum using combined ionomic, metabolomic and transcriptomic analyses

Cadmium (Cd) contamination in marine environment poses great risks to the organisms due to its potential adverse effects. In the present study, the toxicological effects and mechanisms of Cd at environmentally relevant concentrations (5 and 50 μg/L) on clam Ruditapes philippinarum after 21 days were investigated by combined ionomic, metabolomic, and transcriptomic analyses. Results showed that the uptake of Cd significantly decreased the concentrations of Cu, Zn, Sr, Se, and Mo in the whole soft tissue from 50 μg/L Cd-treated clams. Significantly negative correlations were observed between Cd and essential elements (Zn, Sr, Se, and Mo). Altered essential elements homeostasis was associated with the gene regulation of transport and detoxification, including ATP-binding cassette protein subfamily B member 1 (ABCB1) and metallothioneins (MT). The crucial contribution of Se to Cd detoxification was also found in clams. Additionally, gene set enrichment analysis showed that Cd could interfere with proteolysis by peptidases and decrease the translation efficiency at 50 μg/L. Cd inhibited lipid metabolism in clams and increased energy demand by up-regulating glycolysis and TCA cycle. Osmotic pressure was regulated by free amino acids, including alanine, glutamate, taurine, and homarine. Meanwhile, significant alterations of some differentially expressed genes, such as dopamine-β-hydroxylase (DBH), neuroligin (NLGN), NOTCH 1, and chondroitin sulfate proteoglycan 1 (CSPG1) were observed in clams, which implied potential interference with synaptic transmission. Overall, through integrating multiple omics, this study provided new insights into the toxicological mechanisms of Cd, particularly in those mediated by dysregulation of essential element homeostasis.

Population Genetics of Manila Clam (Ruditapes philippinarum) in China Inferred from Microsatellite Markers

The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (N_e). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (H_o) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (H_e) was calculated to be varying from 0.587 to 0.700. F_st values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all F_st values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.

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.

Revealing the potential regulatory relationship between HSP70, HSP90 and HSF genes under temperature stress

Heat Shock Protein (HSPs) gene family members play fundamental roles in different environmental stress tolerances, protect the structure and function of cells, and perform a significant task in cellular homeostasis. In this study, we conducted a genome-wide identification, evolutionary relationship analysis and gene expression analysis of the HSP70, HSP90, and HSF gene families in Ruditapes philippinarum. We identified 83 RpHSP70, 6 RpHSP90, and 3 RpHSF genes in R. philippinarum. The structural characteristics, chromosomal localization, and the gene structure map were constructed to reveal the characteristics of protein structures. Furthermore, the expression profiling of transcriptome data showed the expression pattern of HSP70, HSP90 and HSF genes in Manila clam from different populations, and under high and low temperature stress. In addition, we performed protein-protein interaction network analysis between HSP70, HSP90, and HSF gene family which enabled us to recognize the regulatory relationship between the two HSP gene families and the HSF gene family. Furthermore, the predicted sub-cellular location revealed a diversified subcellular distribution of HSP70, HSP90, and HSF proteins, which may be directly or indirectly associated with functional diversification under heat stress condition.

Transient receptor potential (TRP) channels in the Manila clam (Ruditapes philippinarum): Characterization and expression patterns of the TRP gene family under heat stress in Manila clams based on genome-wide identification

In this study, we identified a total of 40 transient receptor potential genes (RpTRP) in Manila clam by genome-wide identification and classified them into four categories (TRPV, TRPA, TRPM, TRPC) based on gene structure and subfamily relationships. The protein length of RpTRP genes ranges from 281 amino acids to 1601 amino acids. Molecular weight and theoretical PI values range from 182.82 kDa to 32.43 kDa, respectively, with PI values between 5.17 and 9.25. By comparing the expression profiles of TRP genes during heat stress in Manila clams at different latitudes, we found that most genes in the TRP gene family were up-regulated in expression during heat challenge. Therefore, we determined that TRP genes have an important role in the heat stress of Manila clams. This work provides a basis for further studies on the molecular mechanisms of TRP-mediated heat tolerance in Manila clam and for explaining differences in heat tolerance in Manila clam at different latitudes through key differential TRP genes at the molecular level.

Defense System of the Manila Clam Ruditapes philippinarum under High-Temperature and Hydrogen Sulfide Conditions

Hydrogen sulfide (H₂S) acts as an environmental toxin. Despite its toxicity, little is known about the defense strategies of marine bivalves against it. Thus, the tolerance, behavioral characteristics, and physiological response strategies against H₂S treatment in the sentinel organism Manila clam Ruditapes philippinarum were examined. We monitored the survival and behavioral status of Manila clams exposed to different combinations of temperature and H₂S. The physiological response strategies were examined by measuring the enzymatic activity of cytochrome C oxidase (CCO), fumarate reductase (FRD), superoxide dismutase (SOD), and catalase enzymes (CAT). Moreover, adverse effects of H₂S on the tissue and cell structure of Manila clams were also examined under a transmission electron microscope. Manila clams responded to H₂S stress through behavioral and chemical defenses. With exposure to H₂S alone, Manila clams primarily enhanced aerobic respiratory metabolic pathways in the beginning stages by opening the shell and increasing the CCO activity to obtain more oxygen; with increasing exposure time, when aerobic respiration was inhibited, the shell was closed, and FRD, CAT, and SOD were activated. At this point, Manila clams responded to H₂S stress through the anaerobic metabolism and antioxidant defense systems. However, high temperatures (≥28 °C) altered the defense strategy of Manila clams. With co-exposure to high temperatures and high H₂S concentrations (≥20 μmol/L), the Manila clams immediately closed their shells and changed from aerobic respiration to anaerobic metabolism while immediately activating antioxidant defense systems. Nevertheless, this defense strategy was short lived. In addition to this, apparent damage to tissue and cell structures, including mitochondrial ridge dissolution and many vacuoles, was observed in Manila clams exposed to high temperatures and high H₂S concentrations. Thus, prolonged exposure to high temperature and H₂S damages the tissue structure of Manila clams, affecting their behavioral capacity and future survival. In summary, profiling Manila clams' physiological response strategies to H₂S exposure provided ecological behavioral support for our current understanding of H₂S detrimental toxicity on marine bivalves.

Transcriptome sequencing reveals improved ammonia nitrogen tolerance in Zebra II strain of the Manila clam Ruditapes philippinarum

In this research, we identified genes associated with ammonia nitrogen (TAN) stress response and resistance in juveniles of the Zebra II strain and a wild population of the Manila clam Ruditapes philippinarum. Both groups were subjected to a 96 h acute toxicity test using TAN concentrations of 17.617 ± 0.634 and 16.670 ± 0.7 mg/l, respectively. We then collected samples, conducted transcriptome sequencing and screened the sequences for differentially expressed genes (DEGs) related to TAN stress response. We identified 2908 and 2861 DEGs in the Zebra II and wild clam groups, respectively, and the two groups had 626 DEGs in common. The verified DEGs had less of a detoxification effect in the wild population than that in the Zebra II group. Gene Ontology database analysis showed that Zebra II juveniles were mainly enriched in protein phosphorylation, purine nucleoside binding, and kinase activity, whereas the wild population juveniles were primarily enriched in oxidases activity, organic acid metabolic processes, and extracellular regions. Kyoto Encyclopedia of Genes and Genomes pathway analysis mainly highlighted aminoacyl tRNA biosynthesis in Zebra II juveniles and sphingolipid metabolism, FOXO signaling, biosynthesis of aminoacyl tRNA, and other pathways in the wild population. These results show that the toxic effect of TAN on the Manila clam is related to a variety of pathways, which are mainly related to immune response, inflammatory response, metabolic pathways, and nerve conduction. This study provides basic data and theoretical reference for revealing the molecular regulation mechanism of the improved TAN tolerance of Zebra II strain as compared with the wild population of Ruditapes philippinarum.

Characteristic and antibacterial effect of a histone H2A and its preliminary roles in extracellular traps in manila clam Ruditapes philippinarum

In the present study, a histone H2A (designed as RpH2A) was identified and characterized from clam Ruditapes philippinarum, and its open reading frame (ORF) was of 387 bp encoding a polypeptide of 128 amino acids. The deduced amino acid sequence of RpH2A shared high identities ranging from 57.1% to 96.1% with that of other identified H2A. The mRNA expression of RpH2A was up-regulated significantly after Vibrio anguillarum challenge. The recombinant RpH2A protein (rRpH2A) displayed significantly binding affinity to lipopolysaccharide (LPS) and peptidoglycan (PGN) in vitro, and also exhibited antimicrobial properties against Escherichia coli. In addition, the antimicrobial RpH2A was shown to co-localize with extracellular traps (ETs) released from hemocytes induced by E. coli, suggesting that RpH2A might contribute to eliminate invading bacteria in clam ETs. Altogether, our data revealed that RpH2A could function as antimicrobial peptides, which might play a crucial role in the immune responses of hemocytes ETs in clams.

Examination of the potential roles of insulin-like peptide receptor in regulating the growth of Manila clam Ruditapes philippinarum

The role of insulin/insulin-like growth factor (IGF) signaling pathway in the growth regulation of marine invertebrates has not been fully studied. In this study, the economically important species Ruditapes philippinarum was sacrificed to clarify the role of IGF system in the growth regulation of R. philippinarum by real-time quantitative PCR. Systematic bioinformatics analysis can identify the major genes of IGF signaling pathway and insulin-like peptide receptor (ILPR) - mediated signaling pathway in R. philippinarum. The expression levels of IGF and its downstream signaling pathway genes in larger clams were significantly higher than those in small clams, indicating that they were involved in the growth regulation of R. philippinarum. These results suggest that IGF signaling pathway and ILPR mediated signaling pathway to regulate the growth of R. philippinarum.

Effects of high water temperature on physiology, survival, and resistance to high temperature air-exposure in the Manila clam Ruditapes philippinarum

Ruditapes philippinarum is a typical burrowing shellfish, living in the intertidal zone. In natural conditions, the mortality of R. philippinarum is most affected by high water temperatures, high temperature air-exposure, and other environmental stresses. In this study, the mortality rates of the two populations of R. philippinarum under high water temperature stress were recorded, and catalase (CAT), superoxide dismutase (SOD) and total antioxidant capacity (T-AOC) antioxidant enzyme activities in the hepatopancreas were analyzed. The results showed that the survival times of cultured clams were longer than those of wild clams after acute high temperature stress. CAT, SOD, and T-AOC activities increased after acute high water temperature and high temperature air-exposure stress. These antioxidant enzyme activities gradually decreased to their initial levels after 2 days of recovery from these high temperature stresses. Based on these experimental results, we found that the cultured clam population had better heat and high temperature air-exposure resistances than the wild clams. CAT, SOD, and T-AOC enzymes play an important role in the antioxidant processes of R. philippinarum in response to high water temperature and high temperature air-exposure. This study provided a theoretical basis for the development of healthy aquacultural practices for these shellfish.

Comparative transcriptome analysis reveals immunotoxicology induced by three organic UV filters in Manila clam (Ruditapes philippinarum)

Benzophenone-3 (BP-3), 4-methyl-benzylidene camphor (4-MBC) and 2-ethyl-hexyl-4-trimethoxycinnamate (EHMC) are commonly used organic ultraviolet (UV) filters and are frequently detected in water environments. In the present study, we studied the potential adverse impacts of UV filter exposures in Ruditapes philippinarum by investigating transcriptomic profiles and non-specific immune enzyme activities. Transcriptome analysis showed that more genes were differentially regulated in EHMC-treated group, and down-regulated genes (2009) were significantly more than up-regulated ones (410) at day 7. Function annotation revealed that pathways "immune system", "cell growth and death" and "infectious diseases" were significantly enriched. Generally, combined qPCR and biochemical analyses demonstrated that short-term exposure to low dose of UV filters could activate immune responses, whereas the immune system would be restrained after prolonged exposure. Taken together, the present study firstly demonstrated the immunotoxicology induced by BP-3, 4-MBC and EHMC on R. philippinarum, indicating their potential threats to the survival of marine bivalves.

The Ameliorative Effect and Mechanisms of Ruditapes philippinarum Bioactive Peptides on Obesity and Hyperlipidemia Induced by a High-Fat Diet in Mice

In this study, bioactive peptides (RBPs) from Ruditapes philippinarum were prepared by fermentation with Bacillus natto and the effect and mechanisms of RBPs on obesity and hyperlipidemia were explored in mice. We found that RBPs significantly reduced body weight, adipose tissue weight, accumulation of hepatic lipids, and serum levels of total cholesterol (CHO), triglyceride (TG), and low-density lipoprotein (LDL). Mechanistic studies showed that RBPs up-regulated the hepatic expression of genes related to lipolysis, such as hormone-sensitive lipase (HSL), phosphorylated AMP-activated protein kinase (p-AMPK), and peroxisome proliferator-activated receptors α (PPARα), and down-regulated the expression of peroxisome proliferator-activated receptors γ (PPARγ) which is related to lipid synthesis. In addition, RBPs could attenuate obesity and hyperlipidemia by regulating disordered gut microbiota composition, such as increasing the abundance of microflora related to the synthesis of short chain fatty acids (SCFAs) (Bacteroidetes, Prevotellaceas_UCG_001, norank_f_Muribaculaceae, and Odoribacter) and controlling those related to intestinal inflammation (reduced abundance of Deferribacteres and increased abundance of Alistipes and ASF356) to exert anti-obesity and lipid-lowering activities. Our findings laid the foundation for the development and utilization of RBPs as a functional food to ameliorate obesity and hyperlipidemia.

Preparation and Hepatoprotective Activities of Peptides Derived from Mussels (Mytilus edulis) and Clams (Ruditapes philippinarum)

Low molecular weight (<5 kDa) peptides from mussels (Mytilus edulis) (MPs) and the peptides from clams (Ruditapes philippinarum) (CPs) were prepared through enzymatic hydrolysis by proteases (dispase, pepsin, trypsin, alcalase and papain). Both the MPs and the CPs showed excellent in vitro scavenging ability of free radicals including OH, DPPH and ABTS in the concentration range of 0.625−10.000 mg/mL. By contrast, the MPs hydrolyzed by alcalase (MPs-A) and the CPs hydrolyzed by dispase (CPs-D) had the highest antioxidant activities. Furthermore, MPs-A and CPs-D exhibited protective capabilities against oxidative damage induced by H2O2 in HepG2 cells in the concentration range of 25−800 μg/mL. Meanwhile, compared with the corresponding indicators of the negative control (alcohol-fed) mice, lower contents of hepatic MDA and serums ALT and AST, as well as higher activities of hepatic SOD and GSH-PX were observed in experiment mice treated with MPs-A and CPs-D. The present results clearly indicated that Mytilus edulis and Ruditapes philippinarum are good sources of hepatoprotective peptides.

Post-responses of intertidal bivalves to recurrent heatwaves

Heatwaves are becoming hotter, longer and more frequent, threatening the survival of intertidal bivalves and devastating their ecosystems. Yet, substantially overlooked are heatwave-induced post-responses, which are important to assess cascading consequences. Here, we investigated responses of intertidal bivalves, Ruditapes philippinarum, to recurrent heatwaves. Physiological and gene expression analyses demonstrated that the mantle tissue of R. philippinarum did not sensitively respond to heatwaves, but revealed post-responses under recovery scenarios. Of 20 genes related to essential physiology and fitness, 18 were down-regulated during the 1st recovery period, but following repeated exposure, 13 genes were up-regulated, in line with significantly increased activities of energy-metabolizing enzymes, and antioxidant and nonspecific enzymes. The down-regulation of genes involved in biomineralization, nevertheless, was observed under recovery scenarios, implying the trade-off between essential physiological and fitness-related functions. These findings pave the way for understanding the physiological plasticity of marine bivalves in response to intensifying heatwaves.

Isotope Geochemistry for Seafood Traceability and Authentication: The Northern Adriatic Manila Clams Case Study

In Italy, the production of manila clams (Ruditapes philippinarum, Adams and Reeve, 1850) is mainly localized in northern Adriatic lagoons in the Po River delta, where shellfish farming provides important socio-economic revenue. However, in our globalized world, the seafood market is threated by fraudulent activities, in which agri-food products whose provenance is not certified are sold, posing a risk to consumer health. Multi-isotope ratio analysis is commonly used to trace the provenance of goods produced in different countries with different climatic and environmental conditions. Here, we investigated the reliability of this approach in terms of tracing the exact provenance of manila clams harvested in three Adriatic northern lagoons that are close to each other. We also verified the origin of samples bought at a local supermarket with a certificate of provenance. We carried out elemental analyses of carbon (C), nitrogen (N), and sulfur (S) and the respective isotopic ratios (¹³C/¹²C; ¹⁵N/¹⁴N; ³⁴S/³²S) on manila clam tissues, plus isotopic analyses of carbon (¹³C/¹²C), oxygen (¹⁸O/¹⁶O), and strontium (⁸⁷Sr/⁸⁶Sr) on manila clam shells. Each isotopic parameter can be used to identify the marine and continental contributions of water and/or nutrient supplies occurring in the lagoons. Therefore, the combination of isotopic parameters in a linear discriminant analysis (LDA) allowed for the identification of the lagoons in which the manila clams were produced.

Assessing the impact of atmospheric heatwaves on intertidal clams

Heatwaves have become more frequent and intense in the last two decades, resulting in detrimental effects on marine bivalves and ecosystems they sustain. Intertidal clams inhabit the most physiologically challenging habitats in coastal areas and live already near their thermal tolerance limits. However, whether and to what extent atmospheric heatwaves affect intertidal bivalves remain poorly understood. Here, we investigated physiological responses of the Manila clam, Ruditapes philippinarum, to heatwaves at air temperature regimes of 40 °C and 50 °C occurring frequently and occasionally at the present day in the Beibu Gulf, South China Sea. With the increasing intensity of heatwaves and following only two days of aerial exposure, Manila clams suffered 100 % mortality at 50 °C, indicating that they succumb to near future heatwaves, although they survived under various scenarios of moderate heatwaves. The latter is couched in energetic terms across levels of biological organization. Specifically, Manila clams acutely exposed to heatwaves enhanced their standard metabolic rate to fuel essential physiological maintenance, such as increasing activities of SOD, CAT, MDA, and AKP, and expression of HSP70. These strategies occur likely at the expense of fitness-related functions, as best exemplified by significant depressions in activities of enzymes (NKA, CMA, and T-ATP) and expression levels of genes (PT, KHK, CA, CAS, TYR, TNF-BP, and OSER). When heatwaves occurred again, Manila clams can respond and acclimate to thermal stress by implementing a suite of more ATP-efficient and less energy-costly compensatory mechanisms at various levels of biological organization. It is consequently becoming imperative to uncover underlying mechanisms responsible for such positive response and rapid acclimation to recurrent heatwaves.

Genome-wide identification and analysis of HECT E3 ubiquitin ligase gene family in Ruditapes philippinarum and their involvement in the response to heat stress and Vibrio anguillarum infection

E3 ubiquitin ligase (E3s) plays an important role in ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains. However, the role of HECT E3 ubiquitin ligase in mollusk was rarely explored. In this study, we performed a genome-wide analysis of the HECT domain-containing gene in Ruditapes philippinarum to identify and predict the structural and functional characterization of HECT genes in response to abiotic and biotic stress. A total of sixteen members of HECT gene family were identified and analyzed for the gene structure, phylogenetic relation, three-dimensional structure, protein interaction network, and expression patterns. Experimental results demonstrated that Rph.HUWE1, Rph.HECTD1, Rph.Ubr5 were significantly up-regulated in response to heat stress and bacterial challenge. Taken together, our data provide insights into the potential function of HECT E3 ligase in heat stress and Vibrio anguillarum infection.

Source risk, ecological risk, and bioeffect assessment for polycyclic aromatic hydrocarbons (PAHs) in Laizhou Bay and Jiaozhou Bay of Shandong Peninsula, China

In order to incorporate the contribution of pollution sources to ecological risks into environmental monitoring, positive matrix factorization-risk quotient (PMF-RQ) was used to quantify the contribution of different PAH sources to ecological risks, which indicated that the unburned petroleum, vehicular emissions, and diesel combustion were the main sources of PAHs in Laizhou Bay and Jiaozhou Bay, and they were caused by petrochemical industry, maritime shipping, and urban traffic exhaust as the major sources of PAHs for ecological risk. Meanwhile, integrated biomarker response (IBR) and multi-biomarker pollution index (MPI) suggested that September was the most polluted month for PAHs in Laizhou Bay and Jiaozhou Bay and the pollution in Laizhou Bay was significantly higher than that in Jiaozhou Bay. This research was dedicated to explore the monitoring pattern for PAH pollution from the source to bioeffects, and it may have contributed a scientific support to monitoring and governance of marine PAH pollution.

In vitro immunotoxicity and possible mechanisms of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) on Ruditapes philippinarum hemocytes

Marine bivalves can accumulate large amounts of pollutants from sea water, sediments and microalgae due to their filter-feeding habits. BDE-47 is often the most highly concentrated congener in bivalves. BDE-47 has been found to have toxic effects on bivalves, however, the immunotoxicity and the underlying mechanisms of BDE-47 on bivalves are not well understood yet. In this study, isolated hemocytes of Manila clam Ruditapes philippinarum were exposed to five concentrations of BDE-47 (6.25 μM, 12.5 μM, 25 μM, 50 μM, 100 μM), the effects of BDE-47 on hemocyte survival rate, cell viability, granulocyte ratio, phagocytosis, bacteriolytic activity, reactive oxygen species (ROS), lysosomal membrane permeability (LMP), superoxide dismutase (SOD), and phosphorylation state of extracellular regulated protein kinase (ERK) and p38 at 2 h, 6 h and 12 h were studied. The results indicated that BDE-47 exposure declined the hemocyte cell viability, reduced the granulocyte ratio, hampered the hemocyte phagocytosis and bacteriolytic activity, elevated the ROS levels, increased the LMP, significantly changed SOD expression and depressed the phosphorylation levels of ERK and p38. Taken together, the results demonstrated that BDE-47 had significant toxic effects on the immune function, and the immunotoxicity may partly via the overproduction of ROS and the alteration of MAPK signaling pathways.

Apextrin from Ruditapes philippinarum functions as pattern recognition receptor and modulates NF-κB pathway

Apextrin belongs to ApeC-containing proteins (ACPs) and features a signal-peptide, an N-terminal membrane attack complex component/perforin (MACPF) domain, and a C-terminal ApeC domain. Recently, apextrin-like proteins were identified as pattern recognition receptor (PRR), which recognize the bacterial cell wall component and participate in innate immunity. Here, an apextrin (Rpape) was identified and characterized in Ruditapes philippinarum. Our results showed that Rpape mRNA was significantly induced under bacterial challenges. The Rpape recombinant protein exhibited a significant inhibitory effect on gram-positive bacteria (Bacillus subtilis and Staphylococcus aureus) and bound with Vibrio anguillarum, S. aureus and B. subtilis. We found Rpape protein positively activated the NF-κB signaling cascade and increased the activity of Nitric oxide (NO). This study revealed the immunity role of apextrin in R. philippinarum and provided a reference for further study on the role of apextrin in bivalves.

Will extreme weather events influence the toxic impacts of caffeine in coastal systems? Comparison between two widely used bioindicator species

In the recent years, marine heatwaves (MHWs) have caused devastating impacts on marine life. The understanding of the combined effects of these extreme events and anthropogenic pollution is a vital challenge. In particular, the combined effect of MHWs on the toxicity of pharmaceuticals to aquatic life remains unclear. To contribute to these issues, the main goal of the present investigation was to evaluate how MHWs may increase caffeine (CAF) toxicity on the clam Ruditapes philippinarum and the mussel Mytilus galloprovincialis. Bioaccumulation levels and changes on oxidative stress, metabolic capacity and neurotoxic status related biomarkers were investigated. The obtained results revealed the absence of CAF accumulation in both species. However, the used contaminant generated in both bivalve species alteration on neurotransmission, detoxification mechanisms induction as well as cellular damage. The increase of antioxidant defence mechanisms was complemented by an increase of metabolic activity and decrease of energy reserves. The obtained results seemed magnified under a simulated MHWs, suggesting to a climate-induced toxicant sensitivities' response. On this perspective, understanding of how toxicological mechanisms interact with climate-induced stressors will provide a solid platform to improve effect assessments for both humans and wildlife.

Gene Co-Expression Network Analysis Reveals the Correlation Patterns Among Genes in Different Temperature Stress Adaptation of Manila Clam

The Manila clam (Ruditapes philippinarum) is one of the most important aquaculture species and widely distributed along the coasts of China, Japan, and Korea. Due to its wide distribution, it can tolerate a wide range of temperature. Studying the gene expression profiles of clam gills had found differentially expressed genes (DEGs) and pathway involved in temperature stress tolerance. A systematic study of cellular response to temperature stress may provide insights into the mechanism of acquired tolerance. Here, weighted gene co-expression network analysis (WGCNA) was carried out using RNA-seq data from gill transcriptome in response to high and low temperature stress. There are a total 32 gene modules, of which 18 gene modules were identified as temperature-related modules. Blue module was one significantly correlated with temperature which was associated with cellular metabolism, apoptosis pathway, ER stress, and others.

Molecular Mechanisms Underlying Vibrio Tolerance in Ruditapes philippinarum Revealed by Comparative Transcriptome Profiling

The clam Ruditapes philippinarum is an important species in the marine aquaculture industry in China. However, in recent years, the aquaculture of R. philippinarum has been negatively impacted by various bacterial pathogens. In this study, the transcriptome libraries of R. philippinarum showing different levels of resistance to challenge with Vibrio anguillarum were constructed and RNA-seq was performed using the Illumina sequencing platform. Host immune factors were identified that responded to V. anguillarum infection, including C-type lectin domain, glutathione S-transferase 9, lysozyme, methyltransferase FkbM domain, heat shock 70 kDa protein, Ras-like GTP-binding protein RHO, C1q, F-box and BTB/POZ domain protein zf-C2H2. Ten genes were selected and verified by RT-qPCR, and nine of the gene expression results were consistent with those of RNA-seq. The lectin gene in the phagosome pathway was expressed at a significantly higher level after V. anguillarum infection, which might indicate the role of lectin in the immune response to V. anguillarum. Comparing the results from R. philippinarum resistant and nonresistant to V. anguillarum increases our understanding of the resistant genes and key pathways related to Vibrio challenge in this species. The results obtained here provide a reference for future immunological research focusing on the response of R. philippinarum to V. anguillarum infection.

Bottom aquaculture can improve the basic trophic pathways and enhance the secondary production: Implications from benthic food web analysis

To evaluate the impact of bottom aquaculture on benthic ecosystems, characteristics of benthic food web were studied using stable isotope techniques during four seasons in a Manila clam (Ruditapes philippinarum) bottom aquaculture area in a semi-enclosed bay, China. Results showed that although nitrogen stable isotope values of food sources (particulate organic matter and phytoplankton) had significant seasonal differences, there were no significant seasonal changes for benthic food web structure. Manila clam bottom aquaculture can enhance the secondary productivity and improve the basic trophic pathways by providing bio-deposits. Besides particulate organic matter and phytoplankton, Manila clam could feed on self-generated feces with high nitrogen stable isotope values, and benthic micro- and macroalga with high carbon stable isotope values. Secondary productivity of the stations with a high degree of aquaculture was higher than that of stations with a low degree. Bivalve bottom culture may have a positive impact on benthic ecosystem functioning.

Immunotoxicity of Perfluorooctanoic Acid to the Marine Bivalve Species Ruditapes philippinarum

Polyfluorinated alkylated substances are recognized as an important class of pollutants in marine environments. Bivalves are good model organisms for evaluating the toxicity of pollutants and monitoring marine environments. In the present study, immunotoxicity of perfluorooctanoic acid (PFOA) was investigated by measuring biomarkers of the immune profile of Ruditapes philippinarum. In bivalves, hemocytes are an important component of the immune system. Thus, hemocyte proliferation, phagocytosis, cell viability, and immune enzyme activities, which have been applied as marine pollution bioindicators, were identified and observed for changes after exposure to PFOA in R. philippinarum. Based on the integrated biomarker responses method, we selected five biomarkers to evaluate PFOA risk at the multibiomarker level. In addition, the histopathological alterations of hemocytes in bivalves were used as indexes of the response to environmental stress. The subcellular structure of the hemocytes in R. philippinarum changed significantly with PFOA exposure, including hemocyte and nucleus morphological changes, organelle dissolution, cytomembrane and karyotheca swelling, and cytoplasm vacuolization. The present study verifies PFOA immunotoxicity to R. philippinarum at different levels and the integrated assessment of stress levels caused by PFOA in marine environment. Our results will provide new insights into evaluating adverse effects of PFOA and monitoring marine ecosystem. Environ Toxicol Chem 2022;41:426-436. © 2021 SETAC.

Bioaccumulation and function analysis of glutathione S-transferase isoforms in Manila clam Ruditapes philippinarum exposed to different kinds of PAHs

This study analyzed the function of different glutathione S-transferase (GST) isoforms and detoxification metabolism responses in Manila clam, Ruditapes philippinarum, exposed to 4 kinds of polycyclic aromatic hydrocarbons (PAHs) single, and their mixtures for 15 days under laboratory conditions. 13 kinds of GSTs in R. philippinarum were classified, and the results of tissue distribution indicated that 12 kinds of GSTs (except GST sigma 3) expressed most in digestive glands. We detected the mRNA expression levels of aryl hydrocarbon receptor signaling pathway, and detoxification system in digestive glands of clams exposed to benzo[a]pyrene (BaP), chrysene (CHR), benzo[a]anthracene (BaA), benzo[b]fluoranthene (BbF), and BaP + CHR + BaA + BbF, respectively. Among these genes, we selected GST-sigma, GST-omega and GST-pi as potential indicators to BaP; GST-sigma, GST-A and GST-rho to CHR; GST-pi, GST-sigma, GST-A, GST-rho and GST-microsomal to BaA; GST-theta and GST-mu to BbF; while GST-pi and GST-mu to the mixture of BaP, CHR, BaA and BbF. Additionally, the bioaccumulation of PAHs in tissues increased remarkably over time, and showed an obvious dose-effect. Under the same concentration, the bioaccumulation in single exposure group was higher than that in mixture group, and the bioaccumulation of PAHs in tissues with different concentrations of stress was irregular. The results revealed the metabolic differences and bioaccumulation rules in clams exposed to four kinds of PAHs, and provided more valuable information for the PAHs risk assessment.